From 97f82a0d05ed5a9a96f804f88a02135129ecc03e Mon Sep 17 00:00:00 2001
From: Sierra Moxon <sierra.taylor@gmail.com>
Date: Thu, 12 Oct 2023 14:10:46 -0700
Subject: [PATCH] use merged.csv prefixmap so that FB and FlyBase are
 recognized prefixes (#382)

Addresses #383

---------

Co-authored-by: Kevin Schaper <kevinschaper@gmail.com>
---
 backend/poetry.lock                           | 412 ++++++++++++++++--
 backend/pyproject.toml                        |   6 +-
 .../src/monarch_py/service/curie_service.py   |   8 +-
 backend/tests/unit/test_curie_service.py      |  29 ++
 4 files changed, 413 insertions(+), 42 deletions(-)
 create mode 100644 backend/tests/unit/test_curie_service.py

diff --git a/backend/poetry.lock b/backend/poetry.lock
index bc8f92767..baf16c983 100644
--- a/backend/poetry.lock
+++ b/backend/poetry.lock
@@ -1,9 +1,10 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.4.0 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 = [
@@ -19,6 +20,7 @@ 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 = [
@@ -30,6 +32,7 @@ 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 = [
@@ -40,6 +43,7 @@ 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 = [
@@ -61,6 +65,7 @@ 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 = [
@@ -72,6 +77,7 @@ files = [
 name = "arrow"
 version = "1.2.3"
 description = "Better dates & times for Python"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -86,6 +92,7 @@ python-dateutil = ">=2.7.0"
 name = "attrs"
 version = "23.1.0"
 description = "Classes Without Boilerplate"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -104,6 +111,7 @@ 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 = [
@@ -115,6 +123,7 @@ files = [
 name = "bcp47"
 version = "0.0.4"
 description = "Language tags made easy"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -126,6 +135,7 @@ files = [
 name = "beautifulsoup4"
 version = "4.12.2"
 description = "Screen-scraping library"
+category = "main"
 optional = false
 python-versions = ">=3.6.0"
 files = [
@@ -144,6 +154,7 @@ lxml = ["lxml"]
 name = "bibtexparser"
 version = "1.4.1"
 description = "Bibtex parser for python 3"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -153,10 +164,42 @@ files = [
 [package.dependencies]
 pyparsing = ">=2.0.3"
 
+[[package]]
+name = "bioregistry"
+version = "0.10.57"
+description = "Integrated registry of biological databases and nomenclatures"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "bioregistry-0.10.57-py3-none-any.whl", hash = "sha256:b04494de6c43e51e495cbb531ab0b8aca08dbcfc0cfedeac13456e38bfdedae0"},
+    {file = "bioregistry-0.10.57.tar.gz", hash = "sha256:7054b5cfe4d02e346499a3d676ce7ea3448feb68714ba3aa622299a606293f5c"},
+]
+
+[package.dependencies]
+click = "*"
+curies = ">=0.6.0"
+more-click = ">=0.1.2"
+pydantic = "*"
+pystow = ">=0.1.13"
+requests = "*"
+tqdm = "*"
+
+[package.extras]
+align = ["beautifulsoup4", "class-resolver", "defusedxml", "fairsharing-client (>=0.1.0)", "pyyaml", "tabulate"]
+charts = ["jinja2", "matplotlib", "matplotlib-venn", "pandas", "seaborn"]
+docs = ["autodoc-pydantic", "sphinx", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
+export = ["ndex2", "pyyaml", "rdflib", "rdflib-jsonld"]
+gha = ["more-itertools"]
+health = ["click-default-group", "jinja2", "pandas", "pyyaml", "tabulate"]
+tests = ["coverage", "httpx", "more-itertools", "pytest"]
+web = ["bootstrap-flask (<=2.0.0)", "curies[fastapi]", "fastapi", "flask (<2.2.4)", "markdown", "pyyaml", "rdflib", "rdflib-endpoint", "rdflib-jsonld", "uvicorn", "werkzeug (<2.3.0)"]
+
 [[package]]
 name = "black"
 version = "22.12.0"
 description = "The uncompromising code formatter."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -188,10 +231,23 @@ d = ["aiohttp (>=3.7.4)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
+[[package]]
+name = "cachetools"
+version = "5.3.1"
+description = "Extensible memoizing collections and decorators"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "cachetools-5.3.1-py3-none-any.whl", hash = "sha256:95ef631eeaea14ba2e36f06437f36463aac3a096799e876ee55e5cdccb102590"},
+    {file = "cachetools-5.3.1.tar.gz", hash = "sha256:dce83f2d9b4e1f732a8cd44af8e8fab2dbe46201467fc98b3ef8f269092bf62b"},
+]
+
 [[package]]
 name = "cattrs"
 version = "23.1.2"
 description = "Composable complex class support for attrs and dataclasses."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -217,6 +273,7 @@ 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 = [
@@ -228,6 +285,7 @@ files = [
 name = "cffi"
 version = "1.15.1"
 description = "Foreign Function Interface for Python calling C code."
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -304,6 +362,7 @@ pycparser = "*"
 name = "cfgraph"
 version = "0.2.1"
 description = "rdflib collections flattening graph"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -317,6 +376,7 @@ 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 = [
@@ -328,6 +388,7 @@ 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 = [
@@ -412,6 +473,7 @@ files = [
 name = "class-resolver"
 version = "0.4.2"
 description = "Lookup and instantiate classes with style."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -438,6 +500,7 @@ 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 = [
@@ -452,6 +515,7 @@ 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 = [
@@ -463,6 +527,7 @@ 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 = [
@@ -487,6 +552,7 @@ 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 = [
@@ -504,6 +570,7 @@ 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 = [
@@ -514,10 +581,23 @@ files = [
 [package.dependencies]
 packaging = "*"
 
