From a7fbfa1ffb05ab90c0f7711aa819b7e61bb75970 Mon Sep 17 00:00:00 2001 From: Glass Date: Tue, 17 Oct 2023 21:10:24 -0600 Subject: [PATCH] adding links to publications and has_evidence WIP (#410) Closes #408 - adds link fields and logic to has_evidence, publications, and provided_by for Associations model and parsers --- Makefile | 2 +- backend/poetry.lock | 271 +- backend/pyproject.toml | 2 +- backend/src/monarch_py/api/association.py | 2 +- backend/src/monarch_py/api/config.py | 35 +- backend/src/monarch_py/api/histopheno.py | 2 +- backend/src/monarch_py/api/semsim.py | 4 +- backend/src/monarch_py/cli.py | 2 +- backend/src/monarch_py/datamodels/model.py | 44 +- backend/src/monarch_py/datamodels/model.yaml | 32 +- .../implementations/oak/oak_implementation.py | 1 - .../solr/solr_implementation.py | 14 +- .../implementations/solr/solr_parsers.py | 24 +- .../src/monarch_py/service/curie_service.py | 2 +- backend/src/monarch_py/solr_cli.py | 6 +- backend/src/monarch_py/utils/utils.py | 27 +- backend/tests/fixtures/association_counts.py | 13 +- .../fixtures/association_counts_response.py | 6444 +++++++++------ .../tests/fixtures/association_response.py | 6440 +++++++++------ backend/tests/fixtures/association_table.py | 168 +- .../fixtures/association_table_response.py | 86 +- backend/tests/fixtures/associations.py | 7013 +++++++++------- backend/tests/fixtures/autocomplete.py | 33 +- .../tests/fixtures/autocomplete_response.py | 19 +- backend/tests/fixtures/histopheno.py | 40 +- backend/tests/fixtures/histopheno_response.py | 42 +- backend/tests/fixtures/node.py | 25 +- .../fixtures/phenotype_explorer_compare.py | 35 +- backend/tests/fixtures/search.py | 6 +- backend/tests/fixtures/search_response.py | 6 +- backend/tests/unit/test_curie_service.py | 39 +- frontend/fixtures/association-counts.json | 7 +- frontend/fixtures/association-table.json | 169 +- frontend/fixtures/associations.json | 7183 ++++++++++------- frontend/fixtures/autocomplete.json | 36 +- frontend/fixtures/histopheno.json | 80 +- frontend/fixtures/node.json | 19 +- .../fixtures/phenotype-explorer-compare.json | 4285 +--------- frontend/src/api/model.ts | 28 +- frontend/src/pages/metadata.json | 12 +- .../pages/node/SectionAssociationDetails.vue | 16 +- 41 files changed, 16717 insertions(+), 15997 deletions(-) diff --git a/Makefile b/Makefile index d37e56c68..adbd08b77 100644 --- a/Makefile +++ b/Makefile @@ -113,7 +113,7 @@ test-frontend: fixtures: @echo "Generating fixtures..." $(RUN) python scripts/generate_fixtures.py --all-fixtures - $(RUN) black backend/tests/fixtures/ + $(RUN) black -l 120 backend/tests/fixtures/ cd frontend && \ yarn lint diff --git a/backend/poetry.lock b/backend/poetry.lock index baf16c983..7ad0d88f3 100644 --- a/backend/poetry.lock +++ b/backend/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. [[package]] name = "airium" version = "0.2.6" description = "Easy and quick html builder with natural syntax correspondence (python->html). No templates needed. Serves pure pythonic library with no dependencies." -category = "main" optional = false python-versions = "*" files = [ @@ -20,7 +19,6 @@ parse = ["beautifulsoup4 (>=4.10.0,<5.0)", "requests (>=2.12.0,<3)"] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -32,7 +30,6 @@ files = [ name = "antlr4-python3-runtime" version = "4.9.3" description = "ANTLR 4.9.3 runtime for Python 3.7" -category = "main" optional = false python-versions = "*" files = [ @@ -43,7 +40,6 @@ files = [ name = "anyio" version = "3.7.1" description = "High level compatibility layer for multiple asynchronous event loop implementations" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -65,7 +61,6 @@ trio = ["trio (<0.22)"] name = "appdirs" version = "1.4.4" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "main" optional = false python-versions = "*" files = [ @@ -77,7 +72,6 @@ files = [ name = "arrow" version = "1.2.3" description = "Better dates & times for Python" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -92,7 +86,6 @@ python-dateutil = ">=2.7.0" name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -111,7 +104,6 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte name = "babel" version = "2.12.1" description = "Internationalization utilities" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -123,7 +115,6 @@ files = [ name = "bcp47" version = "0.0.4" description = "Language tags made easy" -category = "main" optional = false python-versions = "*" files = [ @@ -135,7 +126,6 @@ files = [ name = "beautifulsoup4" version = "4.12.2" description = "Screen-scraping library" -category = "main" optional = false python-versions = ">=3.6.0" files = [ @@ -154,7 +144,6 @@ lxml = ["lxml"] name = "bibtexparser" version = "1.4.1" description = "Bibtex parser for python 3" -category = "dev" optional = false python-versions = "*" files = [ @@ -168,7 +157,6 @@ pyparsing = ">=2.0.3" name = "bioregistry" version = "0.10.57" description = "Integrated registry of biological databases and nomenclatures" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -199,7 +187,6 @@ web = ["bootstrap-flask (<=2.0.0)", "curies[fastapi]", "fastapi", "flask (<2.2.4 name = "black" version = "22.12.0" description = "The uncompromising code formatter." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -235,7 +222,6 @@ uvloop = ["uvloop (>=0.15.2)"] name = "cachetools" version = "5.3.1" description = "Extensible memoizing collections and decorators" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -247,7 +233,6 @@ files = [ name = "cattrs" version = "23.1.2" description = "Composable complex class support for attrs and dataclasses." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -273,7 +258,6 @@ ujson = ["ujson (>=5.4.0,<6.0.0)"] name = "certifi" version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -285,7 +269,6 @@ files = [ name = "cffi" version = "1.15.1" description = "Foreign Function Interface for Python calling C code." -category = "dev" optional = false python-versions = "*" files = [ @@ -362,7 +345,6 @@ pycparser = "*" name = "cfgraph" version = "0.2.1" description = "rdflib collections flattening graph" -category = "main" optional = false python-versions = "*" files = [ @@ -376,7 +358,6 @@ rdflib = ">=0.4.2" name = "chardet" version = "5.2.0" description = "Universal encoding detector for Python 3" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -388,7 +369,6 @@ files = [ name = "charset-normalizer" version = "3.2.0" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -473,7 +453,6 @@ files = [ name = "class-resolver" version = "0.4.2" description = "Lookup and instantiate classes with style." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -500,7 +479,6 @@ torch-geometric = ["torch", "torch-geometric", "torch-sparse"] name = "click" version = "8.1.7" description = "Composable command line interface toolkit" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -515,7 +493,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -527,7 +504,6 @@ files = [ name = "curies" version = "0.6.4" description = "Idiomatic conversion between URIs and compact URIs (CURIEs)." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -552,7 +528,6 @@ tests = ["coverage", "pytest"] name = "deprecated" version = "1.2.14" description = "Python @deprecated decorator to deprecate old python classes, functions or methods." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -570,7 +545,6 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"] name = "deprecation" version = "2.1.0" description = "A library to handle automated deprecations" -category = "main" optional = false python-versions = "*" files = [ @@ -585,7 +559,6 @@ packaging = "*" name = "distlib" version = "0.3.7" description = "Distribution utilities" -category = "main" optional = false python-versions = "*" files = [ @@ -597,7 +570,6 @@ files = [ name = "docker" version = "6.1.3" description = "A Python library for the Docker Engine API." -category = "main" optional 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Python" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2206,7 +2129,6 @@ files = [ name = "oaklib" version = "0.5.20" description = "Ontology Access Kit: Python library for common ontology operations over a variety of backends" -category = "main" optional = false python-versions = ">=3.9,<4.0.0" files = [ @@ -2253,7 +2175,6 @@ llm = ["llm"] name = "ols-client" version = "0.1.4" description = "A client to the EBI Ontology Lookup Service" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2276,7 +2197,6 @@ tests = ["coverage", "pytest"] name = "ontoportal-client" version = "0.0.4" description = "A client to BioPortal and other OntoPortal instances." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2296,7 +2216,6 @@ tests = ["coverage", "pytest", "unittest-templates"] name = "openpyxl" version = "3.1.2" description = "A Python library to read/write Excel 2010 xlsx/xlsm files" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2311,7 +2230,6 @@ et-xmlfile = "*" name = "outcome" version = "1.2.0" description = "Capture the outcome of Python function calls." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2326,7 +2244,6 @@ attrs = ">=19.2.0" name = "packaging" version = "23.1" description = "Core utilities for Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2338,7 +2255,6 @@ files = [ name = "paginate" version = "0.5.6" description = "Divides large result sets into pages for easier browsing" -category = "main" optional = false python-versions = "*" files = [ @@ -2349,7 +2265,6 @@ files = [ name = "pandas" version = "2.1.0" description = "Powerful data structures for data analysis, time series, and statistics" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2408,7 +2323,6 @@ xml = ["lxml (>=4.8.0)"] name = "pandas" version = "2.1.1" description = "Powerful data 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files = [ @@ -2721,7 +2622,6 @@ email = ["email-validator (>=1.0.3)"] name = "pygments" version = "2.16.1" description = "Pygments is a syntax highlighting package written in Python." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2736,7 +2636,6 @@ plugins = ["importlib-metadata"] name = "pyjsg" version = "0.11.10" description = "Python JSON Schema Grammar interpreter" -category = "main" optional = false python-versions = "*" files = [ @@ -2752,7 +2651,6 @@ jsonasobj = ">=1.2.1" name = "pymdown-extensions" version = "10.3" description = "Extension pack for Python Markdown." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2771,7 +2669,6 @@ extra = ["pygments (>=2.12)"] name = "pyparsing" version = "3.1.1" description = "pyparsing module - Classes and methods to define and execute parsing grammars" -category = "main" optional = false python-versions = ">=3.6.8" files = [ @@ -2786,7 +2683,6 @@ diagrams = ["jinja2", 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-category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4285,7 +4129,6 @@ testing = ["build[virtualenv] (>=0.10)", "covdefaults (>=2.3)", "detect-test-pol name = "tqdm" version = "4.66.1" description = "Fast, Extensible Progress Meter" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4306,7 +4149,6 @@ telegram = ["requests"] name = "trio" version = "0.22.2" description = "A friendly Python library for async concurrency and I/O" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4327,7 +4169,6 @@ sortedcontainers = "*" name = "trio-websocket" version = "0.10.4" description = "WebSocket library for Trio" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4344,7 +4185,6 @@ wsproto = ">=0.14" name = "typer" version = "0.7.0" description = "Typer, build great CLIs. Easy to code. Based on Python type hints." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -4365,7 +4205,6 @@ test = ["black (>=22.3.0,<23.0.0)", "coverage (>=6.2,<7.0)", "isort (>=5.0.6,<6. name = "typer-cli" version = "0.0.13" description = "Run Typer scripts with completion, without having to create a package, using Typer CLI." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4382,7 +4221,6 @@ typer = ">=0.4.0,<=0.7.0" name = "typing-extensions" version = "4.8.0" description = "Backported and Experimental Type Hints for Python 3.8+" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4394,7 +4232,6 @@ files = [ name = "tzdata" version = "2023.3" description = "Provider of IANA time zone data" -category = "main" optional = false python-versions = ">=2" files = [ @@ -4406,7 +4243,6 @@ files = [ name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4421,7 +4257,6 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "url-normalize" version = "1.4.3" description = "URL normalization for Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -4436,7 +4271,6 @@ six = "*" name = "urllib3" version = "2.0.5" description = "HTTP library with thread-safe connection pooling, file post, and more." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4457,7 +4291,6 @@ zstd = ["zstandard (>=0.18.0)"] name = "uvicorn" version = "0.20.0" description = "The lightning-fast ASGI server." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4472,7 +4305,7 @@ h11 = ">=0.8" httptools = {version = ">=0.5.0", optional = true, markers = "extra == \"standard\""} python-dotenv = {version = ">=0.13", optional = true, markers = "extra == \"standard\""} pyyaml = {version = ">=5.1", optional = true, markers = "extra == \"standard\""} -uvloop = {version = ">=0.14.0,<0.15.0 || >0.15.0,<0.15.1 || >0.15.1", optional = true, markers = "sys_platform != \"win32\" and sys_platform != \"cygwin\" and platform_python_implementation != \"PyPy\" and extra == \"standard\""} +uvloop = {version = ">=0.14.0,<0.15.0 || >0.15.0,<0.15.1 || >0.15.1", optional = true, markers = "(sys_platform != \"win32\" and sys_platform != \"cygwin\") and platform_python_implementation != \"PyPy\" and extra == \"standard\""} watchfiles = {version = ">=0.13", optional = true, markers = "extra == \"standard\""} websockets = {version = ">=10.4", optional = true, markers = "extra == \"standard\""} @@ -4483,7 +4316,6 @@ standard = ["colorama (>=0.4)", "httptools (>=0.5.0)", "python-dotenv (>=0.13)", name = "uvloop" version = "0.17.0" description = "Fast implementation of asyncio event loop on top of libuv" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4528,7 +4360,6 @@ test = ["Cython (>=0.29.32,<0.30.0)", "aiohttp", "flake8 (>=3.9.2,<3.10.0)", "my name = "validators" version = "0.22.0" description = "Python Data Validation for Humans™" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4551,7 +4382,6 @@ tooling-extras = ["pyaml (>=23.7.0)", "pypandoc-binary (>=1.11)", "pytest (>=7.4 name = "virtualenv" version = "20.24.5" description = "Virtual Python Environment builder" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4572,7 +4402,6 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess name = "watchdog" version = "3.0.0" description = "Filesystem events monitoring" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4612,7 +4441,6 @@ watchmedo = ["PyYAML (>=3.10)"] name = "watchfiles" version = "0.20.0" description = "Simple, modern and high performance file watching and code reload in python." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4647,7 +4475,6 @@ anyio = ">=3.0.0" name = "webcolors" version = "1.13" description = "A library for working with the color formats defined by HTML and CSS." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4663,7 +4490,6 @@ tests = ["pytest", "pytest-cov"] name = "websocket-client" version = "1.6.3" description = "WebSocket client for Python with low level API options" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4680,7 +4506,6 @@ test = ["websockets"] name = "websockets" version = "11.0.3" description = "An implementation of the WebSocket Protocol (RFC 6455 & 7692)" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4760,7 +4585,6 @@ files = [ name = "win32-setctime" version = "1.1.0" description = "A small Python utility to set file creation time on Windows" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -4775,7 +4599,6 @@ dev = ["black (>=19.3b0)", "pytest (>=4.6.2)"] name = "wrapt" version = "1.15.0" description = "Module for decorators, wrappers and monkey patching." -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" files = [ @@ -4860,7 +4683,6 @@ files = [ name = "wsproto" version = "1.2.0" description = "WebSockets state-machine based protocol implementation" -category = "dev" optional = false python-versions = ">=3.7.0" files = [ @@ -4875,7 +4697,6 @@ h11 = ">=0.9.0,<1" name = "zipp" version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4890,4 +4711,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "c9e158f3706e78d180f43493639dcbe81de5f0ade1f3c2de615c651b372e7db0" +content-hash = "9206d7f577297edb00c7e910b1c3cc803642f2851dc6674efbdb844aa092e933" diff --git a/backend/pyproject.toml b/backend/pyproject.toml index 15be7e914..1ba854e6c 100644 --- a/backend/pyproject.toml +++ b/backend/pyproject.toml @@ -19,7 +19,7 @@ packages = [ python = "^3.9" pydantic = "^1.10.2" curies = "<1" -linkml = "^1.5.5" +linkml = "^1.6.1" prefixmaps = "^0.1.6" requests = "^2.28.1" diff --git a/backend/src/monarch_py/api/association.py b/backend/src/monarch_py/api/association.py index 6e0fe87b8..fd2308a90 100644 --- a/backend/src/monarch_py/api/association.py +++ b/backend/src/monarch_py/api/association.py @@ -12,7 +12,6 @@ @router.get("") -@router.get("/all") async def _get_associations( category: Union[List[str], None] = Query(default=None), subject: Union[List[str], None] = Query(default=None), @@ -35,6 +34,7 @@ async def _get_associations( ) return response + @router.get("/multi") async def _get_multi_entity_associations( entity: Union[List[str], None] = Query(default=None), diff --git a/backend/src/monarch_py/api/config.py b/backend/src/monarch_py/api/config.py index 98f8cfe12..937791701 100644 --- a/backend/src/monarch_py/api/config.py +++ b/backend/src/monarch_py/api/config.py @@ -5,21 +5,20 @@ from pydantic import BaseSettings -from monarch_py.implementations.oak.oak_implementation import OakImplementation from monarch_py.implementations.solr.solr_implementation import SolrImplementation from monarch_py.datamodels.model import TermSetPairwiseSimilarity - class Settings(BaseSettings): solr_host = os.getenv("SOLR_HOST") if os.getenv("SOLR_HOST") else "127.0.0.1" solr_port = os.getenv("SOLR_PORT") if os.getenv("SOLR_PORT") else 8983 solr_url = os.getenv("SOLR_URL") if os.getenv("SOLR_URL") else f"http://{solr_host}:{solr_port}/solr" phenio_db_path = os.getenv("PHENIO_DB_PATH") if os.getenv("PHENIO_DB_PATH") else "/data/phenio.db" - oak_server_host = os.getenv("OAK_SERVER_HOST", '127.0.0.1') + oak_server_host = os.getenv("OAK_SERVER_HOST", "127.0.0.1") oak_server_port = os.getenv("OAK_SERVER_PORT", 18811) + settings = Settings() @@ -35,7 +34,7 @@ def convert_nans(input_dict, to_value=None): """ for k, v in input_dict.items(): for ik, iv in v.items(): - if iv == 'NaN': + if iv == "NaN": input_dict[k][ik] = None return input_dict @@ -57,29 +56,25 @@ def compare(self, subjects, objects): # and just return TermSetPairwiseSimilarity(**data) # remove these similarity maps and fold them into the _best_matches dicts - object_best_matches_similarity_map = convert_nans( - data.pop('object_best_matches_similarity_map') - ) - subject_best_matches_similarity_map = convert_nans( - data.pop('subject_best_matches_similarity_map') - ) + object_best_matches_similarity_map = convert_nans(data.pop("object_best_matches_similarity_map")) + subject_best_matches_similarity_map = convert_nans(data.pop("subject_best_matches_similarity_map")) # convert to a format that can be coerced into a TermSetPairwiseSimilarity converted_data = { **data, **{ # flatten the nested termset dicts - 'subject_termset': {k: v for d in data['subject_termset'] for k, v in d.items()}, - 'object_termset': {k: v for d in data['object_termset'] for k, v in d.items()}, - 'subject_best_matches': { - k: {**v, 'similarity': subject_best_matches_similarity_map[k]} - for k, v in data['subject_best_matches'].items() + "subject_termset": {k: v for d in data["subject_termset"] for k, v in d.items()}, + "object_termset": {k: v for d in data["object_termset"] for k, v in d.items()}, + "subject_best_matches": { + k: {**v, "similarity": subject_best_matches_similarity_map[k]} + for k, v in data["subject_best_matches"].items() + }, + "object_best_matches": { + k: {**v, "similarity": object_best_matches_similarity_map[k]} + for k, v in data["object_best_matches"].items() }, - 'object_best_matches': { - k: {**v, 'similarity': object_best_matches_similarity_map[k]} - for k, v in data['object_best_matches'].items() - } - } + }, } return TermSetPairwiseSimilarity(**converted_data) diff --git a/backend/src/monarch_py/api/histopheno.py b/backend/src/monarch_py/api/histopheno.py index 41517e19f..a17cd208c 100644 --- a/backend/src/monarch_py/api/histopheno.py +++ b/backend/src/monarch_py/api/histopheno.py @@ -15,7 +15,7 @@ async def _get_histopheno( title="ID of the entity to get histopheno data for", examples=["MONDO:0019391"], ) - ) -> HistoPheno: +) -> HistoPheno: """Retrieves the entity with the specified id""" response = solr().get_histopheno(id) if response is None: diff --git a/backend/src/monarch_py/api/semsim.py b/backend/src/monarch_py/api/semsim.py index a34b1b8bd..4a3edb438 100644 --- a/backend/src/monarch_py/api/semsim.py +++ b/backend/src/monarch_py/api/semsim.py @@ -10,8 +10,8 @@ @router.get("/compare/{subjects}/{objects}") def _compare( - subjects: str = Path(...,title="List of subjects for comparison"), - objects: str = Path(...,title="List of objects for comparison"), + subjects: str = Path(..., title="List of subjects for comparison"), + objects: str = Path(..., title="List of objects for comparison"), ): """Get pairwise similarity between two sets of terms diff --git a/backend/src/monarch_py/cli.py b/backend/src/monarch_py/cli.py index 00a0faa47..9b1c0c41d 100644 --- a/backend/src/monarch_py/cli.py +++ b/backend/src/monarch_py/cli.py @@ -114,7 +114,7 @@ def associations( "-f", help="The format of the output (json, yaml, tsv, table)", ), - output: str = typer.Option(None, "--output", "-o", help="The path to the output file"), + output: str = typer.Option(None, "--output", "-O", help="The path to the output file"), ): """ Paginate through associations diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py index 75ebb54b7..1c90e7aa9 100644 --- a/backend/src/monarch_py/datamodels/model.py +++ b/backend/src/monarch_py/datamodels/model.py @@ -45,6 +45,7 @@ class AssociationDirectionEnum(str, Enum): class Association(ConfiguredBaseModel): id: str = Field(...) + category: Optional[str] = Field(None) subject: str = Field(...) original_subject: Optional[str] = Field(None) subject_namespace: Optional[str] = Field( @@ -90,25 +91,32 @@ class Association(ConfiguredBaseModel): object_taxon_label: Optional[str] = Field(None) primary_knowledge_source: Optional[str] = Field(None) aggregator_knowledge_source: Optional[List[str]] = Field(default_factory=list) - category: Optional[str] = Field(None) negated: Optional[bool] = Field(None) + pathway: Optional[str] = Field(None) + evidence_count: Optional[int] = Field( + None, + description="""count of supporting documents, evidence codes, and sources supplying evidence""", + ) + has_evidence: Optional[List[str]] = Field(default_factory=list) + has_evidence_links: Optional[List[ExpandedCurie]] = Field( + default_factory=list, + description="""List of ExpandedCuries with id and url for evidence""", + ) provided_by: Optional[str] = Field(None) provided_by_link: Optional[ExpandedCurie] = Field( None, description="""A link to the docs for the knowledge source that provided the node/edge.""", ) publications: Optional[List[str]] = Field(default_factory=list) + publications_links: Optional[List[ExpandedCurie]] = Field( + default_factory=list, + description="""List of ExpandedCuries with id and url for publications""", + ) qualifiers: Optional[List[str]] = Field(default_factory=list) frequency_qualifier: Optional[str] = Field(None) - has_evidence: Optional[List[str]] = Field(default_factory=list) onset_qualifier: Optional[str] = Field(None) sex_qualifier: Optional[str] = Field(None) stage_qualifier: Optional[str] = Field(None) - evidence_count: Optional[int] = Field( - None, - description="""count of supporting documents, evidence codes, and sources supplying evidence""", - ) - pathway: Optional[str] = Field(None) frequency_qualifier_label: Optional[str] = Field( None, description="""The name of the frequency_qualifier entity""" ) @@ -223,6 +231,7 @@ class DirectionalAssociation(Association): description="""The directionality of the association relative to a given entity for an association_count. If the entity is the subject or in the subject closure, the direction is forwards, if it is the object or in the object closure, the direction is backwards.""", ) id: str = Field(...) + category: Optional[str] = Field(None) subject: str = Field(...) original_subject: Optional[str] = Field(None) subject_namespace: Optional[str] = Field( @@ -268,25 +277,32 @@ class DirectionalAssociation(Association): object_taxon_label: Optional[str] = Field(None) primary_knowledge_source: Optional[str] = Field(None) aggregator_knowledge_source: Optional[List[str]] = Field(default_factory=list) - category: Optional[str] = Field(None) negated: Optional[bool] = Field(None) + pathway: Optional[str] = Field(None) + evidence_count: Optional[int] = Field( + None, + description="""count of supporting documents, evidence codes, and sources supplying evidence""", + ) + has_evidence: Optional[List[str]] = Field(default_factory=list) + has_evidence_links: Optional[List[ExpandedCurie]] = Field( + default_factory=list, + description="""List of ExpandedCuries with id and url for evidence""", + ) provided_by: Optional[str] = Field(None) provided_by_link: Optional[ExpandedCurie] = Field( None, description="""A link to the docs for the knowledge source that provided the node/edge.""", ) publications: Optional[List[str]] = Field(default_factory=list) + publications_links: Optional[List[ExpandedCurie]] = Field( + default_factory=list, + description="""List of ExpandedCuries with id and url for publications""", + ) qualifiers: Optional[List[str]] = Field(default_factory=list) frequency_qualifier: Optional[str] = Field(None) - has_evidence: Optional[List[str]] = Field(default_factory=list) onset_qualifier: Optional[str] = Field(None) sex_qualifier: Optional[str] = Field(None) stage_qualifier: Optional[str] = Field(None) - evidence_count: Optional[int] = Field( - None, - description="""count of supporting documents, evidence codes, and sources supplying evidence""", - ) - pathway: Optional[str] = Field(None) frequency_qualifier_label: Optional[str] = Field( None, description="""The name of the frequency_qualifier entity""" ) diff --git a/backend/src/monarch_py/datamodels/model.yaml b/backend/src/monarch_py/datamodels/model.yaml index e64d91299..7853f375c 100644 --- a/backend/src/monarch_py/datamodels/model.yaml +++ b/backend/src/monarch_py/datamodels/model.yaml @@ -26,6 +26,7 @@ classes: Association: slots: - id + - category - subject - original_subject - subject_namespace @@ -47,29 +48,20 @@ classes: - object_taxon_label - primary_knowledge_source - aggregator_knowledge_source - - category - negated + - pathway + - evidence_count + - has_evidence + - has_evidence_links - provided_by - provided_by_link - publications + - publications_links - qualifiers - frequency_qualifier - - has_evidence - onset_qualifier - sex_qualifier - stage_qualifier - - evidence_count - - pathway - - subject_label - - subject_namespace - - subject_category - - subject_closure - - subject_closure_label - - object_label - - object_namespace - - object_category - - object_closure - - object_closure_label - frequency_qualifier_label - frequency_qualifier_namespace - frequency_qualifier_category @@ -328,6 +320,12 @@ slots: has_evidence: range: string multivalued: true + has_evidence_links: + description: List of ExpandedCuries with id and url for evidence + range: ExpandedCurie + multivalued: true + inlined: true + inlined_as_list: true highlight: description: matching text snippet containing html tags range: string @@ -396,6 +394,12 @@ slots: range: string publications: multivalued: true + publications_links: + description: List of ExpandedCuries with id and url for publications + range: ExpandedCurie + multivalued: true + inlined: true + inlined_as_list: true qualifiers: multivalued: true score: diff --git a/backend/src/monarch_py/implementations/oak/oak_implementation.py b/backend/src/monarch_py/implementations/oak/oak_implementation.py index a1b1b5451..513fc5c93 100644 --- a/backend/src/monarch_py/implementations/oak/oak_implementation.py +++ b/backend/src/monarch_py/implementations/oak/oak_implementation.py @@ -27,7 +27,6 @@ def init_semsim(self, phenio_path: str = None, force_update: bool = False): start = time.time() # self.semsim = get_adapter(f"sqlite:obo:phenio") - if phenio_path: logger.debug(f"Creating semsimian adapter using phenio_path at {phenio_path}") self.semsim = get_adapter(f"semsimian:sqlite:{phenio_path}") diff --git a/backend/src/monarch_py/implementations/solr/solr_implementation.py b/backend/src/monarch_py/implementations/solr/solr_implementation.py index 3e554e7e0..8445ea741 100644 --- a/backend/src/monarch_py/implementations/solr/solr_implementation.py +++ b/backend/src/monarch_py/implementations/solr/solr_implementation.py @@ -10,7 +10,6 @@ AssociationTableResults, CategoryGroupedAssociationResults, Entity, - ExpandedCurie, HistoPheno, MultiEntityAssociationResults, Node, @@ -41,9 +40,8 @@ from monarch_py.interfaces.association_interface import AssociationInterface from monarch_py.interfaces.entity_interface import EntityInterface from monarch_py.interfaces.search_interface import SearchInterface -from monarch_py.service.curie_service import CurieService from monarch_py.service.solr_service import SolrService -from monarch_py.utils.utils import get_provided_by_link +from monarch_py.utils.utils import get_provided_by_link, get_links_for_field @dataclass @@ -113,13 +111,9 @@ def get_entity(self, id: str, extra: bool) -> Optional[Union[Node, Entity]]: node.node_hierarchy = self._get_node_hierarchy(node) node.association_counts = self.get_association_counts(id).items - node.external_links = ( - [ExpandedCurie(id=curie, url=CurieService().expand(curie)) for curie in node.xref] if node.xref else [] - ) - node.provided_by_link = ExpandedCurie( - id=node.provided_by.replace("_nodes", "").replace("_edges", "") if node.provided_by else None, - url=get_provided_by_link(node.provided_by), - ) + node.external_links = get_links_for_field(node.xref) if node.xref else [] + node.provided_by_link = get_provided_by_link(node.provided_by) + return node ### Entity helpers ### diff --git a/backend/src/monarch_py/implementations/solr/solr_parsers.py b/backend/src/monarch_py/implementations/solr/solr_parsers.py index c5208ae73..e1c2ce5fe 100644 --- a/backend/src/monarch_py/implementations/solr/solr_parsers.py +++ b/backend/src/monarch_py/implementations/solr/solr_parsers.py @@ -1,6 +1,8 @@ from typing import Dict, List from loguru import logger +from pydantic import ValidationError + from monarch_py.datamodels.model import ( Association, AssociationCount, @@ -10,7 +12,6 @@ AssociationTableResults, DirectionalAssociation, Entity, - ExpandedCurie, FacetField, FacetValue, HistoBin, @@ -20,8 +21,7 @@ ) from monarch_py.datamodels.solr import HistoPhenoKeys, SolrQueryResult from monarch_py.utils.association_type_utils import get_association_type_mapping_by_query_string -from monarch_py.utils.utils import get_provided_by_link -from pydantic import ValidationError +from monarch_py.utils.utils import get_links_for_field, get_provided_by_link #################### # Parser functions # @@ -40,9 +40,12 @@ def parse_associations( except ValidationError: logger.error(f"Validation error for {doc}") raise ValidationError - association.provided_by_link = ExpandedCurie( - id=association.provided_by.replace("_nodes", "").replace("_edges", ""), - url=get_provided_by_link(association.provided_by), + association.provided_by_link = get_provided_by_link(association.provided_by) if association.provided_by else [] + association.has_evidence_links = ( + get_links_for_field(association.has_evidence) if association.has_evidence else [] + ) + association.publications_links = ( + get_links_for_field(association.publications) if association.publications else [] ) associations.append(association) total = query_result.response.num_found @@ -100,6 +103,15 @@ def parse_association_table( try: direction = get_association_direction(entity, doc) association = DirectionalAssociation(**doc, direction=direction) + association.provided_by_link = ( + get_provided_by_link(association.provided_by) if association.provided_by else [] + ) + association.has_evidence_links = ( + get_links_for_field(association.has_evidence) if association.has_evidence else [] + ) + association.publications_links = ( + get_links_for_field(association.publications) if association.publications else [] + ) associations.append(association) except ValidationError: logger.error(f"Validation error for {doc}") diff --git a/backend/src/monarch_py/service/curie_service.py b/backend/src/monarch_py/service/curie_service.py index e82208aa3..cd62ebe22 100644 --- a/backend/src/monarch_py/service/curie_service.py +++ b/backend/src/monarch_py/service/curie_service.py @@ -1,7 +1,7 @@ ### make a singleton class that uses prefixmap and curies to expand curies from curies import Converter -from prefixmaps.io.parser import load_multi_context, load_context +from prefixmaps.io.parser import load_multi_context class CurieService: diff --git a/backend/src/monarch_py/solr_cli.py b/backend/src/monarch_py/solr_cli.py index 1a921877d..9d11b64af 100644 --- a/backend/src/monarch_py/solr_cli.py +++ b/backend/src/monarch_py/solr_cli.py @@ -171,7 +171,9 @@ def associations( @solr_app.command("multi-entity-associations") def multi_entity_associations( entity: List[str] = typer.Option(None, "--entity", "-e", help="Entity ID to get associations for"), - counterpart_category: List[str] = typer.Option(None, "--counterpart-category", "-c", help="Counterpart category to get associations for"), + counterpart_category: List[str] = typer.Option( + None, "--counterpart-category", "-c", help="Counterpart category to get associations for" + ), limit: int = typer.Option(20, "--limit", "-l"), offset: int = typer.Option(0, "--offset"), fmt: str = typer.Option( @@ -198,7 +200,7 @@ def multi_entity_associations( args = locals() args.pop("fmt", None) args.pop("output", None) - args['limit_per_group'] = args.pop('limit') + args["limit_per_group"] = args.pop("limit") solr = get_solr(update=False) response = solr.get_multi_entity_associations(**args) diff --git a/backend/src/monarch_py/utils/utils.py b/backend/src/monarch_py/utils/utils.py index 9532e2af8..422ff2f04 100644 --- a/backend/src/monarch_py/utils/utils.py +++ b/backend/src/monarch_py/utils/utils.py @@ -5,11 +5,21 @@ import typer import yaml -from monarch_py.datamodels.model import AssociationCountList, ConfiguredBaseModel, Entity, HistoPheno, Node, Results from rich import print_json from rich.console import Console from rich.table import Table +from monarch_py.datamodels.model import ( + AssociationCountList, + ConfiguredBaseModel, + Entity, + ExpandedCurie, + HistoPheno, + Node, + Results, +) +from monarch_py.service.curie_service import CurieService + MONARCH_DATA_URL = "https://data.monarchinitiative.org/monarch-kg-dev" SOLR_DATA_URL = f"{MONARCH_DATA_URL}/latest/solr.tar.gz" SQL_DATA_URL = f"{MONARCH_DATA_URL}/latest/monarch-kg.db.gz" @@ -64,12 +74,21 @@ def set_log_level(log_level: str): loguru.logger.add(sys.stderr, level=log_level) -def get_provided_by_link(provided_by: str) -> str: +### URL fetching methods ### + + +def get_links_for_field(field: List[str]) -> List[ExpandedCurie]: + return [ExpandedCurie(id=curie, url=CurieService().expand(curie.replace("PMID", "PUBMED"))) for curie in field] + + +def get_provided_by_link(provided_by: str) -> List[ExpandedCurie]: """Returns a link to the provided_by resource.""" - pb = provided_by.replace("_nodes", "").replace("_edges", "").split("_") base_url = "https://monarch-initiative.github.io/monarch-ingest/Sources" + pb = provided_by.replace("_nodes", "").replace("_edges", "").split("_") slug = f"{pb[0]}/#{'_'.join(pb[1:])}" - return f"{base_url}/{slug}" + return ExpandedCurie( + id=provided_by.replace("_nodes", "").replace("_edges", "") if provided_by else None, url=f"{base_url}/{slug}" + ) ### Output conversion methods ### diff --git a/backend/tests/fixtures/association_counts.py b/backend/tests/fixtures/association_counts.py index ffd0d3c8c..c9c7da8c6 100644 --- a/backend/tests/fixtures/association_counts.py +++ b/backend/tests/fixtures/association_counts.py @@ -5,15 +5,8 @@ def association_counts(): return { "items": [ - { - "label": "Phenotypes", - "count": 2166, - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - }, - { - "label": "Causal Genes", - "count": 124, - "category": "biolink:CausalGeneToDiseaseAssociation", - }, + {"label": "Phenotypes", "count": 4027, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"}, + {"label": "Causal Genes", "count": 124, "category": "biolink:CausalGeneToDiseaseAssociation"}, + {"label": "Correlated Genes", "count": 151, "category": "biolink:CorrelatedGeneToDiseaseAssociation"}, ] } diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py index 6abf71a00..7af443a25 100644 --- a/backend/tests/fixtures/association_counts_response.py +++ b/backend/tests/fixtures/association_counts_response.py @@ -40,74 +40,41 @@ def association_counts_response(): }, }, "response": { - "num_found": 2823, + "num_found": 4838, "start": 0, "docs": [ { - "id": "urn:uuid:a54e0b8c-af55-459b-ae98-a7e0ae60b190", - "predicate": "biolink:subclass_of", + "id": "urn:uuid:e4e8dbec-cb0c-44e9-b1cb-8be3b357b7b8", + "predicate": "biolink:related_to", "category": "biolink:Association", "aggregator_knowledge_source": ["infores:phenio"], "primary_knowledge_source": "infores:mondo", "provided_by": "phenio_edges", - "subject": "MONDO:0009364", - "object": "MONDO:0000171", + "subject": "MONDO:0018276", + "object": "GO:0006486", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", "MONDO:0018276", - "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0009364", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", - "MONDO:0700070", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], "subject_closure_label": [ "entity", @@ -116,58 +83,122 @@ def association_counts_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", "neuromuscular disease", - "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "myopathy caused by variation in POMT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy", + "object_namespace": "GO", + "object_category": "biolink:BiologicalProcessOrActivity", "object_closure": [ + "GO:0008150", + "BFO:0000003", + "GO:0036211", + "GO:0043413", + "GO:0006486", + "GO:1901564", + "GO:0070085", + "GO:0043412", + "GO:0006807", + "GO:0044238", + "GO:0043170", + "GO:0071704", + "BFO:0000015", + "BFO:0000001", + "GO:0008152", + "GO:0019538", + "BFO:0000001", + "BFO:0000003", + "BFO:0000015", + "GO:0008150", + "GO:0009987", + "GO:0008152", + "GO:0044237", + "GO:0071704", + "GO:0009058", + "GO:0044238", + "GO:0006807", + "GO:0044249", + "GO:0043170", + "GO:1901135", + "GO:1901564", + "GO:1901576", + "GO:0019538", + "GO:0009059", + "GO:1901137", + "GO:0009100", + "GO:1901566", + "GO:0009101", + ], + "object_closure_label": [ + "entity", + "entity", + "occurrent", + "occurrent", + "process", + "process", + "protein glycosylation", + "nitrogen compound metabolic process", + "nitrogen compound metabolic process", + "biological_process", + "biological_process", + "metabolic process", + "metabolic process", + "biosynthetic process", + "macromolecule biosynthetic process", + "glycoprotein metabolic process", + "glycoprotein biosynthetic process", + "cellular process", + "protein metabolic process", + "protein metabolic process", + "protein modification process", + "macromolecule metabolic process", + "macromolecule metabolic process", + "macromolecule modification", + "macromolecule glycosylation", + "cellular metabolic process", + "primary metabolic process", + "primary metabolic process", + "cellular biosynthetic process", + "glycosylation", + "organic substance metabolic process", + "organic substance metabolic process", + "carbohydrate derivative metabolic process", + "carbohydrate derivative biosynthetic process", + "organonitrogen compound metabolic process", + "organonitrogen compound metabolic process", + "organonitrogen compound biosynthetic process", + "organic substance biosynthetic process", + ], + "object_label": "protein glycosylation", + "evidence_count": 0, + }, + { + "id": "uuid:a82ac92f-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:613151", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:613151"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0013155", + "object": "HP:0000486", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", @@ -177,170 +208,305 @@ def association_counts_response(): "MONDO:0005071", "MONDO:0020121", "MONDO:0700068", + "MONDO:0000172", "MONDO:0700223", "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0013155", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", - "MONDO:0020247", "MONDO:0005066", - "MONDO:0005328", + "MONDO:0018277", "MONDO:0019950", "MONDO:0016155", - "MONDO:0700066", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "muscular dystrophy-dystroglycanopathy, type B", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", + "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3", "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", + "congenital muscular dystrophy with cerebellar involvement", "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", "inborn errors of metabolism", "neuromuscular disease", - "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0080581", + "BFO:0000020", + "UPHENO:0002433", + "UPHENO:0003020", + "UPHENO:0079828", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0000707", + "HP:0012373", + "HP:0000496", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0000708", + "HP:0000486", + "UPHENO:0079826", + "UPHENO:0004523", + "HP:0011446", + "HP:0000549", + "UPHENO:0049587", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "BFO:0000141", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "UBERON:0000466", + "GO:0007610", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0000015", + "NBO:0000313", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0006800", + "NBO:0000338", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0001016", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0010222", + "NBO:0000001", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "NBO:0000444", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "immaterial entity", + "behavior", + "biological_process", + "multicellular organismal process", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Strabismus (HPO)", + "Abnormality of eye movement (HPO)", + "Abnormal conjugate eye movement (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal nervous system physiology (HPO)", + "body part movement", + "behavior process", + "kinesthetic behavior", + "eye movement", + "quality", + "non-material anatomical boundary", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "immaterial anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "nervous system", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "anatomical line", + "craniocervical region", + "multicellular anatomical structure", + "anatomical line between pupils", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormality of nervous system physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", + ], + "object_label": "Strabismus (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:6a4b5bf7-4254-49cf-bb21-42549480b64f", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0009667", - "object": "MONDO:0000171", + "id": "uuid:a73a092e-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:615042", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:615042"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0014023", + "object": "HP:0000486", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", "MONDO:0018276", - "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0014023", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0018939", - "MONDO:0020246", - "MONDO:0009667", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", + "MONDO:0017749", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", - "MONDO:0020247", + "MONDO:0005500", "MONDO:0005066", - "MONDO:0005328", "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], "subject_closure_label": [ "entity", @@ -349,1866 +515,261 @@ def association_counts_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3", + "congenital disorder of glycosylation type I", + "congenital muscular dystrophy with intellectual disability and severe epilepsy", "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", + "disorder of multiple glycosylation", "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "muscle-eye-brain disease", "inborn errors of metabolism", "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "human disease", - "hereditary 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morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", + "congenital muscular dystrophy", + "skeletal muscle disorder", + "muscular dystrophy", + "disorder of glycosylation", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "subject_label": "congenital muscular dystrophy with intellectual disability and severe epilepsy", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + 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+ "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", + ], + "object_label": "Strabismus (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:6fc3a05c-fd6a-46e1-8815-25a4a20e9954", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0014071", - "object": "MONDO:0000171", + "id": "uuid:a5790e7e-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:615356", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:615356"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0014144", + "object": "HP:0000486", 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"MONDO:0015286", + "MONDO:0015152", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], "subject_closure_label": [ "entity", @@ -2217,175 +778,482 @@ def association_counts_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "autosomal genetic disease", "musculoskeletal system disorder", - "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "muscle-eye-brain disease", - "inborn errors of metabolism", + "movement disorder", + "autosomal recessive disease", + "autosomal recessive limb-girdle muscular dystrophy type R18", + "autosomal recessive limb-girdle muscular dystrophy", + "progressive muscular dystrophy", + "limb-girdle muscular dystrophy", + "intellectual disability-hyperkinetic movement-truncal ataxia syndrome", "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type R18", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0018282", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0080581", + "BFO:0000020", + "UPHENO:0002433", + "UPHENO:0003020", + "UPHENO:0079828", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0000707", + "HP:0012373", + "HP:0000496", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0000708", + "HP:0000486", + "UPHENO:0079826", + "UPHENO:0004523", + "HP:0011446", + "HP:0000549", + "UPHENO:0049587", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "BFO:0000141", + 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"specifically dependent continuant", + "material entity", + "immaterial entity", + "behavior", + "biological_process", + "multicellular organismal process", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Strabismus (HPO)", + "Abnormality of eye movement (HPO)", + "Abnormal conjugate eye movement (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal nervous system physiology (HPO)", + "body part movement", + "behavior process", + "kinesthetic behavior", + "eye movement", + "quality", + "non-material anatomical boundary", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical 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"abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", + ], + "object_label": "Strabismus (HPO)", + "evidence_count": 2, + }, + { + "id": "uuid:abeb7ac4-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:617404", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:617404"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0024607", + "object": "HP:0000486", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0024607", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", "neuromuscular disease", - "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", + "congenital muscular dystrophy with cataracts and intellectual disability", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "subject_label": "congenital muscular dystrophy with cataracts and intellectual disability", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0080581", + "BFO:0000020", + "UPHENO:0002433", + "UPHENO:0003020", + "UPHENO:0079828", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0000707", + "HP:0012373", + "HP:0000496", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0000708", + "HP:0000486", + "UPHENO:0079826", + "UPHENO:0004523", + "HP:0011446", + "HP:0000549", + "UPHENO:0049587", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "BFO:0000141", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "UBERON:0000466", + "GO:0007610", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0000015", + "NBO:0000313", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0006800", + "NBO:0000338", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0001016", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0010222", + "NBO:0000001", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "NBO:0000444", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "immaterial entity", + "behavior", + "biological_process", + "multicellular organismal process", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Strabismus (HPO)", + "Abnormality of eye movement (HPO)", + "Abnormal conjugate eye movement (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal nervous system physiology (HPO)", + "body part movement", + "behavior process", + "kinesthetic behavior", + "eye movement", + "quality", + "non-material anatomical boundary", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "immaterial anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "nervous system", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "anatomical line", + "craniocervical region", + "multicellular anatomical structure", + "anatomical line between pupils", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormality of nervous system physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", + ], + "object_label": "Strabismus (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:a20f59e6-2468-4f26-a789-04cd5d5bd97f", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0014101", - "object": "MONDO:0000171", + "id": "uuid:abeb7be1-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:614643", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:614643"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0013835", + "object": "HP:0000490", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ @@ -2403,12 +1271,12 @@ def association_counts_response(): "MONDO:0005283", "MONDO:0020238", "BFO:0000002", - "MONDO:0014101", "MONDO:0016185", "MONDO:0000171", "BFO:0000017", "MONDO:0018869", "BFO:0000020", + "MONDO:0013835", "MONDO:0016157", "MONDO:0017745", "BFO:0000016", @@ -2460,7 +1328,7 @@ def association_counts_response(): "retinal disorder", "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -2496,135 +1364,514 @@ def association_counts_response(): "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0018282", + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0000490", + "HP:0012372", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0049367", + "UPHENO:0002764", + "UPHENO:0018424", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0018390", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0020584", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "HP:0100886", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Deeply set eye (HPO)", + "Abnormal eye morphology (HPO)", + "Abnormality of globe location (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal location of anatomical entity", + "abnormal location of eyeball of camera-type eye", + "abnormal anatomical entity morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity topology in independent continuant", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology", + ], + "object_label": "Deeply set eye (HPO)", + "evidence_count": 2, + }, + { + "id": "uuid:aa6b44e5-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:226670", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:226670"], + "has_evidence": ["ECO:0000501"], + "subject": "MONDO:0009181", + "object": "HP:0000491", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0016198", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0006617", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", + "MONDO:0017610", + "MONDO:0006025", + "MONDO:0016106", + "MONDO:0002051", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", + "MONDO:0100118", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", + "MONDO:0002254", + "MONDO:0009181", + "MONDO:0019276", + "MONDO:0005093", "OGMS:0000031", - "MONDO:0015327", + "MONDO:0019268", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", + "MONDO:0006541", + "MONDO:0015152", + "BFO:0000001", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "autosomal genetic disease", + "integumentary system disorder", "musculoskeletal system disorder", - "congenital nervous system disorder", + "syndromic disease", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", + "skin disorder", "myopathy", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", + "autosomal recessive disease", + "epidermolysis bullosa", + "vesiculobullous skin disease", + "epidermolysis bullosa simplex 5B, with muscular dystrophy", + "autosomal recessive limb-girdle muscular dystrophy", + "progressive muscular dystrophy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", + "qualitative or quantitative defects of plectin", + "limb-girdle muscular dystrophy", + "epidermolysis bullosa simplex", "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", + "epidermal disease", + "inherited epidermolysis bullosa", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", + "hereditary skin disorder", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "subject_label": "epidermolysis bullosa simplex 5B, with muscular dystrophy", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082682", + "UPHENO:0082875", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0080377", + "UPHENO:0054970", + "UPHENO:0002948", + "HP:0004328", + "UPHENO:0020998", + "UPHENO:0001001", + "UPHENO:0074763", + "UPHENO:0074632", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "HP:0010978", + "UPHENO:0002764", + "UPHENO:0021662", + "UPHENO:0082723", + "UPHENO:0001002", + "HP:0012647", + "HP:0000118", + "BFO:0000002", + "HP:0100533", + "UPHENO:0080221", + "UPHENO:0083263", + "BFO:0000020", + "HP:0000481", + "UPHENO:0003020", + "UPHENO:0049584", + "HP:0000234", + "UPHENO:0002332", + "HP:0002715", + "UPHENO:0015280", + "UPHENO:0080693", + "HP:0000271", + "HP:0012373", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002263", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0049588", + "HP:0000491", + "UPHENO:0020584", + "UPHENO:0059829", + "UPHENO:0080662", + "UPHENO:0076692", + "UPHENO:0074685", + "UPHENO:0076684", + "UPHENO:0049587", + "BFO:0000001", + "HP:0012649", + "PATO:0000001", + "UPHENO:0074572", + "HP:0011495", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0050896", + "PR:000050567", + "UBERON:0000465", + "GO:0006950", + "UBERON:0000483", + "UBERON:0012430", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0000964", + "GO:0006952", + "UBERON:0019304", + "UBERON:0010371", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "GO:0006954", + "UBERON:0007625", + "UBERON:0015808", + "UBERON:0000019", + "UBERON:0010313", + "UBERON:0010230", + "UBERON:0010409", + "UBERON:0000479", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0002405", + "UBERON:0001772", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000060", + "UBERON:0004923", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "response to stress", + "defense response", + "inflammatory response", + "biological_process", + "response to stimulus", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormal cornea morphology (HPO)", + "Keratitis (HPO)", + "Abnormality of the immune system (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormality of immune system physiology (HPO)", + "Abnormal corneal epithelium morphology (HPO)", + "Abnormal eye morphology (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal inflammatory response (HPO)", + "Increased inflammatory response (HPO)", + "Inflammatory abnormality of the eye (HPO)", + "quality", + "protein-containing material entity", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical wall", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "tissue", + "epithelium", + "cornea", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "corneal epithelium", + "anterior segment of eyeball", + "visual system", + "immune system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "organ component layer", + "pigment epithelium of eye", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "neural crest-derived structure", + "structure with developmental contribution from neural crest", + "ecto-epithelium", + "ocular surface region", + "subdivision of organism along main body axis", + "tunica fibrosa of eyeball", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "eye epithelium", + "sensory organ epithelium", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of immune system physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal immune system", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal cornea morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal corneal epithelium morphology", + "abnormal inflammatory response", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal response to stress", + "increased biological_process", + "abnormal biological_process in independent continuant", + "increased biological_process in independent continuant", + "increased inflammatory response in eyeball of camera-type eye", + "increased inflammatory response in independent continuant", + "increased biological_process in eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "increased inflammatory response", + "abnormal anatomical entity morphology", + "changed biological_process rate in independent continuant", + "changed biological_process rate", + "increased qualitatively biological_process", + "increased qualitatively inflammatory response", + "abnormal multicellular organism morphology", + "increased qualitatively biological_process in independent continuant", + "increased qualitatively inflammatory response in independent continuant", + "abnormality of anatomical entity physiology", + "increased qualitatively response to stimulus", + ], + "object_label": "Keratitis (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:f7c423b7-6f4c-4663-9ead-41d529a7cf2b", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0014120", - "object": "MONDO:0000171", + "id": "uuid:a74a1018-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:253800", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:253800"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0009678", + "object": "HP:0000496", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0700067", "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", "MONDO:0017741", - "MONDO:0014120", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", @@ -2653,10 +1900,12 @@ def association_counts_response(): "MONDO:0002081", "MONDO:0016184", "MONDO:0016156", + "MONDO:0018939", "MONDO:0020246", "MONDO:0021147", "MONDO:0044137", "MONDO:0019755", + "MONDO:0009678", "OGMS:0000031", "MONDO:0015327", "MONDO:0003847", @@ -2691,7 +1940,7 @@ def association_counts_response(): "retinal disorder", "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -2707,6 +1956,7 @@ def association_counts_response(): "qualitative or quantitative defects of alpha-dystroglycan", "lissencephaly spectrum disorders", "cobblestone lissencephaly", + "muscle-eye-brain disease", "inborn errors of metabolism", "neuromuscular disease", "developmental defect during embryogenesis", @@ -2722,15 +1972,206 @@ def association_counts_response(): "vitreous body disorder", "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", + "myopathy caused by variation in FKTN", "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0080581", + "BFO:0000020", + "UPHENO:0002433", + "UPHENO:0003020", + "UPHENO:0079828", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0000707", + "HP:0012373", + "HP:0000496", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0000708", + "UPHENO:0079826", + "UPHENO:0004523", + "HP:0011446", + "UPHENO:0049587", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "GO:0007610", + "UBERON:0000061", + "UBERON:0034923", + "NBO:0000313", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "NBO:0000338", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0001016", + "UBERON:0004456", + "UBERON:0001032", + "NBO:0000001", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "NBO:0000444", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "behavior", + "biological_process", + "multicellular organismal process", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of eye movement (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal nervous system physiology (HPO)", + "body part movement", + "behavior process", + "kinesthetic behavior", + "eye movement", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "nervous system", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormality of nervous system physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", + ], + "object_label": "Abnormality of eye movement (HPO)", + "evidence_count": 2, + }, + { + "id": "uuid:a8bae583-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:236670", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:236670"], + "has_evidence": ["ECO:0000501"], + "subject": "MONDO:0009364", + "object": "HP:0000501", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", @@ -2763,6 +2204,7 @@ def association_counts_response(): "MONDO:0002081", "MONDO:0016184", "MONDO:0016156", + "MONDO:0009364", "MONDO:0020246", "MONDO:0021147", "MONDO:0044137", @@ -2770,6 +2212,7 @@ def association_counts_response(): "OGMS:0000031", "MONDO:0015327", "MONDO:0003847", + "MONDO:0700070", "MONDO:0003939", "MONDO:0002022", "MONDO:0015286", @@ -2783,7 +2226,7 @@ def association_counts_response(): "MONDO:0016155", "MONDO:0700066", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", @@ -2801,6 +2244,7 @@ def association_counts_response(): "retinal disorder", "eye disorder", "myopathy", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -2832,30 +2276,164 @@ def association_counts_response(): "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", "myopathy caused by variation in POMGNT1", + "myopathy caused by variation in POMT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Glaucoma (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], + "object_label": "Glaucoma (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:9d167233-70b8-4d7d-aa5d-f6dac17ba835", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0014140", - "object": "MONDO:0000171", + "id": "uuid:a8aad663-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:613150", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:613150"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0013154", + "object": "HP:0000501", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0700084", "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", "MONDO:0017741", + "MONDO:0013154", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", @@ -2872,6 +2450,7 @@ def association_counts_response(): "MONDO:0018869", "BFO:0000020", "MONDO:0016157", + "MONDO:0700071", "MONDO:0017745", "BFO:0000016", "MONDO:0020120", @@ -2887,7 +2466,6 @@ def association_counts_response(): "MONDO:0018939", "MONDO:0020246", "MONDO:0021147", - "MONDO:0014140", "MONDO:0044137", "MONDO:0019755", "OGMS:0000031", @@ -2924,7 +2502,7 @@ def association_counts_response(): "retinal disorder", "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -2957,15 +2535,159 @@ def association_counts_response(): "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", "myopathy caused by variation in POMGNT1", - "myopathy caused by variation in GMPPB", + "myopathy caused by variation in POMT2", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Glaucoma (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], + "object_label": "Glaucoma (HPO)", + "evidence_count": 2, + }, + { + "id": "uuid:abeb7bed-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:614643", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:614643"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0013835", + "object": "HP:0000501", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", @@ -2985,6 +2707,7 @@ def association_counts_response(): "BFO:0000017", "MONDO:0018869", "BFO:0000020", + "MONDO:0013835", "MONDO:0016157", "MONDO:0017745", "BFO:0000016", @@ -3018,7 +2741,7 @@ def association_counts_response(): "MONDO:0016155", "MONDO:0700066", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", @@ -3036,6 +2759,7 @@ def association_counts_response(): "retinal disorder", "eye disorder", "myopathy", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -3071,18 +2795,151 @@ def association_counts_response(): "hereditary skeletal muscle disorder", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Glaucoma (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], + "object_label": "Glaucoma (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:772849bb-ae4c-4a45-8a2e-b0269106d6e2", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", + "id": "uuid:a619ab58-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:616538", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:616538"], + "has_evidence": ["ECO:0000304"], "subject": "MONDO:0014683", - "object": "MONDO:0000171", + "object": "HP:0000501", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ @@ -3194,161 +3051,451 @@ def association_counts_response(): "disease", ], "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0018282", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Glaucoma (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], + "object_label": "Glaucoma (HPO)", + "evidence_count": 2, + }, + { + "id": "uuid:a8bae681-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:602078", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:602078"], + "has_evidence": ["ECO:0000269"], + "subject": "MONDO:0011181", + "object": "HP:0000505", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", + "MONDO:0004746", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0957003", "BFO:0000017", - "MONDO:0018869", + "MONDO:0011181", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0003569", "MONDO:0700096", - "MONDO:0018838", + "MONDO:0001584", "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", "MONDO:0002022", - "MONDO:0015286", + "MONDO:0015368", "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", + "MONDO:0000462", "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", + "eye adnexa disorder", + "ocular motility disease", "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", - "metabolic disease", + "myopathy of extraocular muscle", "nervous system disorder", - "retinal disorder", "eye disorder", "myopathy", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, 2", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", + "eyelids malposition disorder", "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "subject_label": "fibrosis of extraocular muscles, congenital, 2", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0050620", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "UPHENO:0052164", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0052178", + "BFO:0000020", + "HP:0000504", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "UPHENO:0050236", + "HP:0012373", + "HP:0000505", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049587", + "BFO:0000001", + "PATO:0000001", + "UPHENO:0050622", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "GO:0003008", + "UBERON:0000061", + "UBERON:0034923", + "GO:0050877", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "GO:0007600", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "GO:0050953", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "GO:0007601", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "system process", + "sensory perception", + "visual perception", + "biological_process", + "multicellular organismal process", + "nervous system process", + "sensory perception of light stimulus", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of vision (HPO)", + "Visual impairment (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal biological_process", + "abnormal sensory perception of light stimulus", + "abnormal sensory perception", + "abnormal visual perception", + "decreased qualitatively visual perception", + "decreased qualitatively biological_process", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], + "object_label": "Visual impairment (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:1c12ae85-5540-49db-8bae-44cde2205158", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0011688", - "object": "MONDO:0000172", + "id": "uuid:a93b6d20-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:615249", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:615249"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0014101", + "object": "HP:0000505", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0018282", "MONDO:0000001", + "MONDO:0016182", "MONDO:0017741", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0700068", "MONDO:0700223", "MONDO:0024322", + "MONDO:0005283", + "MONDO:0020238", "BFO:0000002", + "MONDO:0014101", + "MONDO:0016185", + "MONDO:0000171", "BFO:0000017", + "MONDO:0018869", "BFO:0000020", "MONDO:0016157", + "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0018838", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016184", + "MONDO:0016156", + "MONDO:0020246", + "MONDO:0021147", + "MONDO:0044137", + "MONDO:0019755", "OGMS:0000031", + "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", + "MONDO:0020247", "MONDO:0005066", + "MONDO:0005328", "MONDO:0019950", "MONDO:0016155", - "MONDO:0011688", "MONDO:0700066", ], "subject_closure_label": [ @@ -3358,120 +3505,266 @@ def association_counts_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy-dystroglycanopathy, type A", + "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", + "retinal disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy type B5", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", "congenital disorder of glycosylation", + "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "qualitative or quantitative defects of FKRP", "qualitative or quantitative defects of fukutin", + "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", + "qualitative or quantitative defects of protein O-mannosyltransferase 1", + "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", + "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", "qualitative or quantitative defects of alpha-dystroglycan", + "lissencephaly spectrum disorders", + "cobblestone lissencephaly", "inborn errors of metabolism", "neuromuscular disease", + "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "inherited vitreous-retinal disease", + "inherited vitreoretinopathy", + "congenital vitreoretinal dysplasia", + "disorder of development or morphogenesis", "disorder of glycosylation", + "disorder of visual system", + "vitreous body disorder", "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", + "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy type B5", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0050620", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "UPHENO:0052164", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", + "UPHENO:0052178", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "HP:0000504", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "UPHENO:0050236", + "HP:0012373", + "HP:0000505", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049587", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "UPHENO:0050622", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "GO:0003008", + "UBERON:0000061", + "UBERON:0034923", + "GO:0050877", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "GO:0007600", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "GO:0050953", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "GO:0007601", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "occurrent", + "independent continuant", + "process", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "system process", + "sensory perception", + "visual perception", + "biological_process", + "multicellular organismal process", + "nervous system process", + "sensory perception of light stimulus", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of vision (HPO)", + "Visual impairment (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal biological_process", + "abnormal sensory perception of light stimulus", + "abnormal sensory perception", + "abnormal visual perception", + "decreased qualitatively visual perception", + "decreased qualitatively biological_process", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Visual impairment (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:8c3fdf6b-34fc-4154-a332-45e0f699c79c", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0012138", - "object": "MONDO:0000172", + "id": "uuid:a538f419-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:600638", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:600638"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0010912", + "object": "HP:0000508", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0012138", - "MONDO:0018276", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", "MONDO:0700223", + "MONDO:0004746", "BFO:0000002", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0100153", "OGMS:0000031", "MONDO:0003847", + "MONDO:0100154", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "MONDO:0000462", + "MONDO:0005328", + "MONDO:0010912", ], "subject_closure_label": [ "entity", @@ -3480,122 +3773,255 @@ def association_counts_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", + "myopathy of extraocular muscle", "nervous system disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy type B6", - "muscular dystrophy-dystroglycanopathy", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "eyelids malposition disorder", + "disorder of visual system", + "tubulinopathy", + "TUBB3-related tubulinopathy", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy type B6", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0041226", + "UPHENO:0076761", + "UPHENO:0075696", + "UPHENO:0041667", + "UPHENO:0001001", + "UPHENO:0021749", + "UPHENO:0080300", + "UPHENO:0021791", + "UPHENO:0041410", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "HP:0000492", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0041644", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "UPHENO:0015280", + "HP:0000271", + "HP:0012373", + "UPHENO:0082129", + "UPHENO:0081581", + "UPHENO:0001003", + "HP:0000508", + "UPHENO:0002536", + "UPHENO:0020584", + "HP:0032039", + "UPHENO:0076692", + "HP:0030669", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "UPHENO:0075878", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0001711", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0034921", + "UBERON:0000064", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0035639", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormal eyelid morphology (HPO)", + "Ptosis (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal ocular adnexa morphology (HPO)", + "Abnormality of the ocular adnexa (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "eyelid", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "multi organ part structure", + "disconnected anatomical group", + "ocular adnexa", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal ocular adnexa morphology", + "shape anatomical entity", + "drooping anatomical entity", + "drooping eyelid", + "shape eyelid", + "abnormal anatomical entity", + "abnormal ocular adnexa", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal shape of continuant", + "abnormal multicellular organism morphology", + "shape anatomical entity in independent continuant", + "abnormality of anatomical entity physiology", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Ptosis (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:0be3e1fc-b9af-41b0-bf2c-7e4de1ffe2c4", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0013155", - "object": "MONDO:0000172", + "id": "uuid:abcb9e2a-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:609428", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:609428"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0012270", + "object": "HP:0000508", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", - "MONDO:0000172", "MONDO:0700223", - "MONDO:0024322", + "MONDO:0004746", "BFO:0000002", - "MONDO:0013155", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", - "MONDO:0017745", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0012270", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0018277", - "MONDO:0019950", - "MONDO:0016155", + "MONDO:0000462", + "MONDO:0005328", ], "subject_closure_label": [ "entity", @@ -3604,134 +4030,253 @@ def association_counts_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", - "metabolic disease", + "myopathy of extraocular muscle", "nervous system disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3", - "congenital disorder of glycosylation", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "congenital muscular dystrophy with cerebellar involvement", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", + "congenital fibrosis of extraocular muscles", + "Tukel syndrome", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in POMGNT1", + "eyelids malposition disorder", + "disorder of visual system", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "Tukel syndrome", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0041226", + "UPHENO:0076761", + "UPHENO:0075696", + "UPHENO:0041667", + "UPHENO:0001001", + "UPHENO:0021749", + "UPHENO:0080300", + "UPHENO:0021791", + "UPHENO:0041410", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "HP:0000492", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0041644", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "UPHENO:0015280", + "HP:0000271", + "HP:0012373", + "UPHENO:0082129", + "UPHENO:0081581", + "UPHENO:0001003", + "HP:0000508", + "UPHENO:0002536", + "UPHENO:0020584", + "HP:0032039", + "UPHENO:0076692", + "HP:0030669", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "UPHENO:0075878", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0001711", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0034921", + "UBERON:0000064", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0035639", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormal eyelid morphology (HPO)", + "Ptosis (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal ocular adnexa morphology (HPO)", + "Abnormality of the ocular adnexa (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "eyelid", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "multi organ part structure", + "disconnected anatomical group", + "ocular adnexa", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal ocular adnexa morphology", + "shape anatomical entity", + "drooping anatomical entity", + "drooping eyelid", + "shape eyelid", + "abnormal anatomical entity", + "abnormal ocular adnexa", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal shape of continuant", + "abnormal multicellular organism morphology", + "shape anatomical entity in independent continuant", + "abnormality of anatomical entity physiology", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Ptosis (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:8b852151-1710-4175-9e07-4fa11e33704c", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0013156", - "object": "MONDO:0000172", + "id": "uuid:abeb7c5b-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:609612", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:609612"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0012310", + "object": "HP:0000508", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0700067", - "MONDO:0018282", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0012310", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", "MONDO:0700223", - "MONDO:0024322", + "MONDO:0004746", "BFO:0000002", - "MONDO:0018279", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", - "MONDO:0017745", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0013156", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0016155", + "MONDO:0000462", + "MONDO:0005328", ], "subject_closure_label": [ "entity", @@ -3740,131 +4285,518 @@ def association_counts_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", - "metabolic disease", + "myopathy of extraocular muscle", "nervous system disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital without intellectual disability), type B4", - "congenital disorder of glycosylation", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "congenital muscular dystrophy without intellectual disability", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, with synergistic divergence", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKTN", + "eyelids malposition disorder", + "disorder of visual system", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital without intellectual disability), type B4", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "fibrosis of extraocular muscles, congenital, with synergistic divergence", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0041226", + "UPHENO:0076761", + "UPHENO:0075696", + "UPHENO:0041667", + "UPHENO:0001001", + "UPHENO:0021749", + "UPHENO:0080300", + "UPHENO:0021791", + "UPHENO:0041410", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "HP:0000492", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0041644", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "UPHENO:0015280", + "HP:0000271", + "HP:0012373", + "UPHENO:0082129", + "UPHENO:0081581", + "UPHENO:0001003", + "HP:0000508", + "UPHENO:0002536", + "UPHENO:0020584", + "HP:0032039", + "UPHENO:0076692", + "HP:0030669", + "BFO:0000001", + "PATO:0000001", + "UPHENO:0075878", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0001711", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0034921", + "UBERON:0000064", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0035639", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormal eyelid morphology (HPO)", + "Ptosis (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal ocular adnexa morphology (HPO)", + "Abnormality of the ocular adnexa (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "eyelid", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "multi organ part structure", + "disconnected anatomical group", + "ocular adnexa", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal ocular adnexa morphology", + "shape anatomical entity", + "drooping anatomical entity", + "drooping eyelid", + "shape eyelid", + "abnormal anatomical entity", + "abnormal ocular adnexa", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal shape of continuant", + "abnormal multicellular organism morphology", + "shape anatomical entity in independent continuant", + "abnormality of anatomical entity physiology", + ], + "object_label": "Ptosis (HPO)", + "evidence_count": 2, + }, + { + "id": "uuid:a6f9d857-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:160900", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:160900"], + "has_evidence": ["ECO:0000501"], + "subject": "MONDO:0008056", + "object": "HP:0000518", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ + "MONDO:0004994", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0018276", + "MONDO:0016107", "MONDO:0005071", + "MONDO:0005267", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0005045", + "MONDO:0004995", "MONDO:0700223", "BFO:0000002", "BFO:0000017", "BFO:0000020", + "MONDO:0016106", + "MONDO:0005217", + "MONDO:0024573", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0008056", "MONDO:0700096", + "MONDO:0000591", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0002254", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0016120", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "MONDO:0000462", + "MONDO:0005328", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "eye