+[[package]]
+name = "distlib"
+version = "0.3.7"
+description = "Distribution utilities"
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "distlib-0.3.7-py2.py3-none-any.whl", hash = "sha256:2e24928bc811348f0feb63014e97aaae3037f2cf48712d51ae61df7fd6075057"},
+    {file = "distlib-0.3.7.tar.gz", hash = "sha256:9dafe54b34a028eafd95039d5e5d4851a13734540f1331060d31c9916e7147a8"},
+]
+
 [[package]]
 name = "docker"
 version = "6.1.3"
 description = "A Python library for the Docker Engine API."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -539,6 +619,7 @@ ssh = ["paramiko (>=2.4.3)"]
 name = "docutils"
 version = "0.18.1"
 description = "Docutils -- Python Documentation Utilities"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -550,6 +631,7 @@ files = [
 name = "editorconfig"
 version = "0.12.3"
 description = "EditorConfig File Locator and Interpreter for Python"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -561,6 +643,7 @@ files = [
 name = "errorhandler"
 version = "2.0.1"
 description = "A logging framework handler that tracks when messages above a certain level have been logged."
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -576,6 +659,7 @@ test = ["coveralls", "nose", "nose-cov", "nose-fixes"]
 name = "et-xmlfile"
 version = "1.1.0"
 description = "An implementation of lxml.xmlfile for the standard library"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -587,6 +671,7 @@ files = [
 name = "eutils"
 version = "0.6.0"
 description = "\"Python interface to NCBI's eutilities API\""
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -606,6 +691,7 @@ dev = ["flake8", "ipython", "mock", "pytest", "pytest-cov", "restview", "setupto
 name = "exceptiongroup"
 version = "1.1.3"
 description = "Backport of PEP 654 (exception groups)"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -620,6 +706,7 @@ test = ["pytest (>=6)"]
 name = "fake-useragent"
 version = "1.2.1"
 description = "Up-to-date simple useragent faker with real world database"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -634,6 +721,7 @@ importlib-resources = {version = ">=5.0", markers = "python_version < \"3.10\""}
 name = "fastapi"
 version = "0.103.1"
 description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -654,6 +742,7 @@ all = ["email-validator (>=2.0.0)", "httpx (>=0.23.0)", "itsdangerous (>=1.1.0)"
 name = "fastobo"
 version = "0.12.2"
 description = "Faultless AST for Open Biomedical Ontologies in Python."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -696,10 +785,28 @@ files = [
     {file = "fastobo-0.12.2.tar.gz", hash = "sha256:2f2779f70ac54874329dddc74cabd86fea88abe56c544c2238076c1d27fe045e"},
 ]
 
+[[package]]
+name = "filelock"
+version = "3.12.4"
+description = "A platform independent file lock."
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "filelock-3.12.4-py3-none-any.whl", hash = "sha256:08c21d87ded6e2b9da6728c3dff51baf1dcecf973b768ef35bcbc3447edb9ad4"},
+    {file = "filelock-3.12.4.tar.gz", hash = "sha256:2e6f249f1f3654291606e046b09f1fd5eac39b360664c27f5aad072012f8bcbd"},
+]
+
+[package.extras]
+docs = ["furo (>=2023.7.26)", "sphinx (>=7.1.2)", "sphinx-autodoc-typehints (>=1.24)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-timeout (>=2.1)"]
+typing = ["typing-extensions (>=4.7.1)"]
+
 [[package]]
 name = "fqdn"
 version = "1.5.1"
 description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4"
 files = [
@@ -711,6 +818,7 @@ files = [
 name = "free-proxy"
 version = "1.1.1"
 description = "Proxy scraper for further use"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -725,6 +833,7 @@ requests = "*"
 name = "funowl"
 version = "0.2.3"
 description = "Python rendering of the OWL Functional syntax"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -744,6 +853,7 @@ rfc3987 = "*"
 name = "ghp-import"
 version = "2.1.0"
 description = "Copy your docs directly to the gh-pages branch."
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -761,6 +871,7 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 name = "graphviz"
 version = "0.20.1"
 description = "Simple Python interface for Graphviz"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -777,6 +888,7 @@ test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>=
 name = "greenlet"
 version = "2.0.1"
 description = "Lightweight in-process concurrent programming"
+category = "main"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
 files = [
@@ -850,6 +962,7 @@ test = ["faulthandler", "objgraph", "psutil"]
 name = "griffe"
 version = "0.36.2"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -864,6 +977,7 @@ colorama = ">=0.4"
 name = "gunicorn"
 version = "21.2.0"
 description = "WSGI HTTP Server for UNIX"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -884,6 +998,7 @@ tornado = ["tornado