adnexa disorder", + "intrinsic cardiomyopathy", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "syndromic disease", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", + "cardiomyopathy", + "cardiovascular disorder", + "hypertrophic cardiomyopathy", "nervous system disorder", + "familial cardiomyopathy", + "heart disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy", + "myotonic dystrophy type 1", + "progressive muscular dystrophy", + "myotonic dystrophy", + "myotonic syndrome", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "eyelids malposition disorder", + "disorder of visual system", + "familial hypertrophic cardiomyopathy", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "subject_label": "myotonic dystrophy type 1", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "HP:0004328", + "UPHENO:0001001", + "UPHENO:0004765", + "HP:0000152", + "HP:0000518", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0020584", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "HP:0000517", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0005389", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0000965", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of the lens (HPO)", + "Cataract (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormal eye morphology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "lens of camera-type eye", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "anterior segment of eyeball", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "transparent eye structure", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal lens of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology", + ], + "object_label": "Cataract (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:d20f485a-4fde-44b8-aa20-20fd2d5902ab", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0013159", - "object": "MONDO:0000172", + "id": "uuid:a8bae558-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:236670", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:236670"], + "has_evidence": ["ECO:0000501"], + "subject": "MONDO:0009364", + "object": "HP:0000518", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0018282", "MONDO:0000001", + "MONDO:0016182", "MONDO:0017741", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0700068", "MONDO:0700223", - "MONDO:0013159", "MONDO:0024322", + "MONDO:0005283", + "MONDO:0020238", "BFO:0000002", + "MONDO:0016185", + "MONDO:0000171", "BFO:0000017", + "MONDO:0018869", "BFO:0000020", + "MONDO:0016157", + "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0018838", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016184", + "MONDO:0016156", + "MONDO:0009364", + "MONDO:0020246", + "MONDO:0021147", + "MONDO:0044137", + "MONDO:0019755", "OGMS:0000031", + "MONDO:0015327", "MONDO:0003847", "MONDO:0700070", "MONDO:0003939", + "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", + "MONDO:0020247", "MONDO:0005066", + "MONDO:0005328", "MONDO:0019950", "MONDO:0016155", + "MONDO:0700066", ], "subject_closure_label": [ "entity", @@ -3873,129 +4805,277 @@ def association_counts_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy-dystroglycanopathy, type A", + "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", + "retinal disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", "congenital disorder of glycosylation", + "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "qualitative or quantitative defects of FKRP", + "qualitative or quantitative defects of fukutin", + "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", + "qualitative or quantitative defects of protein O-mannosyltransferase 1", + "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", + "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", "qualitative or quantitative defects of alpha-dystroglycan", + "lissencephaly spectrum disorders", + "cobblestone lissencephaly", "inborn errors of metabolism", "neuromuscular disease", + "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "inherited vitreous-retinal disease", + "inherited vitreoretinopathy", + "congenital vitreoretinal dysplasia", + "disorder of development or morphogenesis", "disorder of glycosylation", + "disorder of visual system", + "vitreous body disorder", "glycoprotein metabolism disease", + "myopathy caused by variation in FKRP", + "myopathy caused by variation in POMGNT1", "myopathy caused by variation in POMT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "HP:0004328", + "UPHENO:0001001", + "UPHENO:0004765", + "HP:0000152", + "HP:0000518", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0020584", + "UPHENO:0076692", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "HP:0000517", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0005389", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0000965", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of the lens (HPO)", + "Cataract (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormal eye morphology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "lens of camera-type eye", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "anterior segment of eyeball", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "transparent eye structure", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal lens of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Cataract (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:7a5c97ed-311c-4530-bfdf-447bf5c4db72", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0013160", - "object": "MONDO:0000172", + "id": "uuid:a4c7f187-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:253280", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:253280"], + "has_evidence": ["ECO:0000501"], + "subject": "MONDO:0009667", + "object": "HP:0000518", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0018282", "MONDO:0000001", + "MONDO:0016182", "MONDO:0017741", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0700068", "MONDO:0700223", "MONDO:0024322", + "MONDO:0005283", + "MONDO:0020238", "BFO:0000002", + "MONDO:0016185", + "MONDO:0000171", "BFO:0000017", + "MONDO:0018869", "BFO:0000020", - "MONDO:0013160", - "MONDO:0700071", + "MONDO:0016157", + "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0018838", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016184", + "MONDO:0016156", + "MONDO:0018939", + "MONDO:0020246", + "MONDO:0009667", + "MONDO:0021147", + "MONDO:0044137", + "MONDO:0019755", "OGMS:0000031", + "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", + "MONDO:0020247", "MONDO:0005066", + "MONDO:0005328", "MONDO:0019950", "MONDO:0016155", + "MONDO:0700066", ], "subject_closure_label": [ "entity", @@ -4004,83 +5084,207 @@ def association_counts_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy-dystroglycanopathy, type A", + "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", + "retinal disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3", "congenital disorder of glycosylation", + "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "qualitative or quantitative defects of FKRP", + "qualitative or quantitative defects of fukutin", + "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", + "qualitative or quantitative defects of protein O-mannosyltransferase 1", + "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", + "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", "qualitative or quantitative defects of alpha-dystroglycan", + "lissencephaly spectrum disorders", + "cobblestone lissencephaly", + "muscle-eye-brain disease", "inborn errors of metabolism", "neuromuscular disease", + "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "inherited vitreous-retinal disease", + "inherited vitreoretinopathy", + "congenital vitreoretinal dysplasia", + "disorder of development or morphogenesis", "disorder of glycosylation", + "disorder of visual system", + "vitreous body disorder", "glycoprotein metabolism disease", - "myopathy caused by variation in POMT2", + "myopathy caused by variation in FKRP", + "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "HP:0004328", + "UPHENO:0001001", + "UPHENO:0004765", + "HP:0000152", + "HP:0000518", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0020584", + "UPHENO:0076692", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "HP:0000517", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0005389", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0000965", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of the lens (HPO)", + "Cataract (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormal eye morphology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "lens of camera-type eye", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "anterior segment of eyeball", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "transparent eye structure", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal lens of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Cataract (HPO)", "evidence_count": 2, }, ], @@ -4088,7 +5292,7 @@ def association_counts_response(): "facet_counts": { "facet_fields": {}, "facet_queries": { - '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 2166, + '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 4027, '(category:"biolink:GeneToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 0, '(category:"biolink:PairwiseGeneToGeneInteraction") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 0, '(category:"biolink:GeneToPathwayAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 0, @@ -4107,7 +5311,7 @@ def association_counts_response(): '(category:"biolink:ChemicalToPathwayAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 0, '(category:"biolink:MacromolecularMachineToMolecularActivityAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 0, '(category:"biolink:CausalGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 124, - '(category:"biolink:CorrelatedGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 0, + '(category:"biolink:CorrelatedGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 151, }, }, } diff --git a/backend/tests/fixtures/association_response.py b/backend/tests/fixtures/association_response.py index 99d2f2820..cd46f1fee 100644 --- a/backend/tests/fixtures/association_response.py +++ b/backend/tests/fixtures/association_response.py @@ -18,74 +18,41 @@ def association_response(): }, }, "response": { - "num_found": 2823, + "num_found": 4838, "start": 0, "docs": [ { - "id": "urn:uuid:a54e0b8c-af55-459b-ae98-a7e0ae60b190", - "predicate": "biolink:subclass_of", + "id": "urn:uuid:e4e8dbec-cb0c-44e9-b1cb-8be3b357b7b8", + "predicate": "biolink:related_to", "category": "biolink:Association", "aggregator_knowledge_source": ["infores:phenio"], "primary_knowledge_source": "infores:mondo", "provided_by": "phenio_edges", - "subject": "MONDO:0009364", - "object": "MONDO:0000171", + "subject": "MONDO:0018276", + "object": "GO:0006486", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", "MONDO:0018276", - "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0009364", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", - "MONDO:0700070", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], "subject_closure_label": [ "entity", @@ -94,58 +61,122 @@ def association_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", "neuromuscular disease", - "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "myopathy caused by variation in POMT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy", + "object_namespace": "GO", + "object_category": "biolink:BiologicalProcessOrActivity", "object_closure": [ + "GO:0008150", + "BFO:0000003", + "GO:0036211", + "GO:0043413", + "GO:0006486", + "GO:1901564", + "GO:0070085", + "GO:0043412", + "GO:0006807", + "GO:0044238", + "GO:0043170", + "GO:0071704", + "BFO:0000015", + "BFO:0000001", + "GO:0008152", + "GO:0019538", + "BFO:0000001", + "BFO:0000003", + "BFO:0000015", + "GO:0008150", + "GO:0009987", + "GO:0008152", + "GO:0044237", + "GO:0071704", + "GO:0009058", + "GO:0044238", + "GO:0006807", + "GO:0044249", + "GO:0043170", + "GO:1901135", + "GO:1901564", + "GO:1901576", + "GO:0019538", + "GO:0009059", + "GO:1901137", + "GO:0009100", + "GO:1901566", + "GO:0009101", + ], + "object_closure_label": [ + "entity", + "entity", + "occurrent", + "occurrent", + "process", + "process", + "protein glycosylation", + "nitrogen compound metabolic process", + "nitrogen compound metabolic process", + "biological_process", + "biological_process", + "metabolic process", + "metabolic process", + "biosynthetic process", + "macromolecule biosynthetic process", + "glycoprotein metabolic process", + "glycoprotein biosynthetic process", + "cellular process", + "protein metabolic process", + "protein metabolic process", + "protein modification process", + "macromolecule metabolic process", + "macromolecule metabolic process", + "macromolecule modification", + "macromolecule glycosylation", + "cellular metabolic process", + "primary metabolic process", + "primary metabolic process", + "cellular biosynthetic process", + "glycosylation", + "organic substance metabolic process", + "organic substance metabolic process", + "carbohydrate derivative metabolic process", + "carbohydrate derivative biosynthetic process", + "organonitrogen compound metabolic process", + "organonitrogen compound metabolic process", + "organonitrogen compound biosynthetic process", + "organic substance biosynthetic process", + ], + "object_label": "protein glycosylation", + "evidence_count": 0, + }, + { + "id": "uuid:a82ac92f-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:613151", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:613151"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0013155", + "object": "HP:0000486", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", @@ -155,170 +186,305 @@ def association_response(): "MONDO:0005071", "MONDO:0020121", "MONDO:0700068", + "MONDO:0000172", "MONDO:0700223", "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0013155", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", - "MONDO:0020247", "MONDO:0005066", - "MONDO:0005328", + "MONDO:0018277", "MONDO:0019950", "MONDO:0016155", - "MONDO:0700066", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "muscular dystrophy-dystroglycanopathy, type B", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", + "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3", "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", + "congenital muscular dystrophy with cerebellar involvement", "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", "inborn errors of metabolism", "neuromuscular disease", - "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0080581", + "BFO:0000020", + "UPHENO:0002433", + "UPHENO:0003020", + "UPHENO:0079828", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0000707", + "HP:0012373", + "HP:0000496", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0000708", + "HP:0000486", + "UPHENO:0079826", + "UPHENO:0004523", + "HP:0011446", + "HP:0000549", + "UPHENO:0049587", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "BFO:0000141", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "UBERON:0000466", + "GO:0007610", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0000015", + "NBO:0000313", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0006800", + "NBO:0000338", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0001016", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0010222", + "NBO:0000001", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "NBO:0000444", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "immaterial entity", + "behavior", + "biological_process", + "multicellular organismal process", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Strabismus (HPO)", + "Abnormality of eye movement 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pupils", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormality of nervous system physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + 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"Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Strabismus (HPO)", + "Abnormality of eye movement (HPO)", + "Abnormal conjugate eye movement (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal nervous system physiology (HPO)", + "body part movement", + "behavior process", + "kinesthetic behavior", + "eye movement", + "quality", + "non-material anatomical boundary", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "immaterial anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "nervous system", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "anatomical line", + "craniocervical region", + "multicellular anatomical structure", + "anatomical line between pupils", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormality of nervous system physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", + ], + "object_label": "Strabismus (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:6fc3a05c-fd6a-46e1-8815-25a4a20e9954", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0014071", - "object": "MONDO:0000171", + "id": "uuid:a5790e7e-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:615356", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:615356"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0014144", + "object": "HP:0000486", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0016971", + "MONDO:0000429", + "MONDO:0014144", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0014071", - "MONDO:0000171", + "MONDO:0005395", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", + "MONDO:0006025", + "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0018939", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", + "MONDO:0018243", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", + "MONDO:0015152", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], "subject_closure_label": [ "entity", @@ -2195,175 +756,482 @@ def association_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "autosomal genetic disease", "musculoskeletal system disorder", - "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "muscle-eye-brain disease", - "inborn errors of metabolism", + "movement disorder", + "autosomal recessive disease", + "autosomal recessive limb-girdle muscular dystrophy type R18", + "autosomal recessive limb-girdle muscular dystrophy", + "progressive muscular dystrophy", + "limb-girdle muscular dystrophy", + "intellectual disability-hyperkinetic movement-truncal ataxia syndrome", "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type R18", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0018282", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0080581", + "BFO:0000020", + "UPHENO:0002433", + "UPHENO:0003020", + "UPHENO:0079828", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0000707", + "HP:0012373", + "HP:0000496", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0000708", + "HP:0000486", + "UPHENO:0079826", + "UPHENO:0004523", + "HP:0011446", + "HP:0000549", + "UPHENO:0049587", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "BFO:0000141", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "UBERON:0000466", + "GO:0007610", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0000015", + "NBO:0000313", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0006800", + "NBO:0000338", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0001016", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0010222", + "NBO:0000001", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "NBO:0000444", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "immaterial entity", + "behavior", + "biological_process", + "multicellular organismal process", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Strabismus (HPO)", + "Abnormality of eye movement (HPO)", + "Abnormal conjugate eye movement (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal nervous system physiology (HPO)", + "body part movement", + "behavior process", + "kinesthetic behavior", + "eye movement", + "quality", + "non-material anatomical boundary", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "immaterial anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "nervous system", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "anatomical line", + "craniocervical region", + "multicellular anatomical structure", + "anatomical line between pupils", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormality of nervous system physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", + ], + "object_label": "Strabismus (HPO)", + "evidence_count": 2, + }, + { + "id": "uuid:abeb7ac4-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:617404", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:617404"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0024607", + "object": "HP:0000486", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0024607", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", "neuromuscular disease", - "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", + "congenital muscular dystrophy with cataracts and intellectual disability", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "subject_label": "congenital muscular dystrophy with cataracts and intellectual disability", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0080581", + "BFO:0000020", + "UPHENO:0002433", + "UPHENO:0003020", + "UPHENO:0079828", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0000707", + "HP:0012373", + "HP:0000496", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0000708", + "HP:0000486", + "UPHENO:0079826", + "UPHENO:0004523", + "HP:0011446", + "HP:0000549", + "UPHENO:0049587", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "BFO:0000141", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "UBERON:0000466", + "GO:0007610", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0000015", + "NBO:0000313", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0006800", + "NBO:0000338", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0001016", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0010222", + "NBO:0000001", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "NBO:0000444", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "immaterial entity", + "behavior", + "biological_process", + "multicellular organismal process", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Strabismus (HPO)", + "Abnormality of eye movement (HPO)", + "Abnormal conjugate eye movement (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal nervous system physiology (HPO)", + "body part movement", + "behavior process", + "kinesthetic behavior", + "eye movement", + "quality", + "non-material anatomical boundary", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "immaterial anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "nervous system", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "anatomical line", + "craniocervical region", + "multicellular anatomical structure", + "anatomical line between pupils", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormality of nervous system physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", + ], + "object_label": "Strabismus (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:a20f59e6-2468-4f26-a789-04cd5d5bd97f", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0014101", - "object": "MONDO:0000171", + "id": "uuid:abeb7be1-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:614643", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:614643"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0013835", + "object": "HP:0000490", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ @@ -2381,12 +1249,12 @@ def association_response(): "MONDO:0005283", "MONDO:0020238", "BFO:0000002", - "MONDO:0014101", "MONDO:0016185", "MONDO:0000171", "BFO:0000017", "MONDO:0018869", "BFO:0000020", + "MONDO:0013835", "MONDO:0016157", "MONDO:0017745", "BFO:0000016", @@ -2438,7 +1306,7 @@ def association_response(): "retinal disorder", "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -2474,135 +1342,514 @@ def association_response(): "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0018282", + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0000490", + "HP:0012372", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0049367", + "UPHENO:0002764", + "UPHENO:0018424", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0018390", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0020584", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "HP:0100886", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Deeply set eye (HPO)", + "Abnormal eye morphology (HPO)", + "Abnormality of globe location (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal location of anatomical entity", + "abnormal location of eyeball of camera-type eye", + "abnormal anatomical entity morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity topology in independent continuant", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology", + ], + "object_label": "Deeply set eye (HPO)", + "evidence_count": 2, + }, + { + "id": "uuid:aa6b44e5-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:226670", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:226670"], + "has_evidence": ["ECO:0000501"], + "subject": "MONDO:0009181", + "object": "HP:0000491", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0016198", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0006617", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", + "MONDO:0017610", + "MONDO:0006025", + "MONDO:0016106", + "MONDO:0002051", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", + "MONDO:0100118", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", + "MONDO:0002254", + "MONDO:0009181", + "MONDO:0019276", + "MONDO:0005093", "OGMS:0000031", - "MONDO:0015327", + "MONDO:0019268", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", + "MONDO:0006541", + "MONDO:0015152", + "BFO:0000001", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "autosomal genetic disease", + "integumentary system disorder", "musculoskeletal system disorder", - "congenital nervous system disorder", + "syndromic disease", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", + "skin disorder", "myopathy", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", + "autosomal recessive disease", + "epidermolysis bullosa", + "vesiculobullous skin disease", + "epidermolysis bullosa simplex 5B, with muscular dystrophy", + "autosomal recessive limb-girdle muscular dystrophy", + "progressive muscular dystrophy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", + "qualitative or quantitative defects of plectin", + "limb-girdle muscular dystrophy", + "epidermolysis bullosa simplex", "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", + "epidermal disease", + "inherited epidermolysis bullosa", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", + "hereditary skin disorder", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "subject_label": "epidermolysis bullosa simplex 5B, with muscular dystrophy", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082682", + "UPHENO:0082875", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0080377", + "UPHENO:0054970", + "UPHENO:0002948", + "HP:0004328", + "UPHENO:0020998", + "UPHENO:0001001", + "UPHENO:0074763", + "UPHENO:0074632", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "HP:0010978", + "UPHENO:0002764", + "UPHENO:0021662", + "UPHENO:0082723", + "UPHENO:0001002", + "HP:0012647", + "HP:0000118", + "BFO:0000002", + "HP:0100533", + "UPHENO:0080221", + "UPHENO:0083263", + "BFO:0000020", + "HP:0000481", + "UPHENO:0003020", + "UPHENO:0049584", + "HP:0000234", + "UPHENO:0002332", + "HP:0002715", + "UPHENO:0015280", + "UPHENO:0080693", + "HP:0000271", + "HP:0012373", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002263", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0049588", + "HP:0000491", + "UPHENO:0020584", + "UPHENO:0059829", + "UPHENO:0080662", + "UPHENO:0076692", + "UPHENO:0074685", + "UPHENO:0076684", + "UPHENO:0049587", + "BFO:0000001", + "HP:0012649", + "PATO:0000001", + "UPHENO:0074572", + "HP:0011495", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0050896", + "PR:000050567", + "UBERON:0000465", + "GO:0006950", + "UBERON:0000483", + "UBERON:0012430", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0000964", + "GO:0006952", + "UBERON:0019304", + "UBERON:0010371", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "GO:0006954", + "UBERON:0007625", + "UBERON:0015808", + "UBERON:0000019", + "UBERON:0010313", + "UBERON:0010230", + "UBERON:0010409", + "UBERON:0000479", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0002405", + "UBERON:0001772", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000060", + "UBERON:0004923", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "response to stress", + "defense response", + "inflammatory response", + "biological_process", + "response to stimulus", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormal cornea morphology (HPO)", + "Keratitis (HPO)", + "Abnormality of the immune system (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormality of immune system physiology (HPO)", + "Abnormal corneal epithelium morphology (HPO)", + "Abnormal eye morphology (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal inflammatory response (HPO)", + "Increased inflammatory response (HPO)", + "Inflammatory abnormality of the eye (HPO)", + "quality", + "protein-containing material entity", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical wall", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "tissue", + "epithelium", + "cornea", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "corneal epithelium", + "anterior segment of eyeball", + "visual system", + "immune system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "organ component layer", + "pigment epithelium of eye", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "neural crest-derived structure", + "structure with developmental contribution from neural crest", + "ecto-epithelium", + "ocular surface region", + "subdivision of organism along main body axis", + "tunica fibrosa of eyeball", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "eye epithelium", + "sensory organ epithelium", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of immune system physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal immune system", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal cornea morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal corneal epithelium morphology", + "abnormal inflammatory response", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal response to stress", + "increased biological_process", + "abnormal biological_process in independent continuant", + "increased biological_process in independent continuant", + "increased inflammatory response in eyeball of camera-type eye", + "increased inflammatory response in independent continuant", + "increased biological_process in eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "increased inflammatory response", + "abnormal anatomical entity morphology", + "changed biological_process rate in independent continuant", + "changed biological_process rate", + "increased qualitatively biological_process", + "increased qualitatively inflammatory response", + "abnormal multicellular organism morphology", + "increased qualitatively biological_process in independent continuant", + "increased qualitatively inflammatory response in independent continuant", + "abnormality of anatomical entity physiology", + "increased qualitatively response to stimulus", + ], + "object_label": "Keratitis (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:f7c423b7-6f4c-4663-9ead-41d529a7cf2b", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0014120", - "object": "MONDO:0000171", + "id": "uuid:a74a1018-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:253800", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:253800"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0009678", + "object": "HP:0000496", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0700067", "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", "MONDO:0017741", - "MONDO:0014120", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", @@ -2631,10 +1878,12 @@ def association_response(): "MONDO:0002081", "MONDO:0016184", "MONDO:0016156", + "MONDO:0018939", "MONDO:0020246", "MONDO:0021147", "MONDO:0044137", "MONDO:0019755", + "MONDO:0009678", "OGMS:0000031", "MONDO:0015327", "MONDO:0003847", @@ -2669,7 +1918,7 @@ def association_response(): "retinal disorder", "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -2685,6 +1934,7 @@ def association_response(): "qualitative or quantitative defects of alpha-dystroglycan", "lissencephaly spectrum disorders", "cobblestone lissencephaly", + "muscle-eye-brain disease", "inborn errors of metabolism", "neuromuscular disease", "developmental defect during embryogenesis", @@ -2700,15 +1950,206 @@ def association_response(): "vitreous body disorder", "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", + "myopathy caused by variation in FKTN", "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0080581", + "BFO:0000020", + "UPHENO:0002433", + "UPHENO:0003020", + "UPHENO:0079828", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0000707", + "HP:0012373", + "HP:0000496", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0000708", + "UPHENO:0079826", + "UPHENO:0004523", + "HP:0011446", + "UPHENO:0049587", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "GO:0007610", + "UBERON:0000061", + "UBERON:0034923", + "NBO:0000313", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "NBO:0000338", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0001016", + "UBERON:0004456", + "UBERON:0001032", + "NBO:0000001", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "NBO:0000444", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "behavior", + "biological_process", + "multicellular organismal process", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of eye movement (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal nervous system physiology (HPO)", + "body part movement", + "behavior process", + "kinesthetic behavior", + "eye movement", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "nervous system", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormality of nervous system physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", + ], + "object_label": "Abnormality of eye movement (HPO)", + "evidence_count": 2, + }, + { + "id": "uuid:a8bae583-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:236670", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:236670"], + "has_evidence": ["ECO:0000501"], + "subject": "MONDO:0009364", + "object": "HP:0000501", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", @@ -2741,6 +2182,7 @@ def association_response(): "MONDO:0002081", "MONDO:0016184", "MONDO:0016156", + "MONDO:0009364", "MONDO:0020246", "MONDO:0021147", "MONDO:0044137", @@ -2748,6 +2190,7 @@ def association_response(): "OGMS:0000031", "MONDO:0015327", "MONDO:0003847", + "MONDO:0700070", "MONDO:0003939", "MONDO:0002022", "MONDO:0015286", @@ -2761,7 +2204,7 @@ def association_response(): "MONDO:0016155", "MONDO:0700066", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", @@ -2779,6 +2222,7 @@ def association_response(): "retinal disorder", "eye disorder", "myopathy", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -2810,30 +2254,164 @@ def association_response(): "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", "myopathy caused by variation in POMGNT1", + "myopathy caused by variation in POMT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Glaucoma (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], + "object_label": "Glaucoma (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:9d167233-70b8-4d7d-aa5d-f6dac17ba835", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0014140", - "object": "MONDO:0000171", + "id": "uuid:a8aad663-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:613150", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:613150"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0013154", + "object": "HP:0000501", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0700084", "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", "MONDO:0017741", + "MONDO:0013154", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", @@ -2850,6 +2428,7 @@ def association_response(): "MONDO:0018869", "BFO:0000020", "MONDO:0016157", + "MONDO:0700071", "MONDO:0017745", "BFO:0000016", "MONDO:0020120", @@ -2865,7 +2444,6 @@ def association_response(): "MONDO:0018939", "MONDO:0020246", "MONDO:0021147", - "MONDO:0014140", "MONDO:0044137", "MONDO:0019755", "OGMS:0000031", @@ -2902,7 +2480,7 @@ def association_response(): "retinal disorder", "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -2935,15 +2513,159 @@ def association_response(): "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", "myopathy caused by variation in POMGNT1", - "myopathy caused by variation in GMPPB", + "myopathy caused by variation in POMT2", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Glaucoma (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], + "object_label": "Glaucoma (HPO)", + "evidence_count": 2, + }, + { + "id": "uuid:abeb7bed-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:614643", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:614643"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0013835", + "object": "HP:0000501", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", @@ -2963,6 +2685,7 @@ def association_response(): "BFO:0000017", "MONDO:0018869", "BFO:0000020", + "MONDO:0013835", "MONDO:0016157", "MONDO:0017745", "BFO:0000016", @@ -2996,7 +2719,7 @@ def association_response(): "MONDO:0016155", "MONDO:0700066", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", @@ -3014,6 +2737,7 @@ def association_response(): "retinal disorder", "eye disorder", "myopathy", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -3049,18 +2773,151 @@ def association_response(): "hereditary skeletal muscle disorder", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Glaucoma (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], + "object_label": "Glaucoma (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:772849bb-ae4c-4a45-8a2e-b0269106d6e2", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", + "id": "uuid:a619ab58-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:616538", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:616538"], + "has_evidence": ["ECO:0000304"], "subject": "MONDO:0014683", - "object": "MONDO:0000171", + "object": "HP:0000501", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ @@ -3172,161 +3029,451 @@ def association_response(): "disease", ], "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0018282", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Glaucoma (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], + "object_label": "Glaucoma (HPO)", + "evidence_count": 2, + }, + { + "id": "uuid:a8bae681-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:602078", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:602078"], + "has_evidence": ["ECO:0000269"], + "subject": "MONDO:0011181", + "object": "HP:0000505", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", + "MONDO:0004746", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0957003", "BFO:0000017", - "MONDO:0018869", + "MONDO:0011181", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0003569", "MONDO:0700096", - "MONDO:0018838", + "MONDO:0001584", "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", "MONDO:0002022", - "MONDO:0015286", + "MONDO:0015368", "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", + "MONDO:0000462", "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", + "eye adnexa disorder", + "ocular motility disease", "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", - "metabolic disease", + "myopathy of extraocular muscle", "nervous system disorder", - "retinal disorder", "eye disorder", "myopathy", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, 2", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", + "eyelids malposition disorder", "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "subject_label": "fibrosis of extraocular muscles, congenital, 2", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0050620", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "UPHENO:0052164", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0052178", + "BFO:0000020", + "HP:0000504", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "UPHENO:0050236", + "HP:0012373", + "HP:0000505", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049587", + "BFO:0000001", + "PATO:0000001", + "UPHENO:0050622", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "GO:0003008", + "UBERON:0000061", + "UBERON:0034923", + "GO:0050877", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "GO:0007600", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "GO:0050953", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "GO:0007601", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "system process", + "sensory perception", + "visual perception", + "biological_process", + "multicellular organismal process", + "nervous system process", + "sensory perception of light stimulus", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of vision (HPO)", + "Visual impairment (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal biological_process", + "abnormal sensory perception of light stimulus", + "abnormal sensory perception", + "abnormal visual perception", + "decreased qualitatively visual perception", + "decreased qualitatively biological_process", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], + "object_label": "Visual impairment (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:1c12ae85-5540-49db-8bae-44cde2205158", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0011688", - "object": "MONDO:0000172", + "id": "uuid:a93b6d20-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:615249", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:615249"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0014101", + "object": "HP:0000505", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0018282", "MONDO:0000001", + "MONDO:0016182", "MONDO:0017741", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0700068", "MONDO:0700223", "MONDO:0024322", + "MONDO:0005283", + "MONDO:0020238", "BFO:0000002", + "MONDO:0014101", + "MONDO:0016185", + "MONDO:0000171", "BFO:0000017", + "MONDO:0018869", "BFO:0000020", "MONDO:0016157", + "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0018838", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016184", + "MONDO:0016156", + "MONDO:0020246", + "MONDO:0021147", + "MONDO:0044137", + "MONDO:0019755", "OGMS:0000031", + "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", + "MONDO:0020247", "MONDO:0005066", + "MONDO:0005328", "MONDO:0019950", "MONDO:0016155", - "MONDO:0011688", "MONDO:0700066", ], "subject_closure_label": [ @@ -3336,120 +3483,266 @@ def association_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy-dystroglycanopathy, type A", + "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", + "retinal disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy type B5", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", "congenital disorder of glycosylation", + "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "qualitative or quantitative defects of FKRP", "qualitative or quantitative defects of fukutin", + "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", + "qualitative or quantitative defects of protein O-mannosyltransferase 1", + "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", + "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", "qualitative or quantitative defects of alpha-dystroglycan", + "lissencephaly spectrum disorders", + "cobblestone lissencephaly", "inborn errors of metabolism", "neuromuscular disease", + "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "inherited vitreous-retinal disease", + "inherited vitreoretinopathy", + "congenital vitreoretinal dysplasia", + "disorder of development or morphogenesis", "disorder of glycosylation", + "disorder of visual system", + "vitreous body disorder", "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", + "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy type B5", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0050620", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "UPHENO:0052164", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", + "UPHENO:0052178", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "HP:0000504", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "UPHENO:0050236", + "HP:0012373", + "HP:0000505", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049587", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "UPHENO:0050622", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "GO:0003008", + "UBERON:0000061", + "UBERON:0034923", + "GO:0050877", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "GO:0007600", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "GO:0050953", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "GO:0007601", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "occurrent", + "independent continuant", + "process", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "system process", + "sensory perception", + "visual perception", + "biological_process", + "multicellular organismal process", + "nervous system process", + "sensory perception of light stimulus", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of vision (HPO)", + "Visual impairment (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal biological_process", + "abnormal sensory perception of light stimulus", + "abnormal sensory perception", + "abnormal visual perception", + "decreased qualitatively visual perception", + "decreased qualitatively biological_process", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Visual impairment (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:8c3fdf6b-34fc-4154-a332-45e0f699c79c", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0012138", - "object": "MONDO:0000172", + "id": "uuid:a538f419-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:600638", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:600638"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0010912", + "object": "HP:0000508", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0012138", - "MONDO:0018276", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", "MONDO:0700223", + "MONDO:0004746", "BFO:0000002", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0100153", "OGMS:0000031", "MONDO:0003847", + "MONDO:0100154", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "MONDO:0000462", + "MONDO:0005328", + "MONDO:0010912", ], "subject_closure_label": [ "entity", @@ -3458,122 +3751,255 @@ def association_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", + "myopathy of extraocular muscle", "nervous system disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy type B6", - "muscular dystrophy-dystroglycanopathy", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "eyelids malposition disorder", + "disorder of visual system", + "tubulinopathy", + "TUBB3-related tubulinopathy", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy type B6", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0041226", + "UPHENO:0076761", + "UPHENO:0075696", + "UPHENO:0041667", + "UPHENO:0001001", + "UPHENO:0021749", + "UPHENO:0080300", + "UPHENO:0021791", + "UPHENO:0041410", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "HP:0000492", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0041644", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "UPHENO:0015280", + "HP:0000271", + "HP:0012373", + "UPHENO:0082129", + "UPHENO:0081581", + "UPHENO:0001003", + "HP:0000508", + "UPHENO:0002536", + "UPHENO:0020584", + "HP:0032039", + "UPHENO:0076692", + "HP:0030669", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "UPHENO:0075878", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0001711", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0034921", + "UBERON:0000064", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0035639", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormal eyelid morphology (HPO)", + "Ptosis (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal ocular adnexa morphology (HPO)", + "Abnormality of the ocular adnexa (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "eyelid", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "multi organ part structure", + "disconnected anatomical group", + "ocular adnexa", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal ocular adnexa morphology", + "shape anatomical entity", + "drooping anatomical entity", + "drooping eyelid", + "shape eyelid", + "abnormal anatomical entity", + "abnormal ocular adnexa", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal shape of continuant", + "abnormal multicellular organism morphology", + "shape anatomical entity in independent continuant", + "abnormality of anatomical entity physiology", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Ptosis (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:0be3e1fc-b9af-41b0-bf2c-7e4de1ffe2c4", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0013155", - "object": "MONDO:0000172", + "id": "uuid:abcb9e2a-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:609428", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:609428"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0012270", + "object": "HP:0000508", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", - "MONDO:0000172", "MONDO:0700223", - "MONDO:0024322", + "MONDO:0004746", "BFO:0000002", - "MONDO:0013155", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", - "MONDO:0017745", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0012270", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0018277", - "MONDO:0019950", - "MONDO:0016155", + "MONDO:0000462", + "MONDO:0005328", ], "subject_closure_label": [ "entity", @@ -3582,134 +4008,253 @@ def association_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", - "metabolic disease", + "myopathy of extraocular muscle", "nervous system disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3", - "congenital disorder of glycosylation", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "congenital muscular dystrophy with cerebellar involvement", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", + "congenital fibrosis of extraocular muscles", + "Tukel syndrome", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in POMGNT1", + "eyelids malposition disorder", + "disorder of visual system", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "Tukel syndrome", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0041226", + "UPHENO:0076761", + "UPHENO:0075696", + "UPHENO:0041667", + "UPHENO:0001001", + "UPHENO:0021749", + "UPHENO:0080300", + "UPHENO:0021791", + "UPHENO:0041410", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "HP:0000492", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0041644", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "UPHENO:0015280", + "HP:0000271", + "HP:0012373", + "UPHENO:0082129", + "UPHENO:0081581", + "UPHENO:0001003", + "HP:0000508", + "UPHENO:0002536", + "UPHENO:0020584", + "HP:0032039", + "UPHENO:0076692", + "HP:0030669", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "UPHENO:0075878", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0001711", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0034921", + "UBERON:0000064", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0035639", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormal eyelid morphology (HPO)", + "Ptosis (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal ocular adnexa morphology (HPO)", + "Abnormality of the ocular adnexa (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "eyelid", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "multi organ part structure", + "disconnected anatomical group", + "ocular adnexa", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal ocular adnexa morphology", + "shape anatomical entity", + "drooping anatomical entity", + "drooping eyelid", + "shape eyelid", + "abnormal anatomical entity", + "abnormal ocular adnexa", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal shape of continuant", + "abnormal multicellular organism morphology", + "shape anatomical entity in independent continuant", + "abnormality of anatomical entity physiology", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Ptosis (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:8b852151-1710-4175-9e07-4fa11e33704c", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0013156", - "object": "MONDO:0000172", + "id": "uuid:abeb7c5b-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:609612", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:609612"], + "has_evidence": ["ECO:0000304"], + "subject": "MONDO:0012310", + "object": "HP:0000508", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0700067", - "MONDO:0018282", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0012310", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", "MONDO:0700223", - "MONDO:0024322", + "MONDO:0004746", "BFO:0000002", - "MONDO:0018279", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", - "MONDO:0017745", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0013156", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0016155", + "MONDO:0000462", + "MONDO:0005328", ], "subject_closure_label": [ "entity", @@ -3718,131 +4263,518 @@ def association_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", - "metabolic disease", + "myopathy of extraocular muscle", "nervous system disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital without intellectual disability), type B4", - "congenital disorder of glycosylation", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "congenital muscular dystrophy without intellectual disability", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, with synergistic divergence", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKTN", + "eyelids malposition disorder", + "disorder of visual system", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital without intellectual disability), type B4", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "fibrosis of extraocular muscles, congenital, with synergistic divergence", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0041226", + "UPHENO:0076761", + "UPHENO:0075696", + "UPHENO:0041667", + "UPHENO:0001001", + "UPHENO:0021749", + "UPHENO:0080300", + "UPHENO:0021791", + "UPHENO:0041410", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "HP:0000492", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0041644", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "UPHENO:0015280", + "HP:0000271", + "HP:0012373", + "UPHENO:0082129", + "UPHENO:0081581", + "UPHENO:0001003", + "HP:0000508", + "UPHENO:0002536", + "UPHENO:0020584", + "HP:0032039", + "UPHENO:0076692", + "HP:0030669", + "BFO:0000001", + "PATO:0000001", + "UPHENO:0075878", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0001711", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0034921", + "UBERON:0000064", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0035639", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormal eyelid morphology (HPO)", + "Ptosis (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal ocular adnexa morphology (HPO)", + "Abnormality of the ocular adnexa (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "eyelid", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "multi organ part structure", + "disconnected anatomical group", + "ocular adnexa", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal ocular adnexa morphology", + "shape anatomical entity", + "drooping anatomical entity", + "drooping eyelid", + "shape eyelid", + "abnormal anatomical entity", + "abnormal ocular adnexa", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal shape of continuant", + "abnormal multicellular organism morphology", + "shape anatomical entity in independent continuant", + "abnormality of anatomical entity physiology", + ], + "object_label": "Ptosis (HPO)", + "evidence_count": 2, + }, + { + "id": "uuid:a6f9d857-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:160900", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:160900"], + "has_evidence": ["ECO:0000501"], + "subject": "MONDO:0008056", + "object": "HP:0000518", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ + "MONDO:0004994", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0018276", + "MONDO:0016107", "MONDO:0005071", + "MONDO:0005267", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0005045", + "MONDO:0004995", "MONDO:0700223", "BFO:0000002", "BFO:0000017", "BFO:0000020", + "MONDO:0016106", + "MONDO:0005217", + "MONDO:0024573", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0008056", "MONDO:0700096", + "MONDO:0000591", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0002254", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0016120", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "MONDO:0000462", + "MONDO:0005328", ], - "object_closure_label": [ + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "eye adnexa disorder", + "intrinsic cardiomyopathy", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "syndromic disease", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", + "cardiomyopathy", + "cardiovascular disorder", + "hypertrophic cardiomyopathy", "nervous system disorder", + "familial cardiomyopathy", + "heart disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy", + "myotonic dystrophy type 1", + "progressive muscular dystrophy", + "myotonic dystrophy", + "myotonic syndrome", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "eyelids malposition disorder", + "disorder of visual system", + "familial hypertrophic cardiomyopathy", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "subject_label": "myotonic dystrophy type 1", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "HP:0004328", + "UPHENO:0001001", + "UPHENO:0004765", + "HP:0000152", + "HP:0000518", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0020584", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "HP:0000517", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0005389", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0000965", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of the lens (HPO)", + "Cataract (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormal eye morphology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "lens of camera-type eye", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "anterior segment of eyeball", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "transparent eye structure", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal lens of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology", + ], + "object_label": "Cataract (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:d20f485a-4fde-44b8-aa20-20fd2d5902ab", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0013159", - "object": "MONDO:0000172", + "id": "uuid:a8bae558-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:236670", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:236670"], + "has_evidence": ["ECO:0000501"], + "subject": "MONDO:0009364", + "object": "HP:0000518", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0018282", "MONDO:0000001", + "MONDO:0016182", "MONDO:0017741", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0700068", "MONDO:0700223", - "MONDO:0013159", "MONDO:0024322", + "MONDO:0005283", + "MONDO:0020238", "BFO:0000002", + "MONDO:0016185", + "MONDO:0000171", "BFO:0000017", + "MONDO:0018869", "BFO:0000020", + "MONDO:0016157", + "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0018838", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016184", + "MONDO:0016156", + "MONDO:0009364", + "MONDO:0020246", + "MONDO:0021147", + "MONDO:0044137", + "MONDO:0019755", "OGMS:0000031", + "MONDO:0015327", "MONDO:0003847", "MONDO:0700070", "MONDO:0003939", + "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", + "MONDO:0020247", "MONDO:0005066", + "MONDO:0005328", "MONDO:0019950", "MONDO:0016155", + "MONDO:0700066", ], "subject_closure_label": [ "entity", @@ -3851,129 +4783,277 @@ def association_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy-dystroglycanopathy, type A", + "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", + "retinal disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", "congenital disorder of glycosylation", + "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "qualitative or quantitative defects of FKRP", + "qualitative or quantitative defects of fukutin", + "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", + "qualitative or quantitative defects of protein O-mannosyltransferase 1", + "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", + "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", "qualitative or quantitative defects of alpha-dystroglycan", + "lissencephaly spectrum disorders", + "cobblestone lissencephaly", "inborn errors of metabolism", "neuromuscular disease", + "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "inherited vitreous-retinal disease", + "inherited vitreoretinopathy", + "congenital vitreoretinal dysplasia", + "disorder of development or morphogenesis", "disorder of glycosylation", + "disorder of visual system", + "vitreous body disorder", "glycoprotein metabolism disease", + "myopathy caused by variation in FKRP", + "myopathy caused by variation in POMGNT1", "myopathy caused by variation in POMT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "HP:0004328", + "UPHENO:0001001", + "UPHENO:0004765", + "HP:0000152", + "HP:0000518", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0020584", + "UPHENO:0076692", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "HP:0000517", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0005389", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0000965", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of the lens (HPO)", + "Cataract (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormal eye morphology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "lens of camera-type eye", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "anterior segment of eyeball", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "transparent eye structure", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal lens of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Cataract (HPO)", "evidence_count": 2, }, { - "id": "urn:uuid:7a5c97ed-311c-4530-bfdf-447bf5c4db72", - "predicate": "biolink:subclass_of", - "category": "biolink:Association", - "aggregator_knowledge_source": ["infores:phenio"], - "primary_knowledge_source": "infores:mondo", - "provided_by": "phenio_edges", - "subject": "MONDO:0013160", - "object": "MONDO:0000172", + "id": "uuid:a4c7f187-6c84-11ee-9c86-072f86c27f6e", + "original_subject": "OMIM:253280", + "predicate": "biolink:has_phenotype", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "primary_knowledge_source": "infores:hpo-annotations", + "provided_by": "hpoa_disease_to_phenotype_edges", + "publications": ["OMIM:253280"], + "has_evidence": ["ECO:0000501"], + "subject": "MONDO:0009667", + "object": "HP:0000518", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0018282", "MONDO:0000001", + "MONDO:0016182", "MONDO:0017741", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0700068", "MONDO:0700223", "MONDO:0024322", + "MONDO:0005283", + "MONDO:0020238", "BFO:0000002", + "MONDO:0016185", + "MONDO:0000171", "BFO:0000017", + "MONDO:0018869", "BFO:0000020", - "MONDO:0013160", - "MONDO:0700071", + "MONDO:0016157", + "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0018838", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016184", + "MONDO:0016156", + "MONDO:0018939", + "MONDO:0020246", + "MONDO:0009667", + "MONDO:0021147", + "MONDO:0044137", + "MONDO:0019755", "OGMS:0000031", + "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", + "MONDO:0020247", "MONDO:0005066", + "MONDO:0005328", "MONDO:0019950", "MONDO:0016155", + "MONDO:0700066", ], "subject_closure_label": [ "entity", @@ -3982,83 +5062,207 @@ def association_response(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy-dystroglycanopathy, type A", + "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", + "retinal disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3", "congenital disorder of glycosylation", + "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "qualitative or quantitative defects of FKRP", + "qualitative or quantitative defects of fukutin", + "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", + "qualitative or quantitative defects of protein O-mannosyltransferase 1", + "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", + "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", "qualitative or quantitative defects of alpha-dystroglycan", + "lissencephaly spectrum disorders", + "cobblestone lissencephaly", + "muscle-eye-brain disease", "inborn errors of metabolism", "neuromuscular disease", + "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "inherited vitreous-retinal disease", + "inherited vitreoretinopathy", + "congenital vitreoretinal dysplasia", + "disorder of development or morphogenesis", "disorder of glycosylation", + "disorder of visual system", + "vitreous body disorder", "glycoprotein metabolism disease", - "myopathy caused by variation in POMT2", + "myopathy caused by variation in FKRP", + "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2", - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "HP:0004328", + "UPHENO:0001001", + "UPHENO:0004765", + "HP:0000152", + "HP:0000518", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0020584", + "UPHENO:0076692", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "HP:0000517", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0005389", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0000965", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of the lens (HPO)", + "Cataract (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormal eye morphology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "lens of camera-type eye", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "anterior segment of eyeball", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "transparent eye structure", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal lens of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Cataract (HPO)", "evidence_count": 2, }, ], diff --git a/backend/tests/fixtures/association_table.py b/backend/tests/fixtures/association_table.py index 976a79b56..f3d5308b4 100644 --- a/backend/tests/fixtures/association_table.py +++ b/backend/tests/fixtures/association_table.py @@ -6,10 +6,11 @@ def association_table(): return { "limit": 5, "offset": 0, - "total": 2166, + "total": 4027, "items": [ { - "id": "uuid:d92c5da3-5349-11ee-a38e-df3e29a44ac7", + "id": "uuid:aafbc2e0-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0020793", "original_subject": "OMIM:164310", "subject_namespace": "MONDO", @@ -167,32 +168,32 @@ def association_table(): "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, + "pathway": None, + "evidence_count": 4, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], "provided_by": "hpoa_disease_to_phenotype_edges", - "provided_by_link": None, + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", + }, "publications": ["PMID:21242490", "PMID:32493488", "PMID:31332380"], + "publications_links": [ + {"id": "PMID:21242490", "url": "http://identifiers.org/pubmed/21242490"}, + {"id": "PMID:32493488", "url": "http://identifiers.org/pubmed/32493488"}, + {"id": "PMID:31332380", "url": "http://identifiers.org/pubmed/31332380"}, + ], "qualifiers": [], "frequency_qualifier": "HP:0040282", - "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 6, - "pathway": None, "frequency_qualifier_label": "Frequent (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": [ - "HP:0000001", - "HP:0040282", - "HP:0040279", - ], - "frequency_qualifier_closure_label": [ - "All (HPO)", - "Frequency (HPO)", - "Frequent (HPO)", - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -211,7 +212,8 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:d92c5db4-5349-11ee-a38e-df3e29a44ac7", + "id": "uuid:aafbc2f1-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0020793", "original_subject": "OMIM:164310", "subject_namespace": "MONDO", @@ -423,32 +425,32 @@ def association_table(): "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, + "pathway": None, + "evidence_count": 4, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], "provided_by": "hpoa_disease_to_phenotype_edges", - "provided_by_link": None, + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", + }, "publications": ["PMID:21242490", "PMID:32493488", "PMID:31332380"], + "publications_links": [ + {"id": "PMID:21242490", "url": "http://identifiers.org/pubmed/21242490"}, + {"id": "PMID:32493488", "url": "http://identifiers.org/pubmed/32493488"}, + {"id": "PMID:31332380", "url": "http://identifiers.org/pubmed/31332380"}, + ], "qualifiers": [], "frequency_qualifier": "HP:0040282", - "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 6, - "pathway": None, "frequency_qualifier_label": "Frequent (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": [ - "HP:0000001", - "HP:0040282", - "HP:0040279", - ], - "frequency_qualifier_closure_label": [ - "All (HPO)", - "Frequency (HPO)", - "Frequent (HPO)", - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -467,7 +469,8 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:d574cdea-5349-11ee-a38e-df3e29a44ac7", + "id": "uuid:a77a5b0a-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0013049", "original_subject": "OMIM:612937", "subject_namespace": "MONDO", @@ -657,7 +660,9 @@ def association_table(): "entity", "continuant", "continuant", + "occurrent", "independent continuant", + "process", "specifically dependent continuant", "material entity", "gas molecular entity", @@ -686,6 +691,8 @@ def association_table(): "nitrogen molecular entity", "creatine kinase complex", "cellular_component", + "biological_process", + "metabolic process", "protein-containing complex", "transferase complex, transferring phosphorus-containing groups", "catalytic complex", @@ -751,32 +758,31 @@ def association_table(): "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, + "pathway": None, + "evidence_count": 3, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], "provided_by": "hpoa_disease_to_phenotype_edges", - "provided_by_link": None, + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", + }, "publications": ["PMID:19576565", "PMID:28803818"], + "publications_links": [ + {"id": "PMID:19576565", "url": "http://identifiers.org/pubmed/19576565"}, + {"id": "PMID:28803818", "url": "http://identifiers.org/pubmed/28803818"}, + ], "qualifiers": [], "frequency_qualifier": "HP:0040280", - "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 5, - "pathway": None, "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": [ - "HP:0000001", - "HP:0040279", - "HP:0040280", - ], - "frequency_qualifier_closure_label": [ - "All (HPO)", - "Frequency (HPO)", - "Obligate (HPO)", - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -795,7 +801,8 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:da2b4746-5349-11ee-a38e-df3e29a44ac7", + "id": "uuid:abeb7c29-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0009681", "original_subject": "OMIM:254090", "subject_namespace": "MONDO", @@ -951,32 +958,31 @@ def association_table(): "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, + "pathway": None, + "evidence_count": 3, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], "provided_by": "hpoa_disease_to_phenotype_edges", - "provided_by_link": None, + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", + }, "publications": ["PMID:16258657", "OMIM:254090"], + "publications_links": [ + {"id": "PMID:16258657", "url": "http://identifiers.org/pubmed/16258657"}, + {"id": "OMIM:254090", "url": "http://identifiers.org/mim/254090"}, + ], "qualifiers": [], "frequency_qualifier": "HP:0040280", - "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 5, - "pathway": None, "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": [ - "HP:0000001", - "HP:0040279", - "HP:0040280", - ], - "frequency_qualifier_closure_label": [ - "All (HPO)", - "Frequency (HPO)", - "Obligate (HPO)", - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -995,7 +1001,8 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:d8c61fbc-5349-11ee-a38e-df3e29a44ac7", + "id": "uuid:aa9b85eb-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0009676", "original_subject": "OMIM:253601", "subject_namespace": "MONDO", @@ -1149,32 +1156,31 @@ def association_table(): "object_taxon_label": None, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": None, + "pathway": None, + "evidence_count": 3, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], "provided_by": "hpoa_disease_to_phenotype_edges", - "provided_by_link": None, + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", + }, "publications": ["PMID:9731527", "PMID:9009996"], + "publications_links": [ + {"id": "PMID:9731527", "url": "http://identifiers.org/pubmed/9731527"}, + {"id": "PMID:9009996", "url": "http://identifiers.org/pubmed/9009996"}, + ], "qualifiers": [], "frequency_qualifier": "HP:0040280", - "has_evidence": ["ECO:0000269"], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 5, - "pathway": None, "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": [ - "HP:0000001", - "HP:0040279", - "HP:0040280", - ], - "frequency_qualifier_closure_label": [ - "All (HPO)", - "Frequency (HPO)", - "Obligate (HPO)", - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, diff --git a/backend/tests/fixtures/association_table_response.py b/backend/tests/fixtures/association_table_response.py index d737c34db..d6b314286 100644 --- a/backend/tests/fixtures/association_table_response.py +++ b/backend/tests/fixtures/association_table_response.py @@ -22,11 +22,11 @@ def association_table_response(): }, }, "response": { - "num_found": 2166, + "num_found": 4027, "start": 0, "docs": [ { - "id": "uuid:d92c5da3-5349-11ee-a38e-df3e29a44ac7", + "id": "uuid:aafbc2e0-6c84-11ee-9c86-072f86c27f6e", "original_subject": "OMIM:164310", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -186,21 +186,13 @@ def association_table_response(): "object_label": "Distal muscle weakness (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": [ - "HP:0000001", - "HP:0040282", - "HP:0040279", - ], - "frequency_qualifier_closure_label": [ - "All (HPO)", - "Frequency (HPO)", - "Frequent (HPO)", - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"], "frequency_qualifier_label": "Frequent (HPO)", - "evidence_count": 6, + "evidence_count": 4, }, { - "id": "uuid:d92c5db4-5349-11ee-a38e-df3e29a44ac7", + "id": "uuid:aafbc2f1-6c84-11ee-9c86-072f86c27f6e", "original_subject": "OMIM:164310", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -414,21 +406,13 @@ def association_table_response(): "object_label": "Dysphagia (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": [ - "HP:0000001", - "HP:0040282", - "HP:0040279", - ], - "frequency_qualifier_closure_label": [ - "All (HPO)", - "Frequency (HPO)", - "Frequent (HPO)", - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040282", "HP:0040279"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Frequent (HPO)"], "frequency_qualifier_label": "Frequent (HPO)", - "evidence_count": 6, + "evidence_count": 4, }, { - "id": "uuid:d574cdea-5349-11ee-a38e-df3e29a44ac7", + "id": "uuid:a77a5b0a-6c84-11ee-9c86-072f86c27f6e", "original_subject": "OMIM:612937", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -621,7 +605,9 @@ def association_table_response(): "entity", "continuant", "continuant", + "occurrent", "independent continuant", + "process", "specifically dependent continuant", "material entity", "gas molecular entity", @@ -650,6 +636,8 @@ def association_table_response(): "nitrogen molecular entity", "creatine kinase complex", "cellular_component", + "biological_process", + "metabolic process", "protein-containing complex", "transferase complex, transferring phosphorus-containing groups", "catalytic complex", @@ -714,21 +702,13 @@ def association_table_response(): "object_label": "Elevated circulating creatine kinase concentration (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": [ - "HP:0000001", - "HP:0040279", - "HP:0040280", - ], - "frequency_qualifier_closure_label": [ - "All (HPO)", - "Frequency (HPO)", - "Obligate (HPO)", - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], "frequency_qualifier_label": "Obligate (HPO)", - "evidence_count": 5, + "evidence_count": 3, }, { - "id": "uuid:da2b4746-5349-11ee-a38e-df3e29a44ac7", + "id": "uuid:abeb7c29-6c84-11ee-9c86-072f86c27f6e", "original_subject": "OMIM:254090", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -886,21 +866,13 @@ def association_table_response(): "object_label": "Distal joint laxity (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": [ - "HP:0000001", - "HP:0040279", - "HP:0040280", - ], - "frequency_qualifier_closure_label": [ - "All (HPO)", - "Frequency (HPO)", - "Obligate (HPO)", - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], "frequency_qualifier_label": "Obligate (HPO)", - "evidence_count": 5, + "evidence_count": 3, }, { - "id": "uuid:d8c61fbc-5349-11ee-a38e-df3e29a44ac7", + "id": "uuid:aa9b85eb-6c84-11ee-9c86-072f86c27f6e", "original_subject": "OMIM:253601", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -1056,18 +1028,10 @@ def association_table_response(): "object_label": "Proximal muscle weakness (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": [ - "HP:0000001", - "HP:0040279", - "HP:0040280", - ], - "frequency_qualifier_closure_label": [ - "All (HPO)", - "Frequency (HPO)", - "Obligate (HPO)", - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040280"], + "frequency_qualifier_closure_label": ["All (HPO)", "Frequency (HPO)", "Obligate (HPO)"], "frequency_qualifier_label": "Obligate (HPO)", - "evidence_count": 5, + "evidence_count": 3, }, ], }, diff --git a/backend/tests/fixtures/associations.py b/backend/tests/fixtures/associations.py index 49ec81515..968d2fe9c 100644 --- a/backend/tests/fixtures/associations.py +++ b/backend/tests/fixtures/associations.py @@ -6,70 +6,38 @@ def associations(): return { "limit": 20, "offset": 0, - "total": 2823, + "total": 4838, "items": [ { - "id": "urn:uuid:a54e0b8c-af55-459b-ae98-a7e0ae60b190", - "subject": "MONDO:0009364", + "id": "urn:uuid:e4e8dbec-cb0c-44e9-b1cb-8be3b357b7b8", + "category": "biolink:Association", + "subject": "MONDO:0018276", "original_subject": None, "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", "MONDO:0018276", - "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0009364", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", - "MONDO:0700070", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", + "subject_label": "muscular dystrophy-dystroglycanopathy", "subject_closure_label": [ "entity", "continuant", @@ -77,62 +45,159 @@ def associations(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", "neuromuscular disease", - "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "myopathy caused by variation in POMT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], "subject_taxon": None, "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000171", + "predicate": "biolink:related_to", + "object": "GO:0006486", "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "GO", + "object_category": "biolink:BiologicalProcessOrActivity", "object_closure": [ + "GO:0008150", + "BFO:0000003", + "GO:0036211", + "GO:0043413", + "GO:0006486", + "GO:1901564", + "GO:0070085", + "GO:0043412", + "GO:0006807", + "GO:0044238", + "GO:0043170", + "GO:0071704", + "BFO:0000015", + "BFO:0000001", + "GO:0008152", + "GO:0019538", + "BFO:0000001", + "BFO:0000003", + "BFO:0000015", + "GO:0008150", + "GO:0009987", + "GO:0008152", + "GO:0044237", + "GO:0071704", + "GO:0009058", + "GO:0044238", + "GO:0006807", + "GO:0044249", + "GO:0043170", + "GO:1901135", + "GO:1901564", + "GO:1901576", + "GO:0019538", + "GO:0009059", + "GO:1901137", + "GO:0009100", + "GO:1901566", + "GO:0009101", + ], + "object_label": "protein glycosylation", + "object_closure_label": [ + "entity", + "entity", + "occurrent", + "occurrent", + "process", + "process", + "protein glycosylation", + "nitrogen compound metabolic process", + "nitrogen compound metabolic process", + "biological_process", + "biological_process", + "metabolic process", + "metabolic process", + "biosynthetic process", + "macromolecule biosynthetic process", + "glycoprotein metabolic process", + "glycoprotein biosynthetic process", + "cellular process", + "protein metabolic process", + "protein metabolic process", + "protein modification process", + "macromolecule metabolic process", + "macromolecule metabolic process", + "macromolecule modification", + "macromolecule glycosylation", + "cellular metabolic process", + "primary metabolic process", + "primary metabolic process", + "cellular biosynthetic process", + "glycosylation", + "organic substance metabolic process", + "organic substance metabolic process", + "carbohydrate derivative metabolic process", + "carbohydrate derivative biosynthetic process", + "organonitrogen compound metabolic process", + "organonitrogen compound metabolic process", + "organonitrogen compound biosynthetic process", + "organic substance biosynthetic process", + ], + "object_taxon": None, + "object_taxon_label": None, + "primary_knowledge_source": "infores:mondo", + "aggregator_knowledge_source": ["infores:phenio"], + "negated": None, + "pathway": None, + "evidence_count": 0, + "has_evidence": [], + "has_evidence_links": [], + "provided_by": "phenio_edges", + "provided_by_link": { + "id": "phenio", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + }, + "publications": [], + "publications_links": [], + "qualifiers": [], + "frequency_qualifier": None, + "onset_qualifier": None, + "sex_qualifier": None, + "stage_qualifier": None, + "frequency_qualifier_label": None, + "frequency_qualifier_namespace": None, + "frequency_qualifier_category": None, + "frequency_qualifier_closure": [], + "frequency_qualifier_closure_label": [], + "onset_qualifier_label": None, + "onset_qualifier_namespace": None, + "onset_qualifier_category": None, + "onset_qualifier_closure": [], + "onset_qualifier_closure_label": [], + "sex_qualifier_label": None, + "sex_qualifier_namespace": None, + "sex_qualifier_category": None, + "sex_qualifier_closure": [], + "sex_qualifier_closure_label": [], + "stage_qualifier_label": None, + "stage_qualifier_namespace": None, + "stage_qualifier_category": None, + "stage_qualifier_closure": [], + "stage_qualifier_closure_label": [], + }, + { + "id": "uuid:a82ac92f-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0013155", + "original_subject": "OMIM:613151", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", @@ -142,123 +207,287 @@ def associations(): "MONDO:0005071", "MONDO:0020121", "MONDO:0700068", + "MONDO:0000172", "MONDO:0700223", "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0013155", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", - "MONDO:0020247", "MONDO:0005066", - "MONDO:0005328", + "MONDO:0018277", "MONDO:0019950", "MONDO:0016155", - "MONDO:0700066", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", - "object_closure_label": [ + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3", + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "muscular dystrophy-dystroglycanopathy, type B", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", + "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3", "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", + "congenital muscular dystrophy with cerebellar involvement", "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", "inborn errors of metabolism", "neuromuscular disease", - "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0000486", + "original_object": None, + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0080581", + "BFO:0000020", + "UPHENO:0002433", + "UPHENO:0003020", + "UPHENO:0079828", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0000707", + "HP:0012373", + "HP:0000496", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0000708", + "HP:0000486", + "UPHENO:0079826", + "UPHENO:0004523", + "HP:0011446", + "HP:0000549", + "UPHENO:0049587", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "BFO:0000141", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "UBERON:0000466", + "GO:0007610", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0000015", + "NBO:0000313", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0006800", + "NBO:0000338", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0001016", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0010222", + "NBO:0000001", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "NBO:0000444", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_label": "Strabismus (HPO)", + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "immaterial entity", + "behavior", + "biological_process", + "multicellular organismal process", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Strabismus (HPO)", + "Abnormality of eye movement (HPO)", + "Abnormal conjugate eye movement (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal nervous system physiology (HPO)", + "body part movement", + "behavior process", + "kinesthetic behavior", + "eye movement", + "quality", + "non-material anatomical boundary", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "immaterial anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "nervous system", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "anatomical line", + "craniocervical region", + "multicellular anatomical structure", + "anatomical line between pupils", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormality of nervous system physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", + ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:613151"], + "publications_links": [{"id": "OMIM:613151", "url": "http://identifiers.org/mim/613151"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -281,67 +510,42 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "urn:uuid:6a4b5bf7-4254-49cf-bb21-42549480b64f", - "subject": "MONDO:0009667", - "original_subject": None, + "id": "uuid:a73a092e-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0014023", + "original_subject": "OMIM:615042", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", "MONDO:0018276", - "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0014023", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0018939", - "MONDO:0020246", - "MONDO:0009667", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", + "MONDO:0017749", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", - "MONDO:0020247", + "MONDO:0005500", "MONDO:0005066", - "MONDO:0005328", "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3", + "subject_label": "congenital muscular dystrophy with intellectual disability and severe epilepsy", "subject_closure_label": [ "entity", "continuant", @@ -349,188 +553,244 @@ def associations(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3", + "congenital disorder of glycosylation type I", + "congenital muscular dystrophy with intellectual disability and severe epilepsy", "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", + "disorder of multiple glycosylation", "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "muscle-eye-brain disease", "inborn errors of metabolism", "neuromuscular disease", - "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], "subject_taxon": None, "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000171", + "predicate": "biolink:has_phenotype", + "object": "HP:0000486", "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0700068", - "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", - "BFO:0000017", - "MONDO:0018869", + "UPHENO:0080581", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0016139", - "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", - "MONDO:0005336", - "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", - "OGMS:0000031", - "MONDO:0015327", - "MONDO:0003847", - "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", + "UPHENO:0002433", + "UPHENO:0003020", + "UPHENO:0079828", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0000707", + "HP:0012373", + "HP:0000496", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0000708", + "HP:0000486", + "UPHENO:0079826", + "UPHENO:0004523", + "HP:0011446", + "HP:0000549", + "UPHENO:0049587", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", + "PATO:0000001", + "HP:0012638", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "BFO:0000141", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "UBERON:0000466", + "GO:0007610", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0000015", + "NBO:0000313", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0006800", + "NBO:0000338", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0001016", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0010222", + "NBO:0000001", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "NBO:0000444", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "object_label": "Strabismus (HPO)", "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "occurrent", + "independent continuant", + "process", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "metabolic disease", - "nervous system disorder", - "retinal disorder", - "eye disorder", - "myopathy", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", - "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "immaterial entity", + "behavior", + "biological_process", + "multicellular organismal process", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Strabismus (HPO)", + "Abnormality of eye movement (HPO)", + "Abnormal conjugate eye movement (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal nervous system physiology (HPO)", + "body part movement", + "behavior process", + "kinesthetic behavior", + "eye movement", + "quality", + "non-material anatomical boundary", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "immaterial anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "nervous system", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "anatomical line", + "craniocervical region", + "multicellular anatomical structure", + "anatomical line between pupils", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormality of nervous system physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:615042"], + "publications_links": [{"id": "OMIM:615042", "url": "http://identifiers.org/mim/615042"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -553,68 +813,40 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "urn:uuid:7ddd2655-151a-44d4-ab18-6a6f491abcee", - "subject": "MONDO:0009678", - "original_subject": None, + "id": "uuid:a5790e7e-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0014144", + "original_subject": "OMIM:615356", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0700067", - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0016971", + "MONDO:0000429", + "MONDO:0014144", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0005395", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", + "MONDO:0006025", + "MONDO:0016106", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0018939", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", - "MONDO:0009678", + "MONDO:0018243", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", + "MONDO:0015152", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4", + "subject_label": "autosomal recessive limb-girdle muscular dystrophy type R18", "subject_closure_label": [ "entity", "continuant", @@ -622,1823 +854,242 @@ def associations(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "autosomal genetic disease", "musculoskeletal system disorder", - "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "muscle-eye-brain disease", - "inborn errors of metabolism", + "movement disorder", + "autosomal recessive disease", + "autosomal recessive limb-girdle muscular dystrophy type R18", + "autosomal recessive limb-girdle muscular dystrophy", + "progressive muscular dystrophy", + "limb-girdle muscular dystrophy", + "intellectual disability-hyperkinetic movement-truncal ataxia syndrome", "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - 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"disease", - ], - "object_taxon": None, - "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", - "negated": None, - "provided_by": "phenio_edges", - "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", - }, - "publications": [], - "qualifiers": [], - "frequency_qualifier": None, - "has_evidence": [], - "onset_qualifier": None, - "sex_qualifier": None, - "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, - "frequency_qualifier_label": None, - "frequency_qualifier_namespace": None, - "frequency_qualifier_category": None, - "frequency_qualifier_closure": [], - "frequency_qualifier_closure_label": [], - "onset_qualifier_label": None, - "onset_qualifier_namespace": None, - "onset_qualifier_category": None, - "onset_qualifier_closure": [], - "onset_qualifier_closure_label": [], - "sex_qualifier_label": None, - "sex_qualifier_namespace": None, - "sex_qualifier_category": None, - "sex_qualifier_closure": [], - "sex_qualifier_closure_label": [], - "stage_qualifier_label": None, - "stage_qualifier_namespace": None, - "stage_qualifier_category": None, - "stage_qualifier_closure": [], - "stage_qualifier_closure_label": [], - }, - { - "id": "urn:uuid:b862abf0-be63-4b31-a52d-526d73305fbb", - "subject": "MONDO:0014022", - "original_subject": None, - "subject_namespace": "MONDO", - "subject_category": "biolink:Disease", - "subject_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0700068", - "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", - "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", - "BFO:0000017", - "MONDO:0018869", - "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0016139", - "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", - "MONDO:0005336", - "MONDO:0014022", - "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0018939", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", - "OGMS:0000031", - "MONDO:0015327", - "MONDO:0003847", - "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", - ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10", - "subject_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "metabolic disease", - "nervous system disorder", - "retinal disorder", - "eye disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "muscle-eye-brain disease", - "inborn errors of metabolism", - "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "human disease", - "hereditary skeletal muscle disorder", - "disease", - ], - "subject_taxon": None, - "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000171", - "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", - "object_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0700068", - "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", - "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", - "BFO:0000017", - "MONDO:0018869", - "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0016139", - "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", - "MONDO:0005336", - "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", - "OGMS:0000031", - "MONDO:0015327", - "MONDO:0003847", - "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", - ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", - "object_closure_label": [ - "entity", - "continuant", - "disposition", - "realizable entity", - "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "metabolic disease", - "nervous system disorder", - "retinal disorder", - "eye disorder", - "myopathy", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", - "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "immaterial entity", + "behavior", + "biological_process", + "multicellular organismal process", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Strabismus (HPO)", + "Abnormality of eye movement (HPO)", + "Abnormal conjugate eye movement (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal nervous system physiology (HPO)", + "body part movement", + "behavior process", + "kinesthetic behavior", + "eye movement", + "quality", + "non-material anatomical boundary", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "immaterial anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "nervous system", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "anatomical line", + "craniocervical region", + "multicellular anatomical structure", + "anatomical line between pupils", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormality of nervous system physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:615356"], + "publications_links": [{"id": "OMIM:615356", "url": "http://identifiers.org/mim/615356"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -2461,67 +1112,35 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "urn:uuid:6fc3a05c-fd6a-46e1-8815-25a4a20e9954", - "subject": "MONDO:0014071", - "original_subject": None, + "id": "uuid:abeb7ac4-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0024607", + "original_subject": "OMIM:617404", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0024607", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0016185", - "MONDO:0014071", - "MONDO:0000171", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0018939", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11", + "subject_label": "congenital muscular dystrophy with cataracts and intellectual disability", "subject_closure_label": [ "entity", "continuant", @@ -2529,188 +1148,237 @@ def associations(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "muscle-eye-brain disease", - "inborn errors of metabolism", "neuromuscular disease", - "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", + "congenital muscular dystrophy with cataracts and intellectual disability", "human disease", "hereditary skeletal muscle disorder", "disease", ], "subject_taxon": None, "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000171", + "predicate": "biolink:has_phenotype", + "object": "HP:0000486", "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0018282", - "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0700068", - "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", - "BFO:0000017", - "MONDO:0018869", + "UPHENO:0080581", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0016139", - "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", - "MONDO:0005336", - "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", - "OGMS:0000031", - "MONDO:0015327", - "MONDO:0003847", - "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", + "UPHENO:0002433", + "UPHENO:0003020", + "UPHENO:0079828", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0000707", + "HP:0012373", + "HP:0000496", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0000708", + "HP:0000486", + "UPHENO:0079826", + "UPHENO:0004523", + "HP:0011446", + "HP:0000549", + "UPHENO:0049587", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", + "PATO:0000001", + "HP:0012638", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "BFO:0000141", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "UBERON:0000466", + "GO:0007610", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0000015", + "NBO:0000313", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0006800", + "NBO:0000338", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0001016", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0010222", + "NBO:0000001", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "NBO:0000444", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", + "object_label": "Strabismus (HPO)", "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "occurrent", + "independent continuant", + "process", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "metabolic disease", - "nervous system disorder", - "retinal disorder", - "eye disorder", - "myopathy", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", - "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "immaterial entity", + "behavior", + "biological_process", + "multicellular organismal process", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Strabismus (HPO)", + "Abnormality of eye movement (HPO)", + "Abnormal conjugate eye movement (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal nervous system physiology (HPO)", + "body part movement", + "behavior process", + "kinesthetic behavior", + "eye movement", + "quality", + "non-material anatomical boundary", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "immaterial anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "nervous system", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "anatomical line", + "craniocervical region", + "multicellular anatomical structure", + "anatomical line between pupils", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormality of nervous system physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:617404"], + "publications_links": [{"id": "OMIM:617404", "url": "http://identifiers.org/mim/617404"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -2733,9 +1401,10 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "urn:uuid:a20f59e6-2468-4f26-a789-04cd5d5bd97f", - "subject": "MONDO:0014101", - "original_subject": None, + "id": "uuid:abeb7be1-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0013835", + "original_subject": "OMIM:614643", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ @@ -2753,12 +1422,12 @@ def associations(): "MONDO:0005283", "MONDO:0020238", "BFO:0000002", - "MONDO:0014101", "MONDO:0016185", "MONDO:0000171", "BFO:0000017", "MONDO:0018869", "BFO:0000020", + "MONDO:0013835", "MONDO:0016157", "MONDO:0017745", "BFO:0000016", @@ -2792,7 +1461,7 @@ def associations(): "MONDO:0016155", "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", "subject_closure_label": [ "entity", "continuant", @@ -2811,7 +1480,7 @@ def associations(): "retinal disorder", "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -2849,138 +1518,553 @@ def associations(): ], "subject_taxon": None, "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000171", + "predicate": "biolink:has_phenotype", + "object": "HP:0000490", "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0018282", + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0000490", + "HP:0012372", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0049367", + "UPHENO:0002764", + "UPHENO:0018424", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0018390", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0020584", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "HP:0100886", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_label": "Deeply set eye (HPO)", + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Deeply set eye (HPO)", + "Abnormal eye morphology (HPO)", + "Abnormality of globe location (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal location of anatomical entity", + "abnormal location of eyeball of camera-type eye", + "abnormal anatomical entity morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity topology in independent continuant", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology", + ], + "object_taxon": None, + "object_taxon_label": None, + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "negated": None, + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "provided_by": "hpoa_disease_to_phenotype_edges", + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", + }, + "publications": ["OMIM:614643"], + "publications_links": [{"id": "OMIM:614643", "url": "http://identifiers.org/mim/614643"}], + "qualifiers": [], + "frequency_qualifier": None, + "onset_qualifier": None, + "sex_qualifier": None, + "stage_qualifier": None, + "frequency_qualifier_label": None, + "frequency_qualifier_namespace": None, + "frequency_qualifier_category": None, + "frequency_qualifier_closure": [], + "frequency_qualifier_closure_label": [], + "onset_qualifier_label": None, + "onset_qualifier_namespace": None, + "onset_qualifier_category": None, + "onset_qualifier_closure": [], + "onset_qualifier_closure_label": [], + "sex_qualifier_label": None, + "sex_qualifier_namespace": None, + "sex_qualifier_category": None, + "sex_qualifier_closure": [], + "sex_qualifier_closure_label": [], + "stage_qualifier_label": None, + "stage_qualifier_namespace": None, + "stage_qualifier_category": None, + "stage_qualifier_closure": [], + "stage_qualifier_closure_label": [], + }, + { + "id": "uuid:aa6b44e5-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0009181", + "original_subject": "OMIM:226670", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0016198", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", - "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", + "MONDO:0700223", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0006617", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", + "MONDO:0017610", + "MONDO:0006025", + "MONDO:0016106", + "MONDO:0002051", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", + "MONDO:0100118", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", + "MONDO:0002254", + "MONDO:0009181", + "MONDO:0019276", + "MONDO:0005093", "OGMS:0000031", - "MONDO:0015327", + "MONDO:0019268", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", + "MONDO:0006541", + "MONDO:0015152", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", - "object_closure_label": [ + "subject_label": "epidermolysis bullosa simplex 5B, with muscular dystrophy", + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "autosomal genetic disease", + "integumentary system disorder", "musculoskeletal system disorder", - "congenital nervous system disorder", + "syndromic disease", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", + "skin disorder", "myopathy", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", + "autosomal recessive disease", + "epidermolysis bullosa", + "vesiculobullous skin disease", + "epidermolysis bullosa simplex 5B, with muscular dystrophy", + "autosomal recessive limb-girdle muscular dystrophy", + "progressive muscular dystrophy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", + "qualitative or quantitative defects of plectin", + "limb-girdle muscular dystrophy", + "epidermolysis bullosa simplex", "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", + "epidermal disease", + "inherited epidermolysis bullosa", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", + "hereditary skin disorder", "human disease", "hereditary skeletal muscle disorder", "disease", ], + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0000491", + "original_object": None, + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082682", + "UPHENO:0082875", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0080377", + "UPHENO:0054970", + "UPHENO:0002948", + "HP:0004328", + "UPHENO:0020998", + "UPHENO:0001001", + "UPHENO:0074763", + "UPHENO:0074632", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "HP:0010978", + "UPHENO:0002764", + "UPHENO:0021662", + "UPHENO:0082723", + "UPHENO:0001002", + "HP:0012647", + "HP:0000118", + "BFO:0000002", + "HP:0100533", + "UPHENO:0080221", + "UPHENO:0083263", + "BFO:0000020", + "HP:0000481", + "UPHENO:0003020", + "UPHENO:0049584", + "HP:0000234", + "UPHENO:0002332", + "HP:0002715", + "UPHENO:0015280", + "UPHENO:0080693", + "HP:0000271", + "HP:0012373", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002263", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0049588", + "HP:0000491", + "UPHENO:0020584", + "UPHENO:0059829", + "UPHENO:0080662", + "UPHENO:0076692", + "UPHENO:0074685", + "UPHENO:0076684", + "UPHENO:0049587", + "BFO:0000001", + "HP:0012649", + "PATO:0000001", + "UPHENO:0074572", + "HP:0011495", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0050896", + "PR:000050567", + "UBERON:0000465", + "GO:0006950", + "UBERON:0000483", + "UBERON:0012430", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0000964", + "GO:0006952", + "UBERON:0019304", + "UBERON:0010371", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "GO:0006954", + "UBERON:0007625", + "UBERON:0015808", + "UBERON:0000019", + "UBERON:0010313", + "UBERON:0010230", + "UBERON:0010409", + "UBERON:0000479", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0002405", + "UBERON:0001772", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000060", + "UBERON:0004923", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_label": "Keratitis (HPO)", + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "response to stress", + "defense response", + "inflammatory response", + "biological_process", + "response to stimulus", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormal cornea morphology (HPO)", + "Keratitis (HPO)", + "Abnormality of the immune system (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormality of immune system physiology (HPO)", + "Abnormal corneal epithelium morphology (HPO)", + "Abnormal eye morphology (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal inflammatory response (HPO)", + "Increased inflammatory response (HPO)", + "Inflammatory abnormality of the eye (HPO)", + "quality", + "protein-containing material entity", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical wall", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "tissue", + "epithelium", + "cornea", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "corneal epithelium", + "anterior segment of eyeball", + "visual system", + "immune system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "organ component layer", + "pigment epithelium of eye", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "neural crest-derived structure", + "structure with developmental contribution from neural crest", + "ecto-epithelium", + "ocular surface region", + "subdivision of organism along main body axis", + "tunica fibrosa of eyeball", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "eye epithelium", + "sensory organ epithelium", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of immune system physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal immune system", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal cornea morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal corneal epithelium morphology", + "abnormal inflammatory response", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal response to stress", + "increased biological_process", + "abnormal biological_process in independent continuant", + "increased biological_process in independent continuant", + "increased inflammatory response in eyeball of camera-type eye", + "increased inflammatory response in independent continuant", + "increased biological_process in eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "increased inflammatory response", + "abnormal anatomical entity morphology", + "changed biological_process rate in independent continuant", + "changed biological_process rate", + "increased qualitatively biological_process", + "increased qualitatively inflammatory response", + "abnormal multicellular organism morphology", + "increased qualitatively biological_process in independent continuant", + "increased qualitatively inflammatory response in independent continuant", + "abnormality of anatomical entity physiology", + "increased qualitatively response to stimulus", + ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000501"], + "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:226670"], + "publications_links": [{"id": "OMIM:226670", "url": "http://identifiers.org/mim/226670"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -3003,17 +2087,18 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "urn:uuid:f7c423b7-6f4c-4663-9ead-41d529a7cf2b", - "subject": "MONDO:0014120", - "original_subject": None, + "id": "uuid:a74a1018-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0009678", + "original_subject": "OMIM:253800", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0700067", "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", "MONDO:0017741", - "MONDO:0014120", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", @@ -3042,10 +2127,12 @@ def associations(): "MONDO:0002081", "MONDO:0016184", "MONDO:0016156", + "MONDO:0018939", "MONDO:0020246", "MONDO:0021147", "MONDO:0044137", "MONDO:0019755", + "MONDO:0009678", "OGMS:0000031", "MONDO:0015327", "MONDO:0003847", @@ -3062,7 +2149,7 @@ def associations(): "MONDO:0016155", "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4", "subject_closure_label": [ "entity", "continuant", @@ -3081,7 +2168,7 @@ def associations(): "retinal disorder", "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -3097,6 +2184,7 @@ def associations(): "qualitative or quantitative defects of alpha-dystroglycan", "lissencephaly spectrum disorders", "cobblestone lissencephaly", + "muscle-eye-brain disease", "inborn errors of metabolism", "neuromuscular disease", "developmental defect during embryogenesis", @@ -3112,6 +2200,7 @@ def associations(): "vitreous body disorder", "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", + "myopathy caused by variation in FKTN", "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", @@ -3119,12 +2208,235 @@ def associations(): ], "subject_taxon": None, "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000171", + "predicate": "biolink:has_phenotype", + "object": "HP:0000496", "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0080581", + "BFO:0000020", + "UPHENO:0002433", + "UPHENO:0003020", + "UPHENO:0079828", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0000707", + "HP:0012373", + "HP:0000496", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0000708", + "UPHENO:0079826", + "UPHENO:0004523", + "HP:0011446", + "UPHENO:0049587", + "BFO:0000001", + "PATO:0000001", + "HP:0012638", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "GO:0007610", + "UBERON:0000061", + "UBERON:0034923", + "NBO:0000313", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "NBO:0000338", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0001016", + "UBERON:0004456", + "UBERON:0001032", + "NBO:0000001", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "NBO:0000444", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_label": "Abnormality of eye movement (HPO)", + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "behavior", + "biological_process", + "multicellular organismal process", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of eye movement (HPO)", + "Abnormality of the nervous system (HPO)", + "Behavioral abnormality (HPO)", + "Abnormality of higher mental function (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal nervous system physiology (HPO)", + "body part movement", + "behavior process", + "kinesthetic behavior", + "eye movement", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "nervous system", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormality of nervous system physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal nervous system", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal behavior", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal behavior process", + "abnormal eye movement", + "abnormal eye movement", + "abnormal behavior process", + "abnormality of anatomical entity physiology", + ], + "object_taxon": None, + "object_taxon_label": None, + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "negated": None, + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "provided_by": "hpoa_disease_to_phenotype_edges", + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", + }, + "publications": ["OMIM:253800"], + "publications_links": [{"id": "OMIM:253800", "url": "http://identifiers.org/mim/253800"}], + "qualifiers": [], + "frequency_qualifier": None, + "onset_qualifier": None, + "sex_qualifier": None, + "stage_qualifier": None, + "frequency_qualifier_label": None, + "frequency_qualifier_namespace": None, + "frequency_qualifier_category": None, + "frequency_qualifier_closure": [], + "frequency_qualifier_closure_label": [], + "onset_qualifier_label": None, + "onset_qualifier_namespace": None, + "onset_qualifier_category": None, + "onset_qualifier_closure": [], + "onset_qualifier_closure_label": [], + "sex_qualifier_label": None, + "sex_qualifier_namespace": None, + "sex_qualifier_category": None, + "sex_qualifier_closure": [], + "sex_qualifier_closure_label": [], + "stage_qualifier_label": None, + "stage_qualifier_namespace": None, + "stage_qualifier_category": None, + "stage_qualifier_closure": [], + "stage_qualifier_closure_label": [], + }, + { + "id": "uuid:a8bae583-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0009364", + "original_subject": "OMIM:236670", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", @@ -3157,6 +2469,7 @@ def associations(): "MONDO:0002081", "MONDO:0016184", "MONDO:0016156", + "MONDO:0009364", "MONDO:0020246", "MONDO:0021147", "MONDO:0044137", @@ -3164,6 +2477,7 @@ def associations(): "OGMS:0000031", "MONDO:0015327", "MONDO:0003847", + "MONDO:0700070", "MONDO:0003939", "MONDO:0002022", "MONDO:0015286", @@ -3177,8 +2491,8 @@ def associations(): "MONDO:0016155", "MONDO:0700066", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", - "object_closure_label": [ + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", + "subject_closure_label": [ "entity", "continuant", "disposition", @@ -3196,6 +2510,7 @@ def associations(): "retinal disorder", "eye disorder", "myopathy", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -3227,30 +2542,167 @@ def associations(): "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", "myopathy caused by variation in POMGNT1", + "myopathy caused by variation in POMT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0000501", + "original_object": None, + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_label": "Glaucoma (HPO)", + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Glaucoma (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000501"], + "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:236670"], + "publications_links": [{"id": "OMIM:236670", "url": "http://identifiers.org/mim/236670"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -3273,17 +2725,18 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "urn:uuid:9d167233-70b8-4d7d-aa5d-f6dac17ba835", - "subject": "MONDO:0014140", - "original_subject": None, + "id": "uuid:a8aad663-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0700084", "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", "MONDO:0017741", + "MONDO:0013154", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", @@ -3300,6 +2753,7 @@ def associations(): "MONDO:0018869", "BFO:0000020", "MONDO:0016157", + "MONDO:0700071", "MONDO:0017745", "BFO:0000016", "MONDO:0020120", @@ -3315,7 +2769,6 @@ def associations(): "MONDO:0018939", "MONDO:0020246", "MONDO:0021147", - "MONDO:0014140", "MONDO:0044137", "MONDO:0019755", "OGMS:0000031", @@ -3334,7 +2787,7 @@ def associations(): "MONDO:0016155", "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "subject_closure_label": [ "entity", "continuant", @@ -3353,7 +2806,7 @@ def associations(): "retinal disorder", "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -3386,19 +2839,196 @@ def associations(): "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", "myopathy caused by variation in POMGNT1", - "myopathy caused by variation in GMPPB", + "myopathy caused by variation in POMT2", "human disease", "hereditary skeletal muscle disorder", "disease", ], "subject_taxon": None, "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000171", + "predicate": "biolink:has_phenotype", + "object": "HP:0000501", "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_label": "Glaucoma (HPO)", + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Glaucoma (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], + "object_taxon": None, + "object_taxon_label": None, + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "negated": None, + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "provided_by": "hpoa_disease_to_phenotype_edges", + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", + }, + "publications": ["OMIM:613150"], + "publications_links": [{"id": "OMIM:613150", "url": "http://identifiers.org/mim/613150"}], + "qualifiers": [], + "frequency_qualifier": None, + "onset_qualifier": None, + "sex_qualifier": None, + "stage_qualifier": None, + "frequency_qualifier_label": None, + "frequency_qualifier_namespace": None, + "frequency_qualifier_category": None, + "frequency_qualifier_closure": [], + "frequency_qualifier_closure_label": [], + "onset_qualifier_label": None, + "onset_qualifier_namespace": None, + "onset_qualifier_category": None, + "onset_qualifier_closure": [], + "onset_qualifier_closure_label": [], + "sex_qualifier_label": None, + "sex_qualifier_namespace": None, + "sex_qualifier_category": None, + "sex_qualifier_closure": [], + "sex_qualifier_closure_label": [], + "stage_qualifier_label": None, + "stage_qualifier_namespace": None, + "stage_qualifier_category": None, + "stage_qualifier_closure": [], + "stage_qualifier_closure_label": [], + }, + { + "id": "uuid:abeb7bed-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0013835", + "original_subject": "OMIM:614643", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", @@ -3418,6 +3048,7 @@ def associations(): "BFO:0000017", "MONDO:0018869", "BFO:0000020", + "MONDO:0013835", "MONDO:0016157", "MONDO:0017745", "BFO:0000016", @@ -3451,8 +3082,8 @@ def associations(): "MONDO:0016155", "MONDO:0700066", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", - "object_closure_label": [ + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", + "subject_closure_label": [ "entity", "continuant", "disposition", @@ -3470,6 +3101,7 @@ def associations(): "retinal disorder", "eye disorder", "myopathy", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -3505,26 +3137,162 @@ def associations(): "hereditary skeletal muscle disorder", "disease", ], + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0000501", + "original_object": None, + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_label": "Glaucoma (HPO)", + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Glaucoma (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:614643"], + "publications_links": [{"id": "OMIM:614643", "url": "http://identifiers.org/mim/614643"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -3547,9 +3315,10 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "urn:uuid:772849bb-ae4c-4a45-8a2e-b0269106d6e2", + "id": "uuid:a619ab58-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0014683", - "original_subject": None, + "original_subject": "OMIM:616538", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ @@ -3663,138 +3432,445 @@ def associations(): ], "subject_taxon": None, "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000171", + "predicate": "biolink:has_phenotype", + "object": "HP:0000501", "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0018282", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_label": "Glaucoma (HPO)", + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Glaucoma (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], + "object_taxon": None, + "object_taxon_label": None, + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "negated": None, + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "provided_by": "hpoa_disease_to_phenotype_edges", + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", + }, + "publications": ["OMIM:616538"], + "publications_links": [{"id": "OMIM:616538", "url": "http://identifiers.org/mim/616538"}], + "qualifiers": [], + "frequency_qualifier": None, + "onset_qualifier": None, + "sex_qualifier": None, + "stage_qualifier": None, + "frequency_qualifier_label": None, + "frequency_qualifier_namespace": None, + "frequency_qualifier_category": None, + "frequency_qualifier_closure": [], + "frequency_qualifier_closure_label": [], + "onset_qualifier_label": None, + "onset_qualifier_namespace": None, + "onset_qualifier_category": None, + "onset_qualifier_closure": [], + "onset_qualifier_closure_label": [], + "sex_qualifier_label": None, + "sex_qualifier_namespace": None, + "sex_qualifier_category": None, + "sex_qualifier_closure": [], + "sex_qualifier_closure_label": [], + "stage_qualifier_label": None, + "stage_qualifier_namespace": None, + "stage_qualifier_category": None, + "stage_qualifier_closure": [], + "stage_qualifier_closure_label": [], + }, + { + "id": "uuid:a8bae681-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0011181", + "original_subject": "OMIM:602078", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", + "MONDO:0004746", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0957003", "BFO:0000017", - "MONDO:0018869", + "MONDO:0011181", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0003569", "MONDO:0700096", - "MONDO:0018838", + "MONDO:0001584", "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", "OGMS:0000031", - "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", "MONDO:0002022", - "MONDO:0015286", + "MONDO:0015368", "BFO:0000001", "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", + "MONDO:0000462", "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", - "object_closure_label": [ + "subject_label": "fibrosis of extraocular muscles, congenital, 2", + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", + "eye adnexa disorder", + "ocular motility disease", "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", - "metabolic disease", + "myopathy of extraocular muscle", "nervous system disorder", - "retinal disorder", "eye disorder", "myopathy", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, 2", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", + "eyelids malposition disorder", "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease", ], + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0000505", + "original_object": None, + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0050620", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "UPHENO:0052164", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0052178", + "BFO:0000020", + "HP:0000504", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "UPHENO:0050236", + "HP:0012373", + "HP:0000505", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049587", + "BFO:0000001", + "PATO:0000001", + "UPHENO:0050622", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "GO:0003008", + "UBERON:0000061", + "UBERON:0034923", + "GO:0050877", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "GO:0007600", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "GO:0050953", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "GO:0007601", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_label": "Visual impairment (HPO)", + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "system process", + "sensory perception", + "visual perception", + "biological_process", + "multicellular organismal process", + "nervous system process", + "sensory perception of light stimulus", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of vision (HPO)", + "Visual impairment (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal biological_process", + "abnormal sensory perception of light stimulus", + "abnormal sensory perception", + "abnormal visual perception", + "decreased qualitatively visual perception", + "decreased qualitatively biological_process", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", + ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:602078"], + "publications_links": [{"id": "OMIM:602078", "url": "http://identifiers.org/mim/602078"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -3817,47 +3893,67 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "urn:uuid:1c12ae85-5540-49db-8bae-44cde2205158", - "subject": "MONDO:0011688", - "original_subject": None, + "id": "uuid:a93b6d20-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0014101", + "original_subject": "OMIM:615249", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0018282", "MONDO:0000001", + "MONDO:0016182", "MONDO:0017741", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0700068", "MONDO:0700223", "MONDO:0024322", + "MONDO:0005283", + "MONDO:0020238", "BFO:0000002", + "MONDO:0014101", + "MONDO:0016185", + "MONDO:0000171", "BFO:0000017", + "MONDO:0018869", "BFO:0000020", "MONDO:0016157", + "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0018838", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016184", + "MONDO:0016156", + "MONDO:0020246", + "MONDO:0021147", + "MONDO:0044137", + "MONDO:0019755", "OGMS:0000031", + "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", + "MONDO:0020247", "MONDO:0005066", + "MONDO:0005328", "MONDO:0019950", "MONDO:0016155", - "MONDO:0011688", "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy type B5", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", "subject_closure_label": [ "entity", "continuant", @@ -3865,108 +3961,241 @@ def associations(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy-dystroglycanopathy, type A", + "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", + "retinal disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy type B5", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", "congenital disorder of glycosylation", + "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "qualitative or quantitative defects of FKRP", "qualitative or quantitative defects of fukutin", + "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", + "qualitative or quantitative defects of protein O-mannosyltransferase 1", + "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", + "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", "qualitative or quantitative defects of alpha-dystroglycan", + "lissencephaly spectrum disorders", + "cobblestone lissencephaly", "inborn errors of metabolism", "neuromuscular disease", + "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "inherited vitreous-retinal disease", + "inherited vitreoretinopathy", + "congenital vitreoretinal dysplasia", + "disorder of development or morphogenesis", "disorder of glycosylation", + "disorder of visual system", + "vitreous body disorder", "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", + "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], "subject_taxon": None, "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000172", + "predicate": "biolink:has_phenotype", + "object": "HP:0000505", "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0050620", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "UPHENO:0052164", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", + "UPHENO:0052178", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "HP:0000504", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "UPHENO:0050236", + "HP:0012373", + "HP:0000505", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0049587", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "UPHENO:0050622", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0032501", + "UBERON:0000465", + "GO:0003008", + "UBERON:0000061", + "UBERON:0034923", + "GO:0050877", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "GO:0007600", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "GO:0050953", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "GO:0007601", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Visual impairment (HPO)", "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "occurrent", + "independent continuant", + "process", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "system process", + "sensory perception", + "visual perception", + "biological_process", + "multicellular organismal process", + "nervous system process", + "sensory perception of light stimulus", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of vision (HPO)", + "Visual impairment (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal biological_process", + "abnormal sensory perception of light stimulus", + "abnormal sensory perception", + "abnormal visual perception", + "decreased qualitatively visual perception", + "decreased qualitatively biological_process", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology", ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:615249"], + "publications_links": [{"id": "OMIM:615249", "url": "http://identifiers.org/mim/615249"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -3989,36 +4218,48 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "urn:uuid:8c3fdf6b-34fc-4154-a332-45e0f699c79c", - "subject": "MONDO:0012138", - "original_subject": None, + "id": "uuid:a538f419-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0010912", + "original_subject": "OMIM:600638", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0012138", - "MONDO:0018276", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", "MONDO:0700223", + "MONDO:0004746", "BFO:0000002", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0100153", "OGMS:0000031", "MONDO:0003847", + "MONDO:0100154", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "MONDO:0000462", + "MONDO:0005328", + "MONDO:0010912", ], - "subject_label": "muscular dystrophy-dystroglycanopathy type B6", + "subject_label": "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", "subject_closure_label": [ "entity", "continuant", @@ -4026,97 +4267,232 @@ def associations(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", + "myopathy of extraocular muscle", "nervous system disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy type B6", - "muscular dystrophy-dystroglycanopathy", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "eyelids malposition disorder", + "disorder of visual system", + "tubulinopathy", + "TUBB3-related tubulinopathy", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease", ], "subject_taxon": None, "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000172", + "predicate": "biolink:has_phenotype", + "object": "HP:0000508", "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0041226", + "UPHENO:0076761", + "UPHENO:0075696", + "UPHENO:0041667", + "UPHENO:0001001", + "UPHENO:0021749", + "UPHENO:0080300", + "UPHENO:0021791", + "UPHENO:0041410", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "HP:0000492", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0041644", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "UPHENO:0015280", + "HP:0000271", + "HP:0012373", + "UPHENO:0082129", + "UPHENO:0081581", + "UPHENO:0001003", + "HP:0000508", + "UPHENO:0002536", + "UPHENO:0020584", + "HP:0032039", + "UPHENO:0076692", + "HP:0030669", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "UPHENO:0075878", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0001711", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0034921", + "UBERON:0000064", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0035639", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Ptosis (HPO)", "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormal eyelid morphology (HPO)", + "Ptosis (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal ocular adnexa morphology (HPO)", + "Abnormality of the ocular adnexa (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "eyelid", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "multi organ part structure", + "disconnected anatomical group", + "ocular adnexa", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal ocular adnexa morphology", + "shape anatomical entity", + "drooping anatomical entity", + "drooping eyelid", + "shape eyelid", + "abnormal anatomical entity", + "abnormal ocular adnexa", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal shape of continuant", + "abnormal multicellular organism morphology", + "shape anatomical entity in independent continuant", + "abnormality of anatomical entity physiology", ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:600638"], + "publications_links": [{"id": "OMIM:600638", "url": "http://identifiers.org/mim/600638"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -4139,49 +4515,46 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "urn:uuid:0be3e1fc-b9af-41b0-bf2c-7e4de1ffe2c4", - "subject": "MONDO:0013155", - "original_subject": None, + "id": "uuid:abcb9e2a-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0012270", + "original_subject": "OMIM:609428", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", - "MONDO:0000172", "MONDO:0700223", - "MONDO:0024322", + "MONDO:0004746", "BFO:0000002", - "MONDO:0013155", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", - "MONDO:0017745", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0012270", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0018277", - "MONDO:0019950", - "MONDO:0016155", + "MONDO:0000462", + "MONDO:0005328", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3", + "subject_label": "Tukel syndrome", "subject_closure_label": [ "entity", "continuant", @@ -4189,110 +4562,230 @@ def associations(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", - "metabolic disease", + "myopathy of extraocular muscle", "nervous system disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3", - "congenital disorder of glycosylation", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "congenital muscular dystrophy with cerebellar involvement", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", + "congenital fibrosis of extraocular muscles", + "Tukel syndrome", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in POMGNT1", + "eyelids malposition disorder", + "disorder of visual system", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease", ], "subject_taxon": None, "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000172", + "predicate": "biolink:has_phenotype", + "object": "HP:0000508", "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0041226", + "UPHENO:0076761", + "UPHENO:0075696", + "UPHENO:0041667", + "UPHENO:0001001", + "UPHENO:0021749", + "UPHENO:0080300", + "UPHENO:0021791", + "UPHENO:0041410", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "HP:0000492", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0041644", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "UPHENO:0015280", + "HP:0000271", + "HP:0012373", + "UPHENO:0082129", + "UPHENO:0081581", + "UPHENO:0001003", + "HP:0000508", + "UPHENO:0002536", + "UPHENO:0020584", + "HP:0032039", + "UPHENO:0076692", + "HP:0030669", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "UPHENO:0075878", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0001711", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0034921", + "UBERON:0000064", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0035639", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Ptosis (HPO)", "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormal eyelid morphology (HPO)", + "Ptosis (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal ocular adnexa morphology (HPO)", + "Abnormality of the ocular adnexa (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "eyelid", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "multi organ part structure", + "disconnected anatomical group", + "ocular adnexa", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal ocular adnexa morphology", + "shape anatomical entity", + "drooping anatomical entity", + "drooping eyelid", + "shape eyelid", + "abnormal anatomical entity", + "abnormal ocular adnexa", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal shape of continuant", + "abnormal multicellular organism morphology", + "shape anatomical entity in independent continuant", + "abnormality of anatomical entity physiology", ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:609428"], + "publications_links": [{"id": "OMIM:609428", "url": "http://identifiers.org/mim/609428"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -4315,48 +4808,46 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "urn:uuid:8b852151-1710-4175-9e07-4fa11e33704c", - "subject": "MONDO:0013156", - "original_subject": None, + "id": "uuid:abeb7c5b-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0012310", + "original_subject": "OMIM:609612", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0700067", - "MONDO:0018282", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0012310", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", "MONDO:0700223", - "MONDO:0024322", + "MONDO:0004746", "BFO:0000002", - "MONDO:0018279", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", - "MONDO:0017745", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", - "MONDO:0013156", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", - "MONDO:0015286", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0005066", - "MONDO:0019950", - "MONDO:0016155", + "MONDO:0000462", + "MONDO:0005328", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital without intellectual disability), type B4", + "subject_label": "fibrosis of extraocular muscles, congenital, with synergistic divergence", "subject_closure_label": [ "entity", "continuant", @@ -4364,109 +4855,511 @@ def associations(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", - "metabolic disease", + "myopathy of extraocular muscle", "nervous system disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital without intellectual disability), type B4", - "congenital disorder of glycosylation", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "congenital muscular dystrophy without intellectual disability", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, with synergistic divergence", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKTN", + "eyelids malposition disorder", + "disorder of visual system", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease", ], "subject_taxon": None, "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000172", + "predicate": "biolink:has_phenotype", + "object": "HP:0000508", "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0041226", + "UPHENO:0076761", + "UPHENO:0075696", + "UPHENO:0041667", + "UPHENO:0001001", + "UPHENO:0021749", + "UPHENO:0080300", + "UPHENO:0021791", + "UPHENO:0041410", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "HP:0000492", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0041644", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "UPHENO:0015280", + "HP:0000271", + "HP:0012373", + "UPHENO:0082129", + "UPHENO:0081581", + "UPHENO:0001003", + "HP:0000508", + "UPHENO:0002536", + "UPHENO:0020584", + "HP:0032039", + "UPHENO:0076692", + "HP:0030669", + "BFO:0000001", + "PATO:0000001", + "UPHENO:0075878", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0001711", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0034921", + "UBERON:0000064", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0035639", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_label": "Ptosis (HPO)", + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormal eyelid morphology (HPO)", + "Ptosis (HPO)", + "Abnormal eye physiology (HPO)", + "Abnormal ocular adnexa morphology (HPO)", + "Abnormality of the ocular adnexa (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "eyelid", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "multi organ part structure", + "disconnected anatomical group", + "ocular adnexa", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal ocular adnexa morphology", + "shape anatomical entity", + "drooping anatomical entity", + "drooping eyelid", + "shape eyelid", + "abnormal anatomical entity", + "abnormal ocular adnexa", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal shape of continuant", + "abnormal multicellular organism morphology", + "shape anatomical entity in independent continuant", + "abnormality of anatomical entity physiology", + ], + "object_taxon": None, + "object_taxon_label": None, + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "negated": None, + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}], + "provided_by": "hpoa_disease_to_phenotype_edges", + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", + }, + "publications": ["OMIM:609612"], + "publications_links": [{"id": "OMIM:609612", "url": "http://identifiers.org/mim/609612"}], + "qualifiers": [], + "frequency_qualifier": None, + "onset_qualifier": None, + "sex_qualifier": None, + "stage_qualifier": None, + "frequency_qualifier_label": None, + "frequency_qualifier_namespace": None, + "frequency_qualifier_category": None, + "frequency_qualifier_closure": [], + "frequency_qualifier_closure_label": [], + "onset_qualifier_label": None, + "onset_qualifier_namespace": None, + "onset_qualifier_category": None, + "onset_qualifier_closure": [], + "onset_qualifier_closure_label": [], + "sex_qualifier_label": None, + "sex_qualifier_namespace": None, + "sex_qualifier_category": None, + "sex_qualifier_closure": [], + "sex_qualifier_closure_label": [], + "stage_qualifier_label": None, + "stage_qualifier_namespace": None, + "stage_qualifier_category": None, + "stage_qualifier_closure": [], + "stage_qualifier_closure_label": [], + }, + { + "id": "uuid:a6f9d857-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0008056", + "original_subject": "OMIM:160900", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ + "MONDO:0004994", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0018276", + "MONDO:0016107", "MONDO:0005071", + "MONDO:0005267", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0005045", + "MONDO:0004995", "MONDO:0700223", "BFO:0000002", "BFO:0000017", "BFO:0000020", + "MONDO:0016106", + "MONDO:0005217", + "MONDO:0024573", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0008056", "MONDO:0700096", + "MONDO:0000591", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0002254", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0016120", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "MONDO:0000462", + "MONDO:0005328", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", - "object_closure_label": [ + "subject_label": "myotonic dystrophy type 1", + "subject_closure_label": [ "entity", "continuant", "disposition", "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "eye adnexa disorder", + "intrinsic cardiomyopathy", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "syndromic disease", + "eyelid disorder", "hereditary disease", "muscle tissue disorder", + "cardiomyopathy", + "cardiovascular disorder", + "hypertrophic cardiomyopathy", "nervous system disorder", + "familial cardiomyopathy", + "heart disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy", + "myotonic dystrophy type 1", + "progressive muscular dystrophy", + "myotonic dystrophy", + "myotonic syndrome", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "eyelids malposition disorder", + "disorder of visual system", + "familial hypertrophic cardiomyopathy", "human disease", "hereditary skeletal muscle disorder", "disease", ], + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0000518", + "original_object": None, + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "HP:0004328", + "UPHENO:0001001", + "UPHENO:0004765", + "HP:0000152", + "HP:0000518", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0020584", + "UPHENO:0076692", + "BFO:0000001", + "PATO:0000001", + "HP:0000517", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0005389", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0000965", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", + ], + "object_label": "Cataract (HPO)", + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of the lens (HPO)", + "Cataract (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormal eye morphology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "lens of camera-type eye", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "anterior segment of eyeball", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "transparent eye structure", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal lens of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology", + ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000501"], + "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:160900"], + "publications_links": [{"id": "OMIM:160900", "url": "http://identifiers.org/mim/160900"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -4489,46 +5382,68 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "urn:uuid:d20f485a-4fde-44b8-aa20-20fd2d5902ab", - "subject": "MONDO:0013159", - "original_subject": None, + "id": "uuid:a8bae558-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0009364", + "original_subject": "OMIM:236670", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0018282", "MONDO:0000001", + "MONDO:0016182", "MONDO:0017741", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0700068", "MONDO:0700223", - "MONDO:0013159", "MONDO:0024322", + "MONDO:0005283", + "MONDO:0020238", "BFO:0000002", + "MONDO:0016185", + "MONDO:0000171", "BFO:0000017", + "MONDO:0018869", "BFO:0000020", + "MONDO:0016157", + "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0018838", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016184", + "MONDO:0016156", + "MONDO:0009364", + "MONDO:0020246", + "MONDO:0021147", + "MONDO:0044137", + "MONDO:0019755", "OGMS:0000031", + "MONDO:0015327", "MONDO:0003847", "MONDO:0700070", "MONDO:0003939", + "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", + "MONDO:0020247", "MONDO:0005066", + "MONDO:0005328", "MONDO:0019950", "MONDO:0016155", + "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", "subject_closure_label": [ "entity", "continuant", @@ -4536,28 +5451,49 @@ def associations(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy-dystroglycanopathy, type A", + "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", + "retinal disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", "congenital disorder of glycosylation", + "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "qualitative or quantitative defects of FKRP", + "qualitative or quantitative defects of fukutin", + "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", + "qualitative or quantitative defects of protein O-mannosyltransferase 1", + "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", + "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", "qualitative or quantitative defects of alpha-dystroglycan", + "lissencephaly spectrum disorders", + "cobblestone lissencephaly", "inborn errors of metabolism", "neuromuscular disease", + "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "inherited vitreous-retinal disease", + "inherited vitreoretinopathy", + "congenital vitreoretinal dysplasia", + "disorder of development or morphogenesis", "disorder of glycosylation", + "disorder of visual system", + "vitreous body disorder", "glycoprotein metabolism disease", + "myopathy caused by variation in FKRP", + "myopathy caused by variation in POMGNT1", "myopathy caused by variation in POMT1", "human disease", "hereditary skeletal muscle disorder", @@ -4565,78 +5501,182 @@ def associations(): ], "subject_taxon": None, "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000172", + "predicate": "biolink:has_phenotype", + "object": "HP:0000518", "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "HP:0004328", + "UPHENO:0001001", + "UPHENO:0004765", + "HP:0000152", + "HP:0000518", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0020584", + "UPHENO:0076692", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "HP:0000517", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0005389", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0000965", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Cataract (HPO)", "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of the lens (HPO)", + "Cataract (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormal eye morphology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "lens of camera-type eye", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "anterior segment of eyeball", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "transparent eye structure", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal lens of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology", ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000501"], + "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:236670"], + "publications_links": [{"id": "OMIM:236670", "url": "http://identifiers.org/mim/236670"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, @@ -4659,46 +5699,68 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "urn:uuid:7a5c97ed-311c-4530-bfdf-447bf5c4db72", - "subject": "MONDO:0013160", - "original_subject": None, + "id": "uuid:a4c7f187-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0009667", + "original_subject": "OMIM:253280", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0018282", "MONDO:0000001", + "MONDO:0016182", "MONDO:0017741", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0700068", "MONDO:0700223", "MONDO:0024322", + "MONDO:0005283", + "MONDO:0020238", "BFO:0000002", + "MONDO:0016185", + "MONDO:0000171", "BFO:0000017", + "MONDO:0018869", "BFO:0000020", - "MONDO:0013160", - "MONDO:0700071", + "MONDO:0016157", + "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0018838", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016184", + "MONDO:0016156", + "MONDO:0018939", + "MONDO:0020246", + "MONDO:0009667", + "MONDO:0021147", + "MONDO:0044137", + "MONDO:0019755", "OGMS:0000031", + "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", + "MONDO:0020247", "MONDO:0005066", + "MONDO:0005328", "MONDO:0019950", "MONDO:0016155", + "MONDO:0700066", ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3", "subject_closure_label": [ "entity", "continuant", @@ -4706,107 +5768,232 @@ def associations(): "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy-dystroglycanopathy, type A", + "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", + "retinal disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3", "congenital disorder of glycosylation", + "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "qualitative or quantitative defects of FKRP", + "qualitative or quantitative defects of fukutin", + "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", + "qualitative or quantitative defects of protein O-mannosyltransferase 1", + "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", + "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", "qualitative or quantitative defects of alpha-dystroglycan", + "lissencephaly spectrum disorders", + "cobblestone lissencephaly", + "muscle-eye-brain disease", "inborn errors of metabolism", "neuromuscular disease", + "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "inherited vitreous-retinal disease", + "inherited vitreoretinopathy", + "congenital vitreoretinal dysplasia", + "disorder of development or morphogenesis", "disorder of glycosylation", + "disorder of visual system", + "vitreous body disorder", "glycoprotein metabolism disease", - "myopathy caused by variation in POMT2", + "myopathy caused by variation in FKRP", + "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease", ], "subject_taxon": None, "subject_taxon_label": None, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000172", + "predicate": "biolink:has_phenotype", + "object": "HP:0000518", "original_object": None, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "HP:0004328", + "UPHENO:0001001", + "UPHENO:0004765", + "HP:0000152", + "HP:0000518", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0020584", + "UPHENO:0076692", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950", + "PATO:0000001", + "HP:0000517", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0005389", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0000965", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047", ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Cataract (HPO)", "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of the lens (HPO)", + "Cataract (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormal eye morphology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "lens of camera-type eye", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "anterior segment of eyeball", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "transparent eye structure", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal lens of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology", ], "object_taxon": None, "object_taxon_label": None, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": None, - "provided_by": "phenio_edges", + "pathway": None, + "evidence_count": 2, + "has_evidence": ["ECO:0000501"], + "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, - "publications": [], + "publications": ["OMIM:253280"], + "publications_links": [{"id": "OMIM:253280", "url": "http://identifiers.org/mim/253280"}], "qualifiers": [], "frequency_qualifier": None, - "has_evidence": [], "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, - "evidence_count": 2, - "pathway": None, "frequency_qualifier_label": None, "frequency_qualifier_namespace": None, "frequency_qualifier_category": None, diff --git a/backend/tests/fixtures/autocomplete.py b/backend/tests/fixtures/autocomplete.py index ad39472f2..8db1293b8 100644 --- a/backend/tests/fixtures/autocomplete.py +++ b/backend/tests/fixtures/autocomplete.py @@ -232,24 +232,6 @@ def autocomplete(): "highlight": None, "score": None, }, - { - "id": "MONDO:0100136", - "category": "biolink:Disease", - "name": "obsolete Fanconia anemia complementation group M", - "full_name": None, - "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.", - "xref": [], - "provided_by": "phenio_nodes", - "in_taxon": None, - "in_taxon_label": None, - "symbol": None, - "synonym": [ - "FANCM Fanconi anemia", - "Fanconi anemia caused by mutation in FANCM", - ], - "highlight": None, - "score": None, - }, { "id": "MONDO:0010351", "category": "biolink:Disease", @@ -345,6 +327,21 @@ def autocomplete(): "highlight": None, "score": None, }, + { + "id": "MONDO:0100136", + "category": "biolink:Disease", + "name": "obsolete Fanconia anemia complementation group M", + "full_name": None, + "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.", + "xref": [], + "provided_by": "phenio_nodes", + "in_taxon": None, + "in_taxon_label": None, + "symbol": None, + "synonym": ["FANCM Fanconi anemia", "Fanconi anemia caused by mutation in FANCM"], + "highlight": None, + "score": None, + }, { "id": "MONDO:0009213", "category": "biolink:Disease", diff --git a/backend/tests/fixtures/autocomplete_response.py b/backend/tests/fixtures/autocomplete_response.py index 39feb7332..ba1d2809c 100644 --- a/backend/tests/fixtures/autocomplete_response.py +++ b/backend/tests/fixtures/autocomplete_response.py @@ -182,17 +182,6 @@ def autocomplete_response(): ], "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the MAD2L2 gene.", }, - { - "id": "MONDO:0100136", - "category": "biolink:Disease", - "name": "obsolete Fanconia anemia complementation group M", - "provided_by": "phenio_nodes", - "synonym": [ - "FANCM Fanconi anemia", - "Fanconi anemia caused by mutation in FANCM", - ], - "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.", - }, { "id": "MONDO:0010351", "category": "biolink:Disease", @@ -260,6 +249,14 @@ def autocomplete_response(): ], "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the XRCC2 gene.", }, + { + "id": "MONDO:0100136", + "category": "biolink:Disease", + "name": "obsolete Fanconia anemia complementation group M", + "provided_by": "phenio_nodes", + "synonym": ["FANCM Fanconi anemia", "Fanconi anemia caused by mutation in FANCM"], + "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.", + }, { "id": "MONDO:0009213", "category": "biolink:Disease", diff --git a/backend/tests/fixtures/histopheno.py b/backend/tests/fixtures/histopheno.py index 4268bf6c2..290113ed9 100644 --- a/backend/tests/fixtures/histopheno.py +++ b/backend/tests/fixtures/histopheno.py @@ -6,25 +6,25 @@ def histopheno(): return { "id": "MONDO:0020121", "items": [ - {"label": "musculature", "count": 962, "id": "HP:0003011"}, - {"label": "nervous_system", "count": 628, "id": "HP:0000707"}, - {"label": "head_neck", "count": 366, "id": "HP:0000152"}, - {"label": "skeletal_system", "count": 244, "id": "HP:0000924"}, - {"label": "eye", "count": 191, "id": "HP:0000478"}, - {"label": "respiratory", "count": 177, "id": "HP:0002086"}, - {"label": "metabolism_homeostasis", "count": 126, "id": "HP:0001939"}, - {"label": "blood", "count": 113, "id": "HP:0001871"}, - {"label": "cardiovascular_system", "count": 96, "id": "HP:0001626"}, - {"label": "connective_tissue", "count": 87, "id": "HP:0003549"}, - {"label": "digestive_system", "count": 68, "id": "HP:0025031"}, - {"label": "neoplasm", "count": 68, "id": "HP:0002664"}, - {"label": "integument", "count": 20, "id": "HP:0001574"}, - {"label": "ear", "count": 19, "id": "HP:0000598"}, - {"label": "genitourinary_system", "count": 18, "id": "HP:0000119"}, - {"label": "growth", "count": 14, "id": "HP:0001507"}, - {"label": "immune_system", "count": 12, "id": "HP:0002715"}, - {"label": "prenatal_or_birth", "count": 10, "id": "HP:0001197"}, - {"label": "endocrine", "count": 8, "id": "HP:0000818"}, - {"label": "breast", "count": 0, "id": "HP:0000769"}, + {"label": "musculature", "count": 1756, "id": "HP:0003011"}, + {"label": "nervous_system", "count": 1130, "id": "HP:0000707"}, + {"label": "head_neck", "count": 602, "id": "HP:0000152"}, + {"label": "skeletal_system", "count": 493, "id": "HP:0000924"}, + {"label": "respiratory", "count": 320, "id": "HP:0002086"}, + {"label": "eye", "count": 300, "id": "HP:0000478"}, + {"label": "metabolism_homeostasis", "count": 221, "id": "HP:0001939"}, + {"label": "cardiovascular_system", "count": 185, "id": "HP:0001626"}, + {"label": "blood", "count": 184, "id": "HP:0001871"}, + {"label": "connective_tissue", "count": 165, "id": "HP:0003549"}, + {"label": "neoplasm", "count": 150, "id": "HP:0002664"}, + {"label": "digestive_system", "count": 144, "id": "HP:0025031"}, + {"label": "integument", "count": 48, "id": "HP:0001574"}, + {"label": "genitourinary_system", "count": 44, "id": "HP:0000119"}, + {"label": "growth", "count": 33, "id": "HP:0001507"}, + {"label": "ear", "count": 28, "id": "HP:0000598"}, + {"label": "endocrine", "count": 26, "id": "HP:0000818"}, + {"label": "immune_system", "count": 22, "id": "HP:0002715"}, + {"label": "prenatal_or_birth", "count": 21, "id": "HP:0001197"}, + {"label": "breast", "count": 1, "id": "HP:0000769"}, ], } diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py index 1589a4e9f..9061ed2f1 100644 --- a/backend/tests/fixtures/histopheno_response.py +++ b/backend/tests/fixtures/histopheno_response.py @@ -39,30 +39,30 @@ def histopheno_response(): "facet": "true", }, }, - "response": {"num_found": 2699, "start": 0, "docs": []}, + "response": {"num_found": 4563, "start": 0, "docs": []}, "facet_counts": { "facet_fields": {}, "facet_queries": { - 'object_closure:"HP:0000924"': 244, - 'object_closure:"HP:0000707"': 628, - 'object_closure:"HP:0000152"': 366, - 'object_closure:"HP:0001574"': 20, - 'object_closure:"HP:0000478"': 191, - 'object_closure:"HP:0001626"': 96, - 'object_closure:"HP:0001939"': 126, - 'object_closure:"HP:0000119"': 18, - 'object_closure:"HP:0025031"': 68, - 'object_closure:"HP:0002664"': 68, - 'object_closure:"HP:0001871"': 113, - 'object_closure:"HP:0002715"': 12, - 'object_closure:"HP:0000818"': 8, - 'object_closure:"HP:0003011"': 962, - 'object_closure:"HP:0002086"': 177, - 'object_closure:"HP:0000598"': 19, - 'object_closure:"HP:0003549"': 87, - 'object_closure:"HP:0001197"': 10, - 'object_closure:"HP:0001507"': 14, - 'object_closure:"HP:0000769"': 0, + 'object_closure:"HP:0000924"': 493, + 'object_closure:"HP:0000707"': 1130, + 'object_closure:"HP:0000152"': 602, + 'object_closure:"HP:0001574"': 48, + 'object_closure:"HP:0000478"': 300, + 'object_closure:"HP:0001626"': 185, + 'object_closure:"HP:0001939"': 221, + 'object_closure:"HP:0000119"': 44, + 'object_closure:"HP:0025031"': 144, + 'object_closure:"HP:0002664"': 150, + 'object_closure:"HP:0001871"': 184, + 'object_closure:"HP:0002715"': 22, + 'object_closure:"HP:0000818"': 26, + 'object_closure:"HP:0003011"': 1756, + 'object_closure:"HP:0002086"': 320, + 'object_closure:"HP:0000598"': 28, + 'object_closure:"HP:0003549"': 165, + 'object_closure:"HP:0001197"': 21, + 'object_closure:"HP:0001507"': 33, + 'object_closure:"HP:0000769"': 1, }, }, } diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py index 6cb4fdd6c..945d7df4f 100644 --- a/backend/tests/fixtures/node.py +++ b/backend/tests/fixtures/node.py @@ -24,23 +24,16 @@ def node(): "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", }, "association_counts": [ - { - "label": "Phenotypes", - "count": 2166, - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - }, - { - "label": "Causal Genes", - "count": 124, - "category": "biolink:CausalGeneToDiseaseAssociation", - }, + {"label": "Phenotypes", "count": 4027, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"}, + {"label": "Causal Genes", "count": 124, "category": "biolink:CausalGeneToDiseaseAssociation"}, + {"label": "Correlated Genes", "count": 151, "category": "biolink:CorrelatedGeneToDiseaseAssociation"}, ], "node_hierarchy": { "super_classes": [ { - "id": "MONDO:0005336", + "id": "MONDO:0019056", "category": "biolink:Disease", - "name": "myopathy", + "name": "neuromuscular disease", "full_name": None, "description": None, "xref": [], @@ -51,9 +44,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0019056", + "id": "MONDO:0700223", "category": "biolink:Disease", - "name": "neuromuscular disease", + "name": "hereditary skeletal muscle disorder", "full_name": None, "description": None, "xref": [], @@ -64,9 +57,9 @@ def node(): "synonym": [], }, { - "id": "MONDO:0700223", + "id": "MONDO:0005336", "category": "biolink:Disease", - "name": "hereditary skeletal muscle disorder", + "name": "myopathy", "full_name": None, "description": None, "xref": [], diff --git a/backend/tests/fixtures/phenotype_explorer_compare.py b/backend/tests/fixtures/phenotype_explorer_compare.py index 0878d4dfe..660f9f571 100644 --- a/backend/tests/fixtures/phenotype_explorer_compare.py +++ b/backend/tests/fixtures/phenotype_explorer_compare.py @@ -5,11 +5,8 @@ def phenotype_explorer_compare(): return { "subject_termset": { + "MP:0002169": {"id": "MP:0002169", "label": "no abnormal phenotype detected (MPO)"}, "MP:0010771": {"id": "MP:0010771", "label": "integument phenotype (MPO)"}, - "MP:0002169": { - "id": "MP:0002169", - "label": "no abnormal phenotype detected (MPO)", - }, }, "object_termset": {"HP:0004325": {"id": "HP:0004325", "label": "Decreased body weight (HPO)"}}, "subject_best_matches": { @@ -18,7 +15,7 @@ def phenotype_explorer_compare(): "match_source_label": "no abnormal phenotype detected (MPO)", "match_target": "HP:0004325", "match_target_label": "Decreased body weight (HPO)", - "score": 1.5592737301071706, + "score": 1.4431977534690428, "match_subsumer": None, "match_subsumer_label": None, "similarity": { @@ -33,11 +30,11 @@ def phenotype_explorer_compare(): "ancestor_source": None, "object_information_content": None, "subject_information_content": None, - "ancestor_information_content": 1.5592737301071706, + "ancestor_information_content": 1.4431977534690428, "jaccard_similarity": 0.16216216216216217, "cosine_similarity": None, "dice_similarity": None, - "phenodigm_score": 0.50284709353524, + "phenodigm_score": 0.48376861011243283, }, }, "MP:0010771": { @@ -45,7 +42,7 @@ def phenotype_explorer_compare(): "match_source_label": "integument phenotype (MPO)", "match_target": "HP:0004325", "match_target_label": "Decreased body weight (HPO)", - "score": 2.2829964196656634, + "score": 1.4431977534690428, "match_subsumer": None, "match_subsumer_label": None, "similarity": { @@ -55,16 +52,16 @@ def phenotype_explorer_compare(): "object_id": "HP:0004325", "object_label": None, "object_source": None, - "ancestor_id": "UBERON:0000468", + "ancestor_id": "UPHENO:0001003", "ancestor_label": "", "ancestor_source": None, "object_information_content": None, "subject_information_content": None, - "ancestor_information_content": 2.2829964196656634, - "jaccard_similarity": 0.325, + "ancestor_information_content": 1.4431977534690428, + "jaccard_similarity": 0.3333333333333333, "cosine_similarity": None, "dice_similarity": None, - "phenodigm_score": 0.8613790317806329, + "phenodigm_score": 0.6935891563620457, }, }, }, @@ -74,7 +71,7 @@ def phenotype_explorer_compare(): "match_source_label": "Decreased body weight (HPO)", "match_target": "MP:0010771", "match_target_label": "integument phenotype (MPO)", - "score": 2.2829964196656634, + "score": 1.4431977534690428, "match_subsumer": None, "match_subsumer_label": None, "similarity": { @@ -84,20 +81,20 @@ def phenotype_explorer_compare(): "object_id": "MP:0010771", "object_label": None, "object_source": None, - "ancestor_id": "UBERON:0000468", + "ancestor_id": "UPHENO:0001003", "ancestor_label": "", "ancestor_source": None, "object_information_content": None, "subject_information_content": None, - "ancestor_information_content": 2.2829964196656634, - "jaccard_similarity": 0.325, + "ancestor_information_content": 1.4431977534690428, + "jaccard_similarity": 0.3333333333333333, "cosine_similarity": None, "dice_similarity": None, - "phenodigm_score": 0.8613790317806329, + "phenodigm_score": 0.6935891563620457, }, } }, - "average_score": 2.1020657472760402, - "best_score": 2.2829964196656634, + "average_score": 1.4431977534690428, + "best_score": 1.4431977534690428, "metric": "ancestor_information_content", } diff --git a/backend/tests/fixtures/search.py b/backend/tests/fixtures/search.py index 9dbadd904..1adca2437 100644 --- a/backend/tests/fixtures/search.py +++ b/backend/tests/fixtures/search.py @@ -70,11 +70,7 @@ def search(): "in_taxon": None, "in_taxon_label": None, "symbol": None, - "synonym": [ - "FRTS1", - "Fanconi renotubular syndrome 1", - "primary Fanconi renotubular syndrome", - ], + "synonym": ["FRTS1", "Fanconi renotubular syndrome 1", "primary Fanconi renotubular syndrome"], "highlight": None, "score": None, }, diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py index 8e8d878d1..bed27890b 100644 --- a/backend/tests/fixtures/search_response.py +++ b/backend/tests/fixtures/search_response.py @@ -65,11 +65,7 @@ def search_response(): "category": "biolink:Disease", "name": "primary Fanconi syndrome", "provided_by": "phenio_nodes", - "synonym": [ - "FRTS1", - "Fanconi renotubular syndrome 1", - "primary Fanconi renotubular syndrome", - ], + "synonym": ["FRTS1", "Fanconi renotubular syndrome 1", "primary Fanconi renotubular syndrome"], "description": "A condition in which the kidneys do not absorb certain substances into the body. These substances, such as cysteine, fructose, galactose, or glycogen, are lost in the urine. Fanconi syndrome is thought to be caused by genetic and environmental factors, and it may be diagnosed at any age. Symptoms of Fanconi syndrome include increased urine production (which may cause dehydration), weakness, and abnormalities of the bones.", }, { diff --git a/backend/tests/unit/test_curie_service.py b/backend/tests/unit/test_curie_service.py index 925cd1f14..2b6cef03a 100644 --- a/backend/tests/unit/test_curie_service.py +++ b/backend/tests/unit/test_curie_service.py @@ -4,23 +4,28 @@ @pytest.mark.parametrize( ("curie", "expanded_curie_part"), - [("FB:FBgn0000008", "http://identifiers.org/flybase/FBgn0000008"), # this is a little odd, fb vs. flybase, but both resolve - ("FlyBase:FBgn0000008", "http://identifiers.org/fb/FBgn0000008"), - ("MONDO:0005737", "http://purl.obolibrary.org/obo/MONDO_0005737"), - ("OMIM:613647", "http://identifiers.org/mim/613647"), - ("NCBIGene:1017", "https://identifiers.org/ncbigene/1017"), - ("ZFIN:ZDB-GENE-980526-166", "https://identifiers.org/zfin/ZDB-GENE-980526-166"), - ("MGI:1918910", "https://identifiers.org/MGI/1918910"), - ("ENSEMBL:ENSG00000157764", "http://identifiers.org/ensembl/ENSG00000157764"), - ("HP:0000001", "http://purl.obolibrary.org/obo/HP_0000001"), - ("UBERON:0000001", "http://purl.obolibrary.org/obo/UBERON_0000001"), - ("GO:0000001", "http://purl.obolibrary.org/obo/GO_0000001"), - ("CL:0000001", "http://purl.obolibrary.org/obo/CL_0000001"), - ("WormBase:WBGene00000001", "http://identifiers.org/wb/WBGene00000001"), - ("WB:WBGene00000001", "https://identifiers.org/wb/WBGene00000001"), - ("SGD:S000000001", "https://identifiers.org/sgd/S000000001"), - ("RGD:1", "https://identifiers.org/rgd/1"), - ("HGNC:5", "http://identifiers.org/hgnc/5")] + [ + ( + "FB:FBgn0000008", + "http://identifiers.org/flybase/FBgn0000008", + ), # this is a little odd, fb vs. flybase, but both resolve + ("FlyBase:FBgn0000008", "http://identifiers.org/fb/FBgn0000008"), + ("MONDO:0005737", "http://purl.obolibrary.org/obo/MONDO_0005737"), + ("OMIM:613647", "http://identifiers.org/mim/613647"), + ("NCBIGene:1017", "https://identifiers.org/ncbigene/1017"), + ("ZFIN:ZDB-GENE-980526-166", "https://identifiers.org/zfin/ZDB-GENE-980526-166"), + ("MGI:1918910", "https://identifiers.org/MGI/1918910"), + ("ENSEMBL:ENSG00000157764", "http://identifiers.org/ensembl/ENSG00000157764"), + ("HP:0000001", "http://purl.obolibrary.org/obo/HP_0000001"), + ("UBERON:0000001", "http://purl.obolibrary.org/obo/UBERON_0000001"), + ("GO:0000001", "http://purl.obolibrary.org/obo/GO_0000001"), + ("CL:0000001", "http://purl.obolibrary.org/obo/CL_0000001"), + ("WormBase:WBGene00000001", "http://identifiers.org/wb/WBGene00000001"), + ("WB:WBGene00000001", "https://identifiers.org/wb/WBGene00000001"), + ("SGD:S000000001", "https://identifiers.org/sgd/S000000001"), + ("RGD:1", "https://identifiers.org/rgd/1"), + ("HGNC:5", "http://identifiers.org/hgnc/5"), + ], ) def test_curie_expansion(curie, expanded_curie_part): cs = CurieService() diff --git a/frontend/fixtures/association-counts.json b/frontend/fixtures/association-counts.json index 9dbe0e27c..207c58a9c 100644 --- a/frontend/fixtures/association-counts.json +++ b/frontend/fixtures/association-counts.json @@ -2,13 +2,18 @@ "items": [ { "label": "Phenotypes", - "count": 2166, + "count": 4027, "category": "biolink:DiseaseToPhenotypicFeatureAssociation" }, { "label": "Causal Genes", "count": 124, "category": "biolink:CausalGeneToDiseaseAssociation" + }, + { + "label": "Correlated Genes", + "count": 151, + "category": "biolink:CorrelatedGeneToDiseaseAssociation" } ] } diff --git a/frontend/fixtures/association-table.json b/frontend/fixtures/association-table.json index 0c405d1e4..9a9474824 100644 --- a/frontend/fixtures/association-table.json +++ b/frontend/fixtures/association-table.json @@ -1,10 +1,11 @@ { "limit": 5, "offset": 0, - "total": 2166, + "total": 4027, "items": [ { - "id": "uuid:d92c5da3-5349-11ee-a38e-df3e29a44ac7", + "id": "uuid:aafbc2e0-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0020793", "original_subject": "OMIM:164310", "subject_namespace": "MONDO", @@ -162,19 +163,41 @@ "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, + "pathway": null, + "evidence_count": 4, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [ + { + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" + } + ], "provided_by": "hpoa_disease_to_phenotype_edges", - "provided_by_link": null, + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" + }, "publications": ["PMID:21242490", "PMID:32493488", "PMID:31332380"], + "publications_links": [ + { + "id": "PMID:21242490", + "url": "http://identifiers.org/pubmed/21242490" + }, + { + "id": "PMID:32493488", + "url": "http://identifiers.org/pubmed/32493488" + }, + { + "id": "PMID:31332380", + "url": "http://identifiers.org/pubmed/31332380" + } + ], "qualifiers": [], "frequency_qualifier": "HP:0040282", - "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 6, - "pathway": null, "frequency_qualifier_label": "Frequent (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", @@ -202,7 +225,8 @@ "direction": "outgoing" }, { - "id": "uuid:d92c5db4-5349-11ee-a38e-df3e29a44ac7", + "id": "uuid:aafbc2f1-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0020793", "original_subject": "OMIM:164310", "subject_namespace": "MONDO", @@ -414,19 +438,41 @@ "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": 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groups", "catalytic complex", @@ -738,19 +789,37 @@ "object_taxon_label": null, "primary_knowledge_source": "infores:hpo-annotations", "aggregator_knowledge_source": ["infores:monarchinitiative"], - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "negated": null, + "pathway": null, + "evidence_count": 3, + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [ + { + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" + } + ], "provided_by": "hpoa_disease_to_phenotype_edges", - "provided_by_link": null, + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" + }, "publications": ["PMID:19576565", "PMID:28803818"], + "publications_links": [ + { + "id": "PMID:19576565", + "url": "http://identifiers.org/pubmed/19576565" + }, + { + "id": "PMID:28803818", + "url": "http://identifiers.org/pubmed/28803818" + } + ], "qualifiers": [], 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+ "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" + } + ], "provided_by": "hpoa_disease_to_phenotype_edges", - "provided_by_link": null, + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" + }, "publications": ["PMID:16258657", "OMIM:254090"], + "publications_links": [ + { + "id": "PMID:16258657", + "url": "http://identifiers.org/pubmed/16258657" + }, + { + "id": "OMIM:254090", + "url": "http://identifiers.org/mim/254090" + } + ], "qualifiers": [], "frequency_qualifier": "HP:0040280", - "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 5, - "pathway": null, "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", @@ -974,7 +1062,8 @@ "direction": "outgoing" }, { - "id": 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"publications_links": [ + { + "id": "PMID:9731527", + "url": "http://identifiers.org/pubmed/9731527" + }, + { + "id": "PMID:9009996", + "url": "http://identifiers.org/pubmed/9009996" + } + ], "qualifiers": [], "frequency_qualifier": "HP:0040280", - "has_evidence": ["ECO:0000269"], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 5, - "pathway": null, "frequency_qualifier_label": "Obligate (HPO)", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", diff --git a/frontend/fixtures/associations.json b/frontend/fixtures/associations.json index d1b938a93..a49af8e64 100644 --- a/frontend/fixtures/associations.json +++ b/frontend/fixtures/associations.json @@ -1,70 +1,38 @@ { "limit": 20, "offset": 0, - "total": 2823, + "total": 4838, "items": [ { - "id": "urn:uuid:a54e0b8c-af55-459b-ae98-a7e0ae60b190", - "subject": "MONDO:0009364", + "id": "urn:uuid:e4e8dbec-cb0c-44e9-b1cb-8be3b357b7b8", + "category": 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(HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Deeply set eye (HPO)", + "Abnormal eye morphology (HPO)", + "Abnormality of globe location (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal location of anatomical entity", + "abnormal location of eyeball of camera-type eye", + "abnormal anatomical entity morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity topology in independent continuant", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology" + ], "object_taxon": null, "object_taxon_label": null, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, - "provided_by": "phenio_edges", + "pathway": null, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [ + { + "id": "ECO:0000304", + "url": "http://purl.obolibrary.org/obo/ECO_0000304" + } + ], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#" + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": [], + "publications": ["OMIM:614643"], + "publications_links": [ + { + "id": "OMIM:614643", + "url": "http://identifiers.org/mim/614643" + } + ], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": [], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 2, - "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, "frequency_qualifier_category": null, @@ -2728,66 +1751,49 @@ "stage_qualifier_closure_label": [] }, { - "id": "urn:uuid:a20f59e6-2468-4f26-a789-04cd5d5bd97f", - "subject": "MONDO:0014101", - "original_subject": null, + "id": "uuid:aa6b44e5-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0009181", + "original_subject": "OMIM:226670", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0016198", + "MONDO:0016971", + "MONDO:0000429", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", "BFO:0000002", - "MONDO:0014101", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0006617", "BFO:0000017", - "MONDO:0018869", "BFO:0000020", - "MONDO:0016157", - "MONDO:0017745", + "MONDO:0017610", + "MONDO:0006025", + "MONDO:0016106", + "MONDO:0002051", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", - "MONDO:0018838", - "MONDO:0024458", + "MONDO:0100118", "MONDO:0005336", "MONDO:0002081", - "MONDO:0016184", - "MONDO:0016156", - "MONDO:0020246", - "MONDO:0021147", - "MONDO:0044137", - "MONDO:0019755", + "MONDO:0002254", + "MONDO:0009181", + "MONDO:0019276", + "MONDO:0005093", "OGMS:0000031", - "MONDO:0015327", + "MONDO:0019268", "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0015286", - "BFO:0000001", - "MONDO:0002320", - "MONDO:0019052", - "MONDO:0020247", - "MONDO:0005066", - "MONDO:0005328", - "MONDO:0019950", - "MONDO:0016155", - "MONDO:0700066" + "MONDO:0006541", + "MONDO:0015152", + "BFO:0000001" ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", + "subject_label": "epidermolysis bullosa simplex 5B, with muscular dystrophy", "subject_closure_label": [ "entity", "continuant", @@ -2795,61 +1801,355 @@ "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type A", - "disorder of orbital region", + "autosomal genetic disease", + "integumentary system disorder", "musculoskeletal system disorder", - "congenital nervous system disorder", + "syndromic disease", "hereditary disease", "muscle tissue disorder", - "metabolic disease", "nervous system disorder", - "retinal disorder", - "eye disorder", + "skin disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", - "congenital disorder of glycosylation", - "developmental anomaly of metabolic origin", + "autosomal recessive disease", + "epidermolysis bullosa", + "vesiculobullous skin disease", + "epidermolysis bullosa simplex 5B, with muscular dystrophy", + "autosomal recessive limb-girdle muscular dystrophy", + "progressive muscular dystrophy", "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of FKRP", - "qualitative or quantitative defects of fukutin", - "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", - "qualitative or quantitative defects of protein O-mannosyltransferase 1", - "qualitative or quantitative defects of protein O-mannosyltransferase 2", - "disorder of protein O-glycosylation", - "disorder of O-mannosylglycan synthesis", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "lissencephaly spectrum disorders", - "cobblestone lissencephaly", - "inborn errors of metabolism", + "qualitative or quantitative defects of plectin", + "limb-girdle muscular dystrophy", + "epidermolysis bullosa simplex", "neuromuscular disease", - "developmental defect during embryogenesis", - "congenital muscular dystrophy", + "epidermal disease", + "inherited epidermolysis bullosa", "skeletal muscle disorder", "muscular dystrophy", - "inherited vitreous-retinal disease", - "inherited vitreoretinopathy", - "congenital vitreoretinal dysplasia", - "disorder of development or morphogenesis", - "disorder of glycosylation", - "disorder of visual system", - "vitreous body disorder", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", - "myopathy caused by variation in POMGNT1", + "hereditary skin disorder", "human disease", "hereditary skeletal muscle disorder", "disease" ], - "subject_taxon": null, - "subject_taxon_label": null, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000171", - "original_object": null, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", - "object_closure": [ + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": 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"UPHENO:0001003", + "UPHENO:0002263", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0049588", + "HP:0000491", + "UPHENO:0020584", + "UPHENO:0059829", + "UPHENO:0080662", + "UPHENO:0076692", + "UPHENO:0074685", + "UPHENO:0076684", + "UPHENO:0049587", + "BFO:0000001", + "HP:0012649", + "PATO:0000001", + "UPHENO:0074572", + "HP:0011495", + "BFO:0000001", + "BFO:0000003", + "BFO:0000002", + "BFO:0000015", + "BFO:0000004", + "GO:0008150", + "BFO:0000040", + "UBERON:0001062", + "GO:0050896", + "PR:000050567", + "UBERON:0000465", + "GO:0006950", + "UBERON:0000483", + "UBERON:0012430", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0000964", + "GO:0006952", + "UBERON:0019304", + "UBERON:0010371", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "GO:0006954", + "UBERON:0007625", + "UBERON:0015808", + "UBERON:0000019", + "UBERON:0010313", + "UBERON:0010230", + "UBERON:0010409", + "UBERON:0000479", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0002405", + "UBERON:0001772", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000060", + "UBERON:0004923", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047" + ], + "object_label": "Keratitis (HPO)", + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "occurrent", + "independent continuant", + "process", + "specifically dependent continuant", + "material entity", + "response to stress", + "defense response", + "inflammatory response", + "biological_process", + "response to stimulus", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of 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system", + "anatomical entity", + "subdivision of head", + "face", + "corneal epithelium", + "anterior segment of eyeball", + "visual system", + "immune system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "organ component layer", + "pigment epithelium of eye", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "neural crest-derived structure", + "structure with developmental contribution from neural crest", + "ecto-epithelium", + "ocular surface region", + "subdivision of organism along main body axis", + "tunica fibrosa of eyeball", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "eye epithelium", + "sensory organ epithelium", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormality of camera-type eye physiology", + "abnormality of immune system physiology", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal immune system", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal cornea morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal corneal epithelium morphology", + "abnormal inflammatory response", + "abnormal response to stimulus", + "abnormal biological_process", + "abnormal response to stress", + "increased biological_process", + "abnormal biological_process in independent continuant", + "increased biological_process in independent continuant", + "increased inflammatory response in eyeball of camera-type eye", + "increased inflammatory response in independent continuant", + "increased biological_process in eyeball of camera-type eye", + "abnormal anatomical entity", + "abnormal orbital region", + "increased inflammatory response", + "abnormal anatomical entity morphology", + "changed biological_process rate in independent continuant", + "changed biological_process rate", + "increased qualitatively biological_process", + "increased qualitatively inflammatory response", + "abnormal multicellular organism morphology", + "increased qualitatively biological_process in independent continuant", + "increased qualitatively inflammatory response in independent continuant", + "abnormality of anatomical entity physiology", + "increased qualitatively response to stimulus" + ], + "object_taxon": null, + "object_taxon_label": null, + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "negated": null, + "pathway": null, + "evidence_count": 2, + "has_evidence": ["ECO:0000501"], + "has_evidence_links": [ + { + "id": "ECO:0000501", + "url": "http://purl.obolibrary.org/obo/ECO_0000501" + } + ], + "provided_by": "hpoa_disease_to_phenotype_edges", + "provided_by_link": { + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" + }, + "publications": ["OMIM:226670"], + "publications_links": [ + { + "id": "OMIM:226670", + "url": "http://identifiers.org/mim/226670" + } + ], + "qualifiers": [], + "frequency_qualifier": null, + "onset_qualifier": null, + "sex_qualifier": null, + "stage_qualifier": null, + "frequency_qualifier_label": null, + "frequency_qualifier_namespace": null, + "frequency_qualifier_category": null, + "frequency_qualifier_closure": [], + "frequency_qualifier_closure_label": [], + "onset_qualifier_label": null, + "onset_qualifier_namespace": null, + "onset_qualifier_category": null, + "onset_qualifier_closure": [], + "onset_qualifier_closure_label": [], + "sex_qualifier_label": null, + "sex_qualifier_namespace": null, + "sex_qualifier_category": null, + "sex_qualifier_closure": [], + "sex_qualifier_closure_label": [], + "stage_qualifier_label": null, + "stage_qualifier_namespace": null, + "stage_qualifier_category": null, + "stage_qualifier_closure": [], + "stage_qualifier_closure_label": [] + }, + { + "id": "uuid:a74a1018-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0009678", + "original_subject": "OMIM:253800", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ + "MONDO:0700067", "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", @@ -2882,10 +2182,12 @@ "MONDO:0002081", "MONDO:0016184", "MONDO:0016156", + "MONDO:0018939", "MONDO:0020246", "MONDO:0021147", "MONDO:0044137", "MONDO:0019755", + "MONDO:0009678", "OGMS:0000031", "MONDO:0015327", "MONDO:0003847", @@ -2902,8 +2204,8 @@ "MONDO:0016155", "MONDO:0700066" ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", - "object_closure_label": [ + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4", + "subject_closure_label": [ "entity", "continuant", "disposition", @@ -2921,6 +2223,7 @@ "retinal disorder", "eye disorder", "myopathy", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -2936,6 +2239,7 @@ "qualitative or quantitative defects of alpha-dystroglycan", "lissencephaly spectrum disorders", "cobblestone lissencephaly", + "muscle-eye-brain disease", "inborn errors of metabolism", "neuromuscular disease", "developmental defect during embryogenesis", @@ -2951,31 +2255,224 @@ "vitreous body disorder", "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", + "myopathy caused by variation in FKTN", "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease" ], + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0000496", + "original_object": null, + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0049586", + "UPHENO:0001001", + "UPHENO:0049622", + "UPHENO:0080585", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "UPHENO:0080581", + "BFO:0000020", + "UPHENO:0002433", + "UPHENO:0003020", + "UPHENO:0079828", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0000707", + "HP:0012373", + "HP:0000496", + "UPHENO:0001003", + "UPHENO:0002536", + "HP:0000708", + "UPHENO:0079826", + "UPHENO:0004523", + 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"http://purl.obolibrary.org/obo/ECO_0000304" + } + ], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#" + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": [], + "publications": ["OMIM:253800"], + "publications_links": [ + { + "id": "OMIM:253800", + "url": "http://identifiers.org/mim/253800" + } + ], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": [], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 2, - "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, "frequency_qualifier_category": null, @@ -2998,9 +2495,10 @@ "stage_qualifier_closure_label": [] }, { - "id": "urn:uuid:f7c423b7-6f4c-4663-9ead-41d529a7cf2b", - "subject": "MONDO:0014120", - "original_subject": null, + "id": "uuid:a8bae583-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0009364", + "original_subject": "OMIM:236670", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ @@ -3008,7 +2506,6 @@ "MONDO:0000001", "MONDO:0016182", "MONDO:0017741", - "MONDO:0014120", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", @@ -3037,6 +2534,7 @@ "MONDO:0002081", "MONDO:0016184", "MONDO:0016156", + "MONDO:0009364", "MONDO:0020246", "MONDO:0021147", "MONDO:0044137", @@ -3044,6 +2542,7 @@ "OGMS:0000031", "MONDO:0015327", "MONDO:0003847", + "MONDO:0700070", "MONDO:0003939", "MONDO:0002022", "MONDO:0015286", @@ -3057,7 +2556,7 @@ "MONDO:0016155", "MONDO:0700066" ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", "subject_closure_label": [ "entity", "continuant", @@ -3076,7 +2575,7 @@ "retinal disorder", "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -3108,22 +2607,211 @@ "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", "myopathy caused by variation in POMGNT1", + "myopathy caused by variation in POMT1", "human disease", "hereditary skeletal muscle disorder", "disease" ], "subject_taxon": null, "subject_taxon_label": null, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000171", + "predicate": "biolink:has_phenotype", + "object": "HP:0000501", "original_object": null, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + 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"frequency_qualifier_label": null, + "frequency_qualifier_namespace": null, + "frequency_qualifier_category": null, + "frequency_qualifier_closure": [], + "frequency_qualifier_closure_label": [], + "onset_qualifier_label": null, + "onset_qualifier_namespace": null, + "onset_qualifier_category": null, + "onset_qualifier_closure": [], + "onset_qualifier_closure_label": [], + "sex_qualifier_label": null, + "sex_qualifier_namespace": null, + "sex_qualifier_category": null, + "sex_qualifier_closure": [], + "sex_qualifier_closure_label": [], + "stage_qualifier_label": null, + "stage_qualifier_namespace": null, + "stage_qualifier_category": null, + "stage_qualifier_closure": [], + "stage_qualifier_closure_label": [] + }, + { + "id": "uuid:a8aad663-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", "MONDO:0017741", + "MONDO:0013154", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", @@ -3140,6 +2828,7 @@ "MONDO:0018869", "BFO:0000020", "MONDO:0016157", + "MONDO:0700071", "MONDO:0017745", "BFO:0000016", "MONDO:0020120", @@ -3152,6 +2841,7 @@ "MONDO:0002081", "MONDO:0016184", "MONDO:0016156", + "MONDO:0018939", "MONDO:0020246", "MONDO:0021147", "MONDO:0044137", @@ -3172,8 +2862,8 @@ "MONDO:0016155", "MONDO:0700066" ], - "object_label": "muscular dystrophy-dystroglycanopathy, type A", - "object_closure_label": [ + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "subject_closure_label": [ "entity", "continuant", "disposition", @@ -3191,6 +2881,7 @@ "retinal disorder", "eye disorder", "myopathy", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -3206,6 +2897,7 @@ "qualitative or quantitative defects of alpha-dystroglycan", "lissencephaly spectrum disorders", "cobblestone lissencephaly", + "muscle-eye-brain disease", "inborn errors of metabolism", "neuromuscular disease", "developmental defect during embryogenesis", @@ -3222,30 +2914,177 @@ "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", "myopathy caused by variation in POMGNT1", + "myopathy caused by variation in POMT2", "human disease", "hereditary skeletal muscle disorder", "disease" ], + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0000501", + "original_object": null, + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", + "BFO:0000002", + "BFO:0000020", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0002332", + "HP:0000271", + "HP:0012373", + "UPHENO:0001003", + "UPHENO:0002536", + "BFO:0000001", + "PATO:0000001", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047" + ], + "object_label": "Glaucoma (HPO)", + "object_closure_label": [ + "entity", + "entity", + "continuant", + "continuant", + "independent continuant", + "specifically dependent continuant", + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Glaucoma (HPO)", + "Abnormal eye physiology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "visual system", + "orbital region", + "ectoderm-derived 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["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, - "provided_by": "phenio_edges", + "pathway": null, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [ + { + "id": "ECO:0000304", + "url": "http://purl.obolibrary.org/obo/ECO_0000304" + } + ], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#" + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": [], + "publications": ["OMIM:613150"], + "publications_links": [ + { + "id": "OMIM:613150", + "url": "http://identifiers.org/mim/613150" + } + ], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": [], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 2, - "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, "frequency_qualifier_category": null, @@ -3268,13 +3107,13 @@ "stage_qualifier_closure_label": [] }, { - "id": "urn:uuid:9d167233-70b8-4d7d-aa5d-f6dac17ba835", - "subject": "MONDO:0014140", - "original_subject": null, + "id": "uuid:abeb7bed-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0013835", + "original_subject": "OMIM:614643", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0700084", "MONDO:0018282", "MONDO:0000001", "MONDO:0016182", @@ -3294,6 +3133,7 @@ "BFO:0000017", "MONDO:0018869", "BFO:0000020", + "MONDO:0013835", "MONDO:0016157", "MONDO:0017745", "BFO:0000016", @@ -3307,10 +3147,8 @@ "MONDO:0002081", "MONDO:0016184", "MONDO:0016156", - "MONDO:0018939", "MONDO:0020246", "MONDO:0021147", - "MONDO:0014140", "MONDO:0044137", "MONDO:0019755", "OGMS:0000031", @@ -3329,7 +3167,7 @@ "MONDO:0016155", "MONDO:0700066" ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", "subject_closure_label": [ "entity", "continuant", @@ -3348,7 +3186,7 @@ "retinal disorder", "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 7", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -3364,7 +3202,6 @@ "qualitative or quantitative defects of alpha-dystroglycan", "lissencephaly spectrum disorders", "cobblestone lissencephaly", - "muscle-eye-brain disease", "inborn errors of metabolism", "neuromuscular disease", "developmental defect during embryogenesis", @@ -3381,19 +3218,205 @@ "glycoprotein metabolism disease", "myopathy caused by variation in FKRP", "myopathy caused by variation in POMGNT1", - "myopathy caused by variation in GMPPB", "human disease", "hereditary skeletal muscle disorder", "disease" ], "subject_taxon": null, "subject_taxon_label": null, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000171", + "predicate": "biolink:has_phenotype", + "object": "HP:0000501", "original_object": null, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + 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"muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9", + "subject_closure_label": [ "entity", "continuant", "disposition", @@ -3465,6 +3489,7 @@ "retinal disorder", "eye disorder", "myopathy", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -3500,26 +3525,172 @@ "hereditary skeletal muscle disorder", "disease" ], + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0000501", + "original_object": null, + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "HP:0000478", + 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- "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, "frequency_qualifier_category": null, @@ -3542,66 +3713,47 @@ "stage_qualifier_closure_label": [] }, { - "id": "urn:uuid:772849bb-ae4c-4a45-8a2e-b0269106d6e2", - "subject": "MONDO:0014683", - "original_subject": null, + "id": "uuid:a8bae681-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0011181", + "original_subject": "OMIM:602078", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0016182", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0700068", "MONDO:0700223", - "MONDO:0024322", - "MONDO:0005283", - "MONDO:0020238", + "MONDO:0004746", "BFO:0000002", - "MONDO:0016185", - "MONDO:0000171", + "MONDO:0957003", "BFO:0000017", - "MONDO:0018869", + 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"continuant", "disposition", @@ -3735,6 +4087,7 @@ "retinal disorder", "eye disorder", "myopathy", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12", "congenital disorder of glycosylation", "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", @@ -3770,26 +4123,204 @@ "hereditary skeletal muscle disorder", "disease" ], + "subject_taxon": null, + "subject_taxon_label": null, + "predicate": "biolink:has_phenotype", + "object": "HP:0000505", + "original_object": null, + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0000315", + "HP:0000001", + "UPHENO:0050620", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "UPHENO:0001001", + "HP:0000152", + "UPHENO:0052164", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", 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+ "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal biological_process", + "abnormal sensory perception of light stimulus", + "abnormal sensory perception", + "abnormal visual perception", + "decreased qualitatively visual perception", + "decreased qualitatively biological_process", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormality of anatomical entity physiology" + ], "object_taxon": null, "object_taxon_label": null, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, - "provided_by": "phenio_edges", + "pathway": null, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [ + { + "id": "ECO:0000304", + "url": "http://purl.obolibrary.org/obo/ECO_0000304" + } + ], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#" + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": [], + "publications": ["OMIM:615249"], + "publications_links": [ + { + "id": "OMIM:615249", + "url": "http://identifiers.org/mim/615249" + } + ], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": [], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 2, - "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, "frequency_qualifier_category": null, @@ -3812,47 +4343,48 @@ "stage_qualifier_closure_label": [] }, { - "id": "urn:uuid:1c12ae85-5540-49db-8bae-44cde2205158", - "subject": "MONDO:0011688", - "original_subject": null, + "id": "uuid:a538f419-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0010912", + "original_subject": "OMIM:600638", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018282", + "MONDO:0020158", "MONDO:0000001", - "MONDO:0017741", - "MONDO:0018276", - "MONDO:0045010", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", "MONDO:0700223", - "MONDO:0024322", + "MONDO:0004746", "BFO:0000002", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", - "MONDO:0016157", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", - "MONDO:0016139", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0100153", "OGMS:0000031", "MONDO:0003847", + "MONDO:0100154", "MONDO:0003939", - "MONDO:0015286", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0002320", - 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glycosylation", - "qualitative or quantitative protein defects in neuromuscular diseases", - "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", - "qualitative or quantitative defects of fukutin", - "disorder of protein O-glycosylation", - "muscular dystrophy-dystroglycanopathy", - "qualitative or quantitative defects of alpha-dystroglycan", - "inborn errors of metabolism", + "congenital fibrosis of extraocular muscles", + "fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", - "disorder of glycosylation", - "glycoprotein metabolism disease", - "myopathy caused by variation in FKRP", + "eyelids malposition disorder", + "disorder of visual system", + "tubulinopathy", + "TUBB3-related tubulinopathy", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease" ], "subject_taxon": null, "subject_taxon_label": null, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000172", + "predicate": "biolink:has_phenotype", + "object": "HP:0000508", "original_object": null, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0041226", + "UPHENO:0076761", + "UPHENO:0075696", + "UPHENO:0041667", + "UPHENO:0001001", + "UPHENO:0021749", + "UPHENO:0080300", + "UPHENO:0021791", + "UPHENO:0041410", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", + "HP:0000492", + "UPHENO:0002844", + "UPHENO:0002219", + "UPHENO:0001005", + "UPHENO:0002764", + 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morphology", + "abnormal eyelid morphology", + "abnormal ocular adnexa morphology", + "shape anatomical entity", + "drooping anatomical entity", + "drooping eyelid", + "shape eyelid", + "abnormal anatomical entity", + "abnormal ocular adnexa", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal eyelid morphology", + "abnormal shape of continuant", + "abnormal multicellular organism morphology", + "shape anatomical entity in independent continuant", + "abnormality of anatomical entity physiology" ], "object_taxon": null, - "object_taxon_label": null, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "object_taxon_label": null, + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, - "provided_by": "phenio_edges", + "pathway": null, + "evidence_count": 2, + "has_evidence": ["ECO:0000304"], + "has_evidence_links": [ + { + "id": "ECO:0000304", + "url": "http://purl.obolibrary.org/obo/ECO_0000304" + } + ], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#" + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": [], + "publications": ["OMIM:600638"], + "publications_links": [ + { + "id": "OMIM:600638", + "url": "http://identifiers.org/mim/600638" + } + ], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": [], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 2, - "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, "frequency_qualifier_category": null, @@ -3984,36 +4650,46 @@ "stage_qualifier_closure_label": [] }, { - "id": "urn:uuid:8c3fdf6b-34fc-4154-a332-45e0f699c79c", - "subject": "MONDO:0012138", - "original_subject": null, + "id": "uuid:abcb9e2a-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0012270", + "original_subject": "OMIM:609428", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0020158", "MONDO:0000001", - "MONDO:0012138", - "MONDO:0018276", + "MONDO:0007614", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", "MONDO:0700223", + "MONDO:0004746", "BFO:0000002", + "MONDO:0957003", "BFO:0000017", "BFO:0000020", + "MONDO:0016106", + "MONDO:0003382", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", + "MONDO:0003569", "MONDO:0700096", + "MONDO:0001584", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0012270", "OGMS:0000031", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", + "MONDO:0015368", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950" + "MONDO:0000462", + "MONDO:0005328" ], - "subject_label": "muscular dystrophy-dystroglycanopathy type B6", + "subject_label": "Tukel syndrome", "subject_closure_label": [ "entity", "continuant", @@ -4021,97 +4697,240 @@ "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "eye adnexa disorder", + "ocular motility disease", + "disorder of orbital region", "musculoskeletal system disorder", - "congenital nervous system disorder", + "eyelid disorder", + "cranial nerve neuropathy", "hereditary disease", "muscle tissue disorder", + "myopathy of extraocular muscle", "nervous system disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy type B6", - "muscular dystrophy-dystroglycanopathy", + "congenital fibrosis of extraocular muscles", + "Tukel syndrome", + "neuro-ophthalmological disease", + "progressive muscular dystrophy", "neuromuscular disease", - "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "eyelids malposition disorder", + "disorder of visual system", "human disease", "hereditary skeletal muscle disorder", + "hereditary neuro-ophthalmological disease", "disease" ], "subject_taxon": null, "subject_taxon_label": null, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000172", + "predicate": "biolink:has_phenotype", + "object": "HP:0000508", "original_object": null, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0041226", + "UPHENO:0076761", + "UPHENO:0075696", + "UPHENO:0041667", + "UPHENO:0001001", + "UPHENO:0021749", + "UPHENO:0080300", + "UPHENO:0021791", + "UPHENO:0041410", + "HP:0000152", + "UPHENO:0002910", + "HP:0000478", 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null, + "evidence_count": 2, + "has_evidence": ["ECO:0000501"], + "has_evidence_links": [ + { + "id": "ECO:0000501", + "url": "http://purl.obolibrary.org/obo/ECO_0000501" + } + ], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#" + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": [], + "publications": ["OMIM:160900"], + "publications_links": [ + { + "id": "OMIM:160900", + "url": "http://identifiers.org/mim/160900" + } + ], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": [], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 2, - "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, "frequency_qualifier_category": null, @@ -4484,46 +5547,68 @@ "stage_qualifier_closure_label": [] }, { - "id": "urn:uuid:d20f485a-4fde-44b8-aa20-20fd2d5902ab", - "subject": "MONDO:0013159", - "original_subject": null, + "id": "uuid:a8bae558-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0009364", + "original_subject": "OMIM:236670", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0018282", "MONDO:0000001", + "MONDO:0016182", "MONDO:0017741", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0700068", "MONDO:0700223", - "MONDO:0013159", "MONDO:0024322", + "MONDO:0005283", + "MONDO:0020238", "BFO:0000002", + "MONDO:0016185", + "MONDO:0000171", "BFO:0000017", + "MONDO:0018869", "BFO:0000020", + "MONDO:0016157", + "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0018838", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016184", + "MONDO:0016156", + "MONDO:0009364", + "MONDO:0020246", + "MONDO:0021147", + "MONDO:0044137", + "MONDO:0019755", "OGMS:0000031", + "MONDO:0015327", "MONDO:0003847", "MONDO:0700070", "MONDO:0003939", + "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", + "MONDO:0020247", "MONDO:0005066", + "MONDO:0005328", "MONDO:0019950", - "MONDO:0016155" + "MONDO:0016155", + "MONDO:0700066" ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", "subject_closure_label": [ "entity", "continuant", @@ -4531,28 +5616,49 @@ "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy-dystroglycanopathy, type A", + "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", + "retinal disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1", "congenital disorder of glycosylation", + "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "qualitative or quantitative defects of FKRP", + "qualitative or quantitative defects of fukutin", + "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", + "qualitative or quantitative defects of protein O-mannosyltransferase 1", + "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", + "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", "qualitative or quantitative defects of alpha-dystroglycan", + "lissencephaly spectrum disorders", + "cobblestone lissencephaly", "inborn errors of metabolism", "neuromuscular disease", + "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "inherited vitreous-retinal disease", + "inherited vitreoretinopathy", + "congenital vitreoretinal dysplasia", + "disorder of development or morphogenesis", "disorder of glycosylation", + "disorder of visual system", + "vitreous body disorder", "glycoprotein metabolism disease", + "myopathy caused by variation in FKRP", + "myopathy caused by variation in POMGNT1", "myopathy caused by variation in POMT1", "human disease", "hereditary skeletal muscle disorder", @@ -4560,78 +5666,192 @@ ], "subject_taxon": null, "subject_taxon_label": null, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000172", + "predicate": "biolink:has_phenotype", + "object": "HP:0000518", "original_object": null, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "HP:0004328", + "UPHENO:0001001", + "UPHENO:0004765", + "HP:0000152", + "HP:0000518", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0020584", + "UPHENO:0076692", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950" + "PATO:0000001", + "HP:0000517", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0005389", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0000965", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047" ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Cataract (HPO)", "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of the lens (HPO)", + "Cataract (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormal eye morphology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "lens of camera-type eye", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "anterior segment of eyeball", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "transparent eye structure", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal lens of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology" ], "object_taxon": null, "object_taxon_label": null, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, - "provided_by": "phenio_edges", + "pathway": null, + "evidence_count": 2, + "has_evidence": ["ECO:0000501"], + "has_evidence_links": [ + { + "id": "ECO:0000501", + "url": "http://purl.obolibrary.org/obo/ECO_0000501" + } + ], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#" + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": [], + "publications": ["OMIM:236670"], + "publications_links": [ + { + "id": "OMIM:236670", + "url": "http://identifiers.org/mim/236670" + } + ], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": [], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 2, - "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, "frequency_qualifier_category": null, @@ -4654,46 +5874,68 @@ "stage_qualifier_closure_label": [] }, { - "id": "urn:uuid:7a5c97ed-311c-4530-bfdf-447bf5c4db72", - "subject": "MONDO:0013160", - "original_subject": null, + "id": "uuid:a4c7f187-6c84-11ee-9c86-072f86c27f6e", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0009667", + "original_subject": "OMIM:253280", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ "MONDO:0018282", "MONDO:0000001", + "MONDO:0016182", "MONDO:0017741", "MONDO:0018276", "MONDO:0045010", "MONDO:0005071", "MONDO:0020121", - "MONDO:0000172", + "MONDO:0700068", "MONDO:0700223", "MONDO:0024322", + "MONDO:0005283", + "MONDO:0020238", "BFO:0000002", + "MONDO:0016185", + "MONDO:0000171", "BFO:0000017", + "MONDO:0018869", "BFO:0000020", - "MONDO:0013160", - "MONDO:0700071", + "MONDO:0016157", + "MONDO:0017745", "BFO:0000016", "MONDO:0020120", "MONDO:0019056", "MONDO:0016139", "MONDO:0700096", + "MONDO:0018838", + "MONDO:0024458", "MONDO:0005336", "MONDO:0002081", + "MONDO:0016184", + "MONDO:0016156", + "MONDO:0018939", + "MONDO:0020246", + "MONDO:0009667", + "MONDO:0021147", + "MONDO:0044137", + "MONDO:0019755", "OGMS:0000031", + "MONDO:0015327", "MONDO:0003847", "MONDO:0003939", + "MONDO:0002022", "MONDO:0015286", "BFO:0000001", "MONDO:0002320", "MONDO:0019052", + "MONDO:0020247", "MONDO:0005066", + "MONDO:0005328", "MONDO:0019950", - "MONDO:0016155" + "MONDO:0016155", + "MONDO:0700066" ], - "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3", "subject_closure_label": [ "entity", "continuant", @@ -4701,107 +5943,242 @@ "realizable entity", "specifically dependent continuant", "disease", - "muscular dystrophy-dystroglycanopathy, type B", + "muscular dystrophy-dystroglycanopathy, type A", + "disorder of orbital region", "musculoskeletal system disorder", "congenital nervous system disorder", "hereditary disease", "muscle tissue disorder", "metabolic disease", "nervous system disorder", + "retinal disorder", + "eye disorder", "myopathy", - "muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3", "congenital disorder of glycosylation", + "developmental anomaly of metabolic origin", "qualitative or quantitative protein defects in neuromuscular diseases", "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "qualitative or quantitative defects of FKRP", + "qualitative or quantitative defects of fukutin", + "qualitative or quantitative defects of protein O-mannose beta1, 2N-acetylglucosaminyltransferase", + "qualitative or quantitative defects of protein O-mannosyltransferase 1", + "qualitative or quantitative defects of protein O-mannosyltransferase 2", "disorder of protein O-glycosylation", + "disorder of O-mannosylglycan synthesis", "muscular dystrophy-dystroglycanopathy", "qualitative or quantitative defects of alpha-dystroglycan", + "lissencephaly spectrum disorders", + "cobblestone lissencephaly", + "muscle-eye-brain disease", "inborn errors of metabolism", "neuromuscular disease", + "developmental defect during embryogenesis", "congenital muscular dystrophy", "skeletal muscle disorder", "muscular dystrophy", + "inherited vitreous-retinal disease", + "inherited vitreoretinopathy", + "congenital vitreoretinal dysplasia", + "disorder of development or morphogenesis", "disorder of glycosylation", + "disorder of visual system", + "vitreous body disorder", "glycoprotein metabolism disease", - "myopathy caused by variation in POMT2", + "myopathy caused by variation in FKRP", + "myopathy caused by variation in POMGNT1", "human disease", "hereditary skeletal muscle disorder", "disease" ], "subject_taxon": null, "subject_taxon_label": null, - "predicate": "biolink:subclass_of", - "object": "MONDO:0000172", + "predicate": "biolink:has_phenotype", + "object": "HP:0000518", "original_object": null, - "object_namespace": "MONDO", - "object_category": "biolink:Disease", + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "MONDO:0000001", - "MONDO:0018276", - "MONDO:0005071", - "MONDO:0020121", - "MONDO:0000172", - "MONDO:0700223", + "HP:0000315", + "HP:0000001", + "UPHENO:0075997", + "HP:0012372", + "UPHENO:0075696", + "HP:0004328", + "UPHENO:0001001", + "UPHENO:0004765", + "HP:0000152", + "HP:0000518", + "UPHENO:0002910", + "HP:0000478", + "UPHENO:0021474", + "UPHENO:0002844", + "UPHENO:0001005", + "UPHENO:0002764", + "UPHENO:0001002", + "HP:0000118", "BFO:0000002", - "BFO:0000017", "BFO:0000020", - "BFO:0000016", - "MONDO:0020120", - "MONDO:0019056", - "MONDO:0700096", - "MONDO:0005336", - "MONDO:0002081", - "OGMS:0000031", - "MONDO:0003847", - "MONDO:0003939", + "UPHENO:0003020", + "HP:0000234", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0081581", + "UPHENO:0001003", + "UPHENO:0002536", + "UPHENO:0021038", + "UPHENO:0020584", + "UPHENO:0076692", "BFO:0000001", - "MONDO:0002320", - "MONDO:0019950" + "PATO:0000001", + "HP:0000517", + "BFO:0000001", + "BFO:0000002", + "BFO:0000004", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0000465", + "UBERON:0000061", + "UBERON:0034923", + "UBERON:0015212", + "UBERON:0010314", + "UBERON:0004121", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0005389", + "UBERON:0015203", + "UBERON:0000019", + "UBERON:0000965", + "UBERON:0010230", + "UBERON:0000475", + "UBERON:0000062", + "UBERON:0000468", + "UBERON:0000064", + "UBERON:0001801", + "UBERON:0004456", + "UBERON:0001032", + "UBERON:0000153", + "UBERON:0011676", + "UBERON:0013701", + "UBERON:0007811", + "UBERON:0001444", + "UBERON:0000020", + "UBERON:0013702", + "UBERON:0000063", + "UBERON:0002104", + "http://uri.neuinfo.org/nif/nifstd/FMAID_7191", + "UBERON:0000033", + "UBERON:0004088", + "UBERON:0000970", + "UBERON:0001456", + "UBERON:0000047" ], - "object_label": "muscular dystrophy-dystroglycanopathy, type B", + "object_label": "Cataract (HPO)", "object_closure_label": [ + "entity", "entity", "continuant", - "disposition", - "realizable entity", + "continuant", + "independent continuant", "specifically dependent continuant", - "disease", - "muscular dystrophy-dystroglycanopathy, type B", - "musculoskeletal system disorder", - "congenital nervous system disorder", - "hereditary disease", - "muscle tissue disorder", - "nervous system disorder", - "myopathy", - "muscular dystrophy-dystroglycanopathy", - "neuromuscular disease", - "congenital muscular dystrophy", - "skeletal muscle disorder", - "muscular dystrophy", - "human disease", - "hereditary skeletal muscle disorder", - "disease" + "material entity", + "All (HPO)", + "Phenotypic abnormality (HPO)", + "Abnormality of head or neck (HPO)", + "Abnormality of the head (HPO)", + "Abnormality of the face (HPO)", + "Abnormality of the orbital region (HPO)", + "Abnormality of the eye (HPO)", + "Abnormality of the lens (HPO)", + "Cataract (HPO)", + "Abnormal anterior eye segment morphology (HPO)", + "Abnormal eye morphology (HPO)", + "quality", + "camera-type eye", + "sense organ", + "head", + "simple eye", + "anatomical structure", + "organ", + "organ subunit", + "organ part", + "anterior region of body", + "material anatomical entity", + "anatomical system", + "multicellular organism", + "organism subdivision", + "lens of camera-type eye", + "eye", + "sensory system", + "anatomical entity", + "subdivision of head", + "face", + "anterior segment of eyeball", + "visual system", + "orbital region", + "ectoderm-derived structure", + "entire sense organ system", + "transparent eye structure", + "craniocervical region", + "multicellular anatomical structure", + "eyeball of camera-type eye", + "structure with developmental contribution from neural crest", + "subdivision of organism along main body axis", + "main body axis", + "body proper", + "non-connected functional system", + "lateral structure", + "disconnected anatomical group", + "phenotype", + "Phenotypic abnormality", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "abnormal anatomical entity", + "abnormal craniocervical region", + "abnormal head", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal lens of camera-type eye", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "abnormal anterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal anatomical entity", + "abnormal orbital region", + "abnormal anatomical entity morphology", + "abnormal multicellular organism morphology" ], "object_taxon": null, "object_taxon_label": null, - "primary_knowledge_source": "infores:mondo", - "aggregator_knowledge_source": ["infores:phenio"], - "category": "biolink:Association", + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], "negated": null, - "provided_by": "phenio_edges", + "pathway": null, + "evidence_count": 2, + "has_evidence": ["ECO:0000501"], + "has_evidence_links": [ + { + "id": "ECO:0000501", + "url": "http://purl.obolibrary.org/obo/ECO_0000501" + } + ], + "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { - "id": "phenio", - "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#" + "id": "hpoa_disease_to_phenotype", + "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype" }, - "publications": [], + "publications": ["OMIM:253280"], + "publications_links": [ + { + "id": "OMIM:253280", + "url": "http://identifiers.org/mim/253280" + } + ], "qualifiers": [], "frequency_qualifier": null, - "has_evidence": [], "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, - "evidence_count": 2, - "pathway": null, "frequency_qualifier_label": null, "frequency_qualifier_namespace": null, "frequency_qualifier_category": null, diff --git a/frontend/fixtures/autocomplete.json b/frontend/fixtures/autocomplete.json index 6798fe2d9..a012da724 100644 --- a/frontend/fixtures/autocomplete.json +++ b/frontend/fixtures/autocomplete.json @@ -227,24 +227,6 @@ "highlight": null, "score": null }, - { - "id": "MONDO:0100136", - "category": "biolink:Disease", - "name": "obsolete Fanconia anemia complementation group M", - "full_name": null, - "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.", - "xref": [], - "provided_by": "phenio_nodes", - "in_taxon": null, - "in_taxon_label": null, - "symbol": null, - "synonym": [ - "FANCM Fanconi anemia", - "Fanconi anemia caused by mutation in FANCM" - ], - "highlight": null, - "score": null - }, { "id": "MONDO:0010351", "category": "biolink:Disease", @@ -340,6 +322,24 @@ "highlight": null, "score": null }, + { + "id": "MONDO:0100136", + "category": "biolink:Disease", + "name": "obsolete Fanconia anemia complementation group M", + "full_name": null, + "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.", + "xref": [], + "provided_by": "phenio_nodes", + "in_taxon": null, + "in_taxon_label": null, + "symbol": null, + "synonym": [ + "FANCM Fanconi anemia", + "Fanconi anemia caused by mutation in FANCM" + ], + "highlight": null, + "score": null + }, { "id": "MONDO:0009213", "category": "biolink:Disease", diff --git a/frontend/fixtures/histopheno.json b/frontend/fixtures/histopheno.json index fb9e20a1c..1cecaea78 100644 --- a/frontend/fixtures/histopheno.json +++ b/frontend/fixtures/histopheno.json @@ -3,102 +3,102 @@ "items": [ { "label": "musculature", - "count": 962, + "count": 1756, "id": "HP:0003011" }, { "label": "nervous_system", - "count": 628, + "count": 1130, "id": "HP:0000707" }, { "label": "head_neck", - "count": 366, + "count": 602, "id": "HP:0000152" }, { "label": "skeletal_system", - "count": 244, + "count": 493, "id": "HP:0000924" }, - { - "label": "eye", - "count": 191, - "id": "HP:0000478" - }, { "label": "respiratory", - "count": 177, + "count": 320, "id": "HP:0002086" }, { - "label": "metabolism_homeostasis", - "count": 126, - "id": "HP:0001939" + "label": "eye", + "count": 300, + "id": "HP:0000478" }, { - "label": "blood", - "count": 113, - "id": "HP:0001871" + "label": "metabolism_homeostasis", + "count": 221, + "id": "HP:0001939" }, { "label": "cardiovascular_system", - "count": 96, + "count": 185, "id": "HP:0001626" }, { - "label": "connective_tissue", - "count": 87, - "id": "HP:0003549" + "label": "blood", + "count": 184, + "id": "HP:0001871" }, { - "label": "digestive_system", - "count": 68, - "id": "HP:0025031" + "label": "connective_tissue", + "count": 165, + "id": "HP:0003549" }, { "label": "neoplasm", - "count": 68, + "count": 150, "id": "HP:0002664" }, { - "label": "integument", - "count": 20, - "id": "HP:0001574" + "label": "digestive_system", + "count": 144, + "id": "HP:0025031" }, { - "label": "ear", - "count": 19, - "id": "HP:0000598" + "label": "integument", + "count": 48, + "id": "HP:0001574" }, { "label": "genitourinary_system", - "count": 18, + "count": 44, "id": "HP:0000119" }, { "label": "growth", - "count": 14, + "count": 33, "id": "HP:0001507" }, + { + "label": "ear", + "count": 28, + "id": "HP:0000598" + }, + { + "label": "endocrine", + "count": 26, + "id": "HP:0000818" + }, { "label": "immune_system", - "count": 12, + "count": 22, "id": "HP:0002715" }, { "label": "prenatal_or_birth", - "count": 10, + "count": 21, "id": "HP:0001197" }, - { - "label": "endocrine", - "count": 8, - "id": "HP:0000818" - }, { "label": "breast", - "count": 0, + "count": 1, "id": "HP:0000769" } ] diff --git a/frontend/fixtures/node.json b/frontend/fixtures/node.json index 6b7d7328a..3658bcac1 100644 --- a/frontend/fixtures/node.json +++ b/frontend/fixtures/node.json @@ -21,21 +21,26 @@ "association_counts": [ { "label": "Phenotypes", - "count": 2166, + "count": 4027, "category": "biolink:DiseaseToPhenotypicFeatureAssociation" }, { "label": "Causal Genes", "count": 124, "category": "biolink:CausalGeneToDiseaseAssociation" + }, + { + "label": "Correlated Genes", + "count": 151, + "category": "biolink:CorrelatedGeneToDiseaseAssociation" } ], "node_hierarchy": { "super_classes": [ { - "id": "MONDO:0005336", + "id": "MONDO:0019056", "category": "biolink:Disease", - "name": "myopathy", + "name": "neuromuscular disease", "full_name": null, "description": null, "xref": [], @@ -46,9 +51,9 @@ "synonym": [] }, { - "id": "MONDO:0019056", + "id": "MONDO:0700223", "category": "biolink:Disease", - "name": "neuromuscular disease", + "name": "hereditary skeletal muscle disorder", "full_name": null, "description": null, "xref": [], @@ -59,9 +64,9 @@ "synonym": [] }, { - "id": "MONDO:0700223", + "id": "MONDO:0005336", "category": "biolink:Disease", - "name": "hereditary skeletal muscle disorder", + "name": "myopathy", "full_name": null, "description": null, "xref": [], diff --git a/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json index b19a253ec..47898790d 100644 --- a/frontend/fixtures/phenotype-explorer-compare.json +++ b/frontend/fixtures/phenotype-explorer-compare.json @@ -1,4291 +1,106 @@ { "subject_termset": { - "HP:0200055": { - "id": "HP:0200055", - "label": "Small hand (HPO)" + "MP:0002169": { + "id": "MP:0002169", + "label": "no abnormal phenotype detected (MPO)" }, - "HP:0008065": { - "id": "HP:0008065", - "label": "Aplasia/Hypoplasia of the skin (HPO)" - }, - "HP:0002209": { - "id": "HP:0002209", - "label": "Sparse scalp hair (HPO)" - }, - "HP:0002861": { - "id": "HP:0002861", - "label": "Melanoma (HPO)" - }, - "HP:0000275": { - "id": "HP:0000275", - "label": "Narrow face (HPO)" - }, - "HP:0001608": { - "id": "HP:0001608", - "label": "Abnormality of the voice (HPO)" - }, - "HP:0005177": { - "id": "HP:0005177", - "label": "Premature arteriosclerosis (HPO)" - }, - "HP:0001635": { - "id": "HP:0001635", - "label": "Congestive heart failure (HPO)" - }, - "HP:0003777": { - "id": "HP:0003777", - "label": "Pili torti (HPO)" - }, - "HP:0000518": { - "id": "HP:0000518", - "label": "Cataract (HPO)" - }, - "HP:0002216": { - "id": "HP:0002216", - "label": "Premature graying of hair (HPO)" - }, - "HP:0004322": { - "id": "HP:0004322", - "label": "Short stature (HPO)" - }, - "HP:0010721": { - "id": "HP:0010721", - "label": "Abnormal hair whorl (HPO)" - }, - "HP:0001601": { - "id": "HP:0001601", - "label": "Laryngomalacia (HPO)" - }, - "HP:0001620": { - "id": "HP:0001620", - "label": "High pitched voice (HPO)" - }, - "HP:0000819": { - "id": "HP:0000819", - "label": "Diabetes mellitus (HPO)" - }, - "HP:0000869": { - "id": "HP:0000869", - "label": "Secondary amenorrhea (HPO)" - }, - "HP:0002669": { - "id": "HP:0002669", - "label": "Osteosarcoma (HPO)" - }, - "HP:0002858": { - "id": "HP:0002858", - "label": "Meningioma (HPO)" - }, - "HP:0002211": { - "id": "HP:0002211", - "label": "White forelock (HPO)" - }, - "HP:0002155": { - "id": "HP:0002155", - "label": "Hypertriglyceridemia (HPO)" - }, - "HP:0004349": { - "id": "HP:0004349", - "label": "Reduced bone mineral density (HPO)" - }, - "HP:0001533": { - "id": "HP:0001533", - "label": "Slender build (HPO)" - }, - "HP:0009726": { - "id": "HP:0009726", - "label": "Renal neoplasm (HPO)" - }, - "HP:0005978": { - "id": "HP:0005978", - "label": "Type II diabetes mellitus (HPO)" - }, - "HP:0007703": { - "id": "HP:0007703", - "label": "Abnormality of retinal pigmentation (HPO)" - }, - "HP:0100324": { - "id": "HP:0100324", - "label": "Scleroderma (HPO)" - }, - "HP:0100578": { - "id": "HP:0100578", - "label": "Lipoatrophy (HPO)" - }, - "HP:0012056": { - "id": "HP:0012056", - "label": "Cutaneous melanoma (HPO)" - }, - "HP:0002621": { - "id": "HP:0002621", - "label": "Atherosclerosis (HPO)" - }, - "HP:0001838": { - "id": "HP:0001838", - "label": "Rocker bottom foot (HPO)" - }, - "HP:0007618": { - "id": "HP:0007618", - "label": "Subcutaneous calcification (HPO)" - }, - "HP:0031956": { - "id": "HP:0031956", - "label": "Elevated circulating aspartate aminotransferase concentration (HPO)" - }, - "HP:0002293": { - "id": "HP:0002293", - "label": "Alopecia of scalp (HPO)" - }, - "HP:0003419": { - "id": "HP:0003419", - "label": "Low back pain (HPO)" - }, - "HP:0000962": { - "id": "HP:0000962", - "label": "Hyperkeratosis (HPO)" - }, - "HP:0012060": { - "id": "HP:0012060", - "label": "Acral lentiginous melanoma (HPO)" - }, - "HP:0000939": { - "id": "HP:0000939", - "label": "Osteoporosis (HPO)" - }, - "HP:0003202": { - "id": "HP:0003202", - "label": "Skeletal muscle atrophy (HPO)" - }, - "HP:0010468": { - "id": "HP:0010468", - "label": "Aplasia/Hypoplasia of the testes (HPO)" - }, - "HP:0000546": { - "id": "HP:0000546", - "label": "Retinal degeneration (HPO)" - }, - "HP:0100649": { - "id": "HP:0100649", - "label": "Neoplasm of the oral cavity (HPO)" - }, - "HP:0002860": { - "id": "HP:0002860", - "label": "Squamous cell carcinoma (HPO)" - }, - "HP:0003002": { - "id": "HP:0003002", - "label": "Breast carcinoma (HPO)" - }, - "HP:0000035": { - "id": "HP:0000035", - "label": "Abnormal testis morphology (HPO)" - }, - "HP:0009125": { - "id": "HP:0009125", - "label": "Lipodystrophy (HPO)" - }, - "HP:0100526": { - "id": "HP:0100526", - "label": "Neoplasm of the lung (HPO)" - }, - "HP:0200042": { - "id": "HP:0200042", - "label": "Skin ulcer (HPO)" - }, - "HP:0004415": { - "id": "HP:0004415", - "label": "Pulmonary artery stenosis (HPO)" - }, - "HP:0002890": { - "id": "HP:0002890", - "label": "Thyroid carcinoma (HPO)" - }, - "HP:0007495": { - "id": "HP:0007495", - "label": "Prematurely aged appearance (HPO)" - }, - "HP:0000765": { - "id": "HP:0000765", - "label": "Abnormal thorax morphology (HPO)" - }, - "HP:0011001": { - "id": "HP:0011001", - "label": "Increased bone mineral density (HPO)" - }, - "HP:0000444": { - "id": "HP:0000444", - "label": "Convex nasal ridge (HPO)" - }, - "HP:0000135": { - "id": "HP:0000135", - "label": "Hypogonadism (HPO)" - }, - "HP:0000822": { - "id": "HP:0000822", - "label": "Hypertension (HPO)" - }, - "HP:0000934": { - "id": "HP:0000934", - "label": "Chondrocalcinosis (HPO)" - }, - "HP:0100242": { - "id": "HP:0100242", - "label": "Sarcoma (HPO)" - }, - "HP:0100615": { - "id": "HP:0100615", - "label": "Ovarian neoplasm (HPO)" - }, - "HP:0100585": { - "id": "HP:0100585", - "label": "Telangiectasia of the skin (HPO)" - }, - "HP:0100659": { - "id": "HP:0100659", - "label": "Abnormal cerebral vascular morphology (HPO)" - }, - "HP:0000320": { - "id": "HP:0000320", - "label": "Bird-like facies (HPO)" - }, - "HP:0040217": { - "id": "HP:0040217", - "label": "Elevated hemoglobin A1c (HPO)" - }, - "HP:0000855": { - "id": "HP:0000855", - "label": "Insulin resistance (HPO)" - }, - "HP:0001387": { - "id": "HP:0001387", - "label": "Joint stiffness (HPO)" - }, - "HP:0031964": { - "id": "HP:0031964", - "label": "Elevated circulating alanine aminotransferase concentration (HPO)" - }, - "HP:0100833": { - "id": "HP:0100833", - "label": "Neoplasm of the small intestine (HPO)" - }, - "HP:0002672": { - "id": "HP:0002672", - "label": "Gastrointestinal carcinoma (HPO)" - }, - "HP:0005328": { - "id": "HP:0005328", - "label": "Progeroid facial appearance (HPO)" - }, - "HP:0000144": { - "id": "HP:0000144", - "label": "Decreased fertility (HPO)" - }, - "HP:0002664": { - "id": "HP:0002664", - "label": "Neoplasm (HPO)" - }, - "HP:0100679": { - "id": "HP:0100679", - "label": "Lack of skin elasticity (HPO)" + "MP:0010771": { + "id": "MP:0010771", + "label": "integument phenotype (MPO)" } }, "object_termset": { - "HP:0012378": { - "id": "HP:0012378", - "label": "Fatigue (HPO)" - }, - "HP:0002315": { - "id": "HP:0002315", - "label": "Headache (HPO)" - }, - "HP:0000023": { - "id": "HP:0000023", - "label": "Inguinal hernia (HPO)" - }, - "HP:0001653": { - "id": "HP:0001653", - "label": "Mitral regurgitation (HPO)" - }, - "HP:0001760": { - "id": "HP:0001760", - "label": "Abnormal foot morphology (HPO)" - }, - "HP:0005294": { - "id": "HP:0005294", - "label": "Arterial dissection (HPO)" - }, - "HP:0006243": { - "id": "HP:0006243", - "label": "Phalangeal dislocation (HPO)" - }, - "HP:0001704": { - "id": "HP:0001704", - "label": "Tricuspid valve prolapse (HPO)" - }, - "HP:0003771": { - "id": "HP:0003771", - "label": "Pulp calcification (HPO)" - }, - "HP:0001075": { - "id": "HP:0001075", - "label": "Atrophic scars (HPO)" - }, - "HP:0012450": { - "id": "HP:0012450", - "label": "Chronic constipation (HPO)" - }, - "HP:0000993": { - "id": "HP:0000993", - "label": "Molluscoid pseudotumors (HPO)" - }, - "HP:0001634": { - "id": "HP:0001634", - "label": "Mitral valve prolapse (HPO)" - }, - "HP:0001073": { - "id": "HP:0001073", - "label": "Cigarette-paper scars (HPO)" - }, - "HP:0000978": { - "id": "HP:0000978", - "label": "Bruising susceptibility (HPO)" - }, - "HP:0001065": { - "id": "HP:0001065", - "label": "Striae distensae (HPO)" - }, - "HP:0000286": { - "id": "HP:0000286", - "label": "Epicanthus (HPO)" - }, - "HP:0003083": { - "id": "HP:0003083", - "label": "Dislocated radial head (HPO)" - }, - "HP:0004872": { - "id": "HP:0004872", - "label": "Incisional hernia (HPO)" - }, - "HP:0004944": { - "id": "HP:0004944", - "label": "Dilatation of the cerebral artery (HPO)" - }, - "HP:0002035": { - "id": "HP:0002035", - "label": "Rectal prolapse (HPO)" - }, - "HP:0002616": { - "id": "HP:0002616", - "label": "Aortic root aneurysm (HPO)" - }, - "HP:0002761": { - "id": "HP:0002761", - "label": "Generalized joint laxity (HPO)" - }, - "HP:0009763": { - "id": "HP:0009763", - "label": "Limb pain (HPO)" - }, - "HP:0025014": { - "id": "HP:0025014", - "label": "Subcutaneous spheroids (HPO)" - }, - "HP:0001252": { - "id": "HP:0001252", - "label": "Hypotonia (HPO)" - }, - "HP:0031653": { - "id": "HP:0031653", - "label": "Abnormal heart valve physiology (HPO)" - }, - "HP:0001058": { - "id": "HP:0001058", - "label": "Poor wound healing (HPO)" - }, - "HP:0002829": { - "id": "HP:0002829", - "label": "Arthralgia (HPO)" - }, - "HP:0001324": { - "id": "HP:0001324", - "label": "Muscle weakness (HPO)" - }, - "HP:0003394": { - "id": "HP:0003394", - "label": "Muscle spasm (HPO)" - }, - "HP:0001537": { - "id": "HP:0001537", - "label": "Umbilical hernia (HPO)" - }, - "HP:0010750": { - "id": "HP:0010750", - "label": "Dermatochalasis (HPO)" - }, - "HP:0002999": { - "id": "HP:0002999", - "label": "Patellar dislocation (HPO)" - }, - "HP:0010754": { - "id": "HP:0010754", - "label": "Abnormality of the temporomandibular joint (HPO)" - }, - "HP:0031364": { - "id": "HP:0031364", - "label": "Ecchymosis (HPO)" - }, - "HP:0000974": { - "id": "HP:0000974", - "label": "Hyperextensible skin (HPO)" - }, - "HP:0001030": { - "id": "HP:0001030", - "label": "Fragile skin (HPO)" - }, - "HP:0000481": { - "id": "HP:0000481", - "label": "Abnormal cornea morphology (HPO)" - }, - "HP:0003834": { - "id": "HP:0003834", - "label": "Shoulder dislocation (HPO)" - }, - "HP:0000938": { - "id": "HP:0000938", - "label": "Osteopenia (HPO)" - }, - "HP:0003010": { - "id": "HP:0003010", - "label": "Prolonged bleeding time (HPO)" - }, - "HP:0007495": { - "id": "HP:0007495", - "label": "Prematurely aged appearance (HPO)" - }, - "HP:0001763": { - "id": "HP:0001763", - "label": "Pes planus (HPO)" - }, - "HP:0010749": { - "id": "HP:0010749", - "label": "Blepharochalasis (HPO)" - }, - "HP:0002020": { - "id": "HP:0002020", - "label": "Gastroesophageal reflux (HPO)" - }, - "HP:0030009": { - "id": "HP:0030009", - "label": "Cervical insufficiency (HPO)" - }, - "HP:0000139": { - "id": "HP:0000139", - "label": "Uterine prolapse (HPO)" - }, - 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"HP:0001278", - "label": "Orthostatic hypotension (HPO)" - }, - "HP:0002036": { - "id": "HP:0002036", - "label": "Hiatus hernia (HPO)" - }, - "HP:0000015": { - "id": "HP:0000015", - "label": "Bladder diverticulum (HPO)" - }, - "HP:0002018": { - "id": "HP:0002018", - "label": "Nausea (HPO)" - }, - "HP:0001788": { - "id": "HP:0001788", - "label": "Premature rupture of membranes (HPO)" - }, - "HP:0001270": { - "id": "HP:0001270", - "label": "Motor delay (HPO)" + "HP:0004325": { + "id": "HP:0004325", + "label": "Decreased body weight (HPO)" } }, "subject_best_matches": { - "HP:0000035": { - "match_source": "HP:0000035", - "match_source_label": "Abnormal testis morphology (HPO)", - "match_target": "HP:0030009", - "match_target_label": "Cervical insufficiency (HPO)", - "score": 10.48204782739082, - "match_subsumer": null, - "match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0000035", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0030009", - 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"match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0006243", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0001838", - "object_label": null, - "object_source": null, - "ancestor_id": "HP:0001367", - "ancestor_label": "", - "ancestor_source": null, - "object_information_content": null, - "subject_information_content": null, - "ancestor_information_content": 9.004930281885281, - "jaccard_similarity": 0.40625, - "cosine_similarity": null, - "dice_similarity": null, - "phenodigm_score": 1.91265598762974 - } - }, - "HP:0007495": { - "match_source": "HP:0007495", - "match_source_label": "Prematurely aged appearance (HPO)", - "match_target": "HP:0005328", - "match_target_label": "Progeroid facial appearance (HPO)", - "score": 14.418232729793377, - "match_subsumer": null, - "match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0007495", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0005328", - "object_label": null, - "object_source": null, - "ancestor_id": "HP:0007495", - "ancestor_label": "Prematurely aged appearance (HPO)", - "ancestor_source": null, - "object_information_content": null, - "subject_information_content": null, - "ancestor_information_content": 14.418232729793377, - "jaccard_similarity": 0.972972972972973, - "cosine_similarity": null, - "dice_similarity": null, - "phenodigm_score": 3.7454706999419027 - } - }, - "HP:0009763": { - "match_source": "HP:0009763", - "match_source_label": "Limb pain (HPO)", - "match_target": "HP:0003419", - "match_target_label": "Low back pain (HPO)", - "score": 12.074278328576016, - "match_subsumer": null, - "match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0009763", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0003419", - "object_label": null, - "object_source": null, - "ancestor_id": "HP:0012531", - "ancestor_label": "", - "ancestor_source": null, - "object_information_content": null, - "subject_information_content": null, - "ancestor_information_content": 12.074278328576016, - "jaccard_similarity": 0.5185185185185185, - "cosine_similarity": null, - "dice_similarity": null, - "phenodigm_score": 2.5021464607639357 - } - }, - "HP:0010749": { - "match_source": "HP:0010749", - "match_source_label": "Blepharochalasis (HPO)", - "match_target": "HP:0000275", - "match_target_label": "Narrow face (HPO)", - "score": 12.311317525876866, - "match_subsumer": null, - "match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0010749", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0000275", - "object_label": null, - "object_source": null, - "ancestor_id": "HP:0001999", - "ancestor_label": "", - "ancestor_source": null, - "object_information_content": null, - "subject_information_content": null, - "ancestor_information_content": 12.311317525876866, - "jaccard_similarity": 0.37735849056603776, - "cosine_similarity": null, - "dice_similarity": null, - "phenodigm_score": 2.1554072001466684 - } - }, - "HP:0010750": { - "match_source": "HP:0010750", - "match_source_label": "Dermatochalasis (HPO)", - "match_target": "HP:0000546", - "match_target_label": "Retinal degeneration (HPO)", - "score": 7.709281511796768, - "match_subsumer": null, - "match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0010750", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0000546", - "object_label": null, - "object_source": null, - "ancestor_id": "HP:0000315", - "ancestor_label": "", - "ancestor_source": null, - "object_information_content": null, - "subject_information_content": null, - "ancestor_information_content": 7.709281511796768, - "jaccard_similarity": 0.57, - "cosine_similarity": null, - "dice_similarity": null, - "phenodigm_score": 2.096256296764343 - } - }, - "HP:0010754": { - "match_source": "HP:0010754", - "match_source_label": "Abnormality of the temporomandibular joint (HPO)", - "match_target": "HP:0100649", - "match_target_label": "Neoplasm of the oral cavity (HPO)", - "score": 9.152888163272383, - "match_subsumer": null, - "match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0010754", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0100649", - "object_label": null, - "object_source": null, - "ancestor_id": "HP:0031816", - "ancestor_label": "", - "ancestor_source": null, - "object_information_content": null, - "subject_information_content": null, - "ancestor_information_content": 9.152888163272383, - "jaccard_similarity": 0.41353383458646614, - "cosine_similarity": null, - "dice_similarity": null, - "phenodigm_score": 1.9455150833902846 - } - }, - "HP:0012378": { - "match_source": "HP:0012378", - "match_source_label": "Fatigue (HPO)", - "match_target": "HP:0003419", - "match_target_label": "Low back pain (HPO)", - "score": 11.324256581584363, - "match_subsumer": null, - "match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0012378", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0003419", - "object_label": null, - "object_source": null, - "ancestor_id": "HP:0025142", - "ancestor_label": "", - "ancestor_source": null, - "object_information_content": null, - "subject_information_content": null, - "ancestor_information_content": 11.324256581584363, - "jaccard_similarity": 0.36, - "cosine_similarity": null, - "dice_similarity": null, - "phenodigm_score": 2.0190919665459446 - } - }, - "HP:0012450": { - "match_source": "HP:0012450", - "match_source_label": "Chronic constipation (HPO)", - "match_target": "HP:0002672", - "match_target_label": "Gastrointestinal carcinoma (HPO)", - "score": 7.826350815132431, - "match_subsumer": null, - "match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0012450", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0002672", - "object_label": null, - "object_source": null, - "ancestor_id": "HP:0025031", - "ancestor_label": "", - "ancestor_source": null, - "object_information_content": null, - "subject_information_content": null, - "ancestor_information_content": 7.826350815132431, - "jaccard_similarity": 0.5106382978723404, - "cosine_similarity": null, - "dice_similarity": null, - "phenodigm_score": 1.9991084159672352 - } - }, - "HP:0025014": { - "match_source": "HP:0025014", - "match_source_label": "Subcutaneous spheroids (HPO)", - "match_target": "HP:0200042", - "match_target_label": "Skin ulcer (HPO)", - "score": 10.72635502515571, - "match_subsumer": null, - "match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0025014", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0200042", - "object_label": null, - "object_source": null, - "ancestor_id": "HP:0011355", - "ancestor_label": "", - "ancestor_source": null, - "object_information_content": null, - "subject_information_content": null, - "ancestor_information_content": 10.72635502515571, - "jaccard_similarity": 0.8974358974358975, - "cosine_similarity": null, - "dice_similarity": null, - "phenodigm_score": 3.102614389223492 - } - }, - "HP:0025019": { - "match_source": "HP:0025019", - "match_source_label": "Arterial rupture (HPO)", - "match_target": "HP:0001635", - "match_target_label": "Congestive heart failure (HPO)", - "score": 9.47121402147955, - "match_subsumer": null, - "match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0025019", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0001635", - "object_label": null, - "object_source": null, - "ancestor_id": "HP:0011025", - "ancestor_label": "", - "ancestor_source": null, - "object_information_content": null, - "subject_information_content": null, - "ancestor_information_content": 9.47121402147955, - "jaccard_similarity": 0.42028985507246375, - "cosine_similarity": null, - "dice_similarity": null, - "phenodigm_score": 1.995157930703213 - } - }, - "HP:0025509": { - "match_source": "HP:0025509", - "match_source_label": "Piezogenic pedal papules (HPO)", - "match_target": "HP:0008065", - "match_target_label": "Aplasia/Hypoplasia of the skin (HPO)", - "score": 10.72635502515571, - "match_subsumer": null, - "match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0025509", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0008065", - "object_label": null, - "object_source": null, - "ancestor_id": "HP:0011355", - "ancestor_label": "", - "ancestor_source": null, - "object_information_content": null, - "subject_information_content": null, - "ancestor_information_content": 10.72635502515571, - "jaccard_similarity": 0.8536585365853658, - "cosine_similarity": null, - "dice_similarity": null, - "phenodigm_score": 3.025994800667957 - } - }, - "HP:0030009": { - "match_source": "HP:0030009", - "match_source_label": "Cervical insufficiency (HPO)", - "match_target": "HP:0100615", - "match_target_label": "Ovarian neoplasm (HPO)", - "score": 11.350488123157543, - "match_subsumer": null, - "match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0030009", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0100615", - "object_label": null, - "object_source": null, - "ancestor_id": "HP:0000008", - "ancestor_label": "", - "ancestor_source": null, - "object_information_content": null, - "subject_information_content": null, - "ancestor_information_content": 11.350488123157543, - "jaccard_similarity": 0.6301369863013698, - "cosine_similarity": null, - "dice_similarity": null, - "phenodigm_score": 2.674390094764783 - } - }, - "HP:0031364": { - "match_source": "HP:0031364", - "match_source_label": "Ecchymosis (HPO)", - "match_target": "HP:0007618", - "match_target_label": "Subcutaneous calcification (HPO)", - "score": 14.533709947213314, - "match_subsumer": null, - "match_subsumer_label": null, - "similarity": { - "subject_id": "HP:0031364", - "subject_label": null, - "subject_source": null, - "object_id": "HP:0007618", - "object_label": null, - "object_source": null, - "ancestor_id": "UBERON:0011818", - "ancestor_label": "", - "ancestor_source": null, - "object_information_content": null, - "subject_information_content": null, - "ancestor_information_content": 14.533709947213314, - "jaccard_similarity": 0.4222222222222222, - "cosine_similarity": null, - "dice_similarity": null, - "phenodigm_score": 2.47718697539076 - } - }, - "HP:0031653": { - "match_source": "HP:0031653", - "match_source_label": "Abnormal heart valve physiology (HPO)", - "match_target": "HP:0001635", - "match_target_label": "Congestive heart failure (HPO)", - "score": 9.47121402147955, + } + }, + "object_best_matches": { + "HP:0004325": { + "match_source": "HP:0004325", + "match_source_label": "Decreased body weight (HPO)", + "match_target": "MP:0010771", + "match_target_label": "integument phenotype (MPO)", + "score": 1.4431977534690428, "match_subsumer": null, "match_subsumer_label": null, "similarity": { - "subject_id": "HP:0031653", + "subject_id": "HP:0004325", "subject_label": null, "subject_source": null, - "object_id": "HP:0001635", + "object_id": "MP:0010771", "object_label": null, "object_source": null, - "ancestor_id": "HP:0011025", + "ancestor_id": "UPHENO:0001003", "ancestor_label": "", "ancestor_source": null, "object_information_content": null, "subject_information_content": null, - "ancestor_information_content": 9.47121402147955, - "jaccard_similarity": 0.3972602739726027, + "ancestor_information_content": 1.4431977534690428, + "jaccard_similarity": 0.3333333333333333, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.9397260314348834 + "phenodigm_score": 0.6935891563620457 } } }, - "average_score": 9.923734289544301, - "best_score": 17.11867244793447, + "average_score": 1.4431977534690428, + "best_score": 1.4431977534690428, "metric": "ancestor_information_content" } diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts index fdbb5e69e..eca5afefd 100644 --- a/frontend/src/api/model.ts +++ b/frontend/src/api/model.ts @@ -24,6 +24,7 @@ export enum AssociationDirectionEnum { export interface Association { id: string, + category?: string, subject: string, original_subject?: string, /** The namespace/prefix of the subject entity */ @@ -55,21 +56,24 @@ export interface Association { object_taxon_label?: string, primary_knowledge_source?: string, aggregator_knowledge_source?: string[], - category?: string, negated?: boolean, + pathway?: string, + /** count of supporting documents, evidence codes, and sources supplying evidence */ + evidence_count?: number, + has_evidence?: string[], + /** List of ExpandedCuries with id and url for evidence */ + has_evidence_links?: ExpandedCurie[], provided_by?: string, /** A link to the docs for the knowledge source that provided the node/edge. */ provided_by_link?: ExpandedCurie, publications?: string[], + /** List of ExpandedCuries with id and url for publications */ + publications_links?: ExpandedCurie[], qualifiers?: string[], frequency_qualifier?: string, - has_evidence?: string[], onset_qualifier?: string, sex_qualifier?: string, stage_qualifier?: string, - /** count of supporting documents, evidence codes, and sources supplying evidence */ - evidence_count?: number, - pathway?: string, /** The name of the frequency_qualifier entity */ frequency_qualifier_label?: string, /** The namespace/prefix of the frequency_qualifier entity */ @@ -180,6 +184,7 @@ export interface DirectionalAssociation extends Association { /** The directionality of the association relative to a given entity for an association_count. If the entity is the subject or in the subject closure, the direction is forwards, if it is the object or in the object closure, the direction is backwards. */ direction: string, id: string, + category?: string, subject: string, original_subject?: string, /** The namespace/prefix of the subject entity */ @@ -211,21 +216,24 @@ export interface DirectionalAssociation extends Association { object_taxon_label?: string, primary_knowledge_source?: string, aggregator_knowledge_source?: string[], - category?: string, negated?: boolean, + pathway?: string, + /** count of supporting documents, evidence codes, and sources supplying evidence */ + evidence_count?: number, + has_evidence?: string[], + /** List of ExpandedCuries with id and url for evidence */ + has_evidence_links?: ExpandedCurie[], provided_by?: string, /** A link to the docs for the knowledge source that provided the node/edge. */ provided_by_link?: ExpandedCurie, publications?: string[], + /** List of ExpandedCuries with id and url for publications */ + publications_links?: ExpandedCurie[], qualifiers?: string[], frequency_qualifier?: string, - has_evidence?: string[], onset_qualifier?: string, sex_qualifier?: string, stage_qualifier?: string, - /** count of supporting documents, evidence codes, and sources supplying evidence */ - evidence_count?: number, - pathway?: string, /** The name of the frequency_qualifier entity */ frequency_qualifier_label?: string, /** The namespace/prefix of the frequency_qualifier entity */ diff --git a/frontend/src/pages/metadata.json b/frontend/src/pages/metadata.json index 92e06651e..016c23d13 100644 --- a/frontend/src/pages/metadata.json +++ b/frontend/src/pages/metadata.json @@ -3,7 +3,7 @@ { "label": "Genes", "icon": "category-gene", - "count": 565986 + "count": 558334 }, { "label": "Phenotypes", @@ -18,29 +18,29 @@ { "label": "Total Nodes", "icon": "node", - "count": 806761 + "count": 838004 } ], "association": [ { "label": "Gene to Disease", "icon": "association-gene-to-disease", - "count": 7092 + "count": 15032 }, { "label": "Gene to Phenotype", "icon": "association-gene-to-phenotype", - "count": 832349 + "count": 881975 }, { "label": "Disease to Phenotype", "icon": "association-disease-to-phenotype", - "count": 129270 + "count": 240274 }, { "label": "Total Associations", "icon": "association", - "count": 8260697 + "count": 10049533 } ] } diff --git a/frontend/src/pages/node/SectionAssociationDetails.vue b/frontend/src/pages/node/SectionAssociationDetails.vue index fccba5091..248d0c23a 100644 --- a/frontend/src/pages/node/SectionAssociationDetails.vue +++ b/frontend/src/pages/node/SectionAssociationDetails.vue @@ -35,10 +35,11 @@ :full="true" > - {{ source }}{{ source.id }} @@ -60,12 +61,13 @@ :full="true" > - - {{ publication }} - + {{ publication.id }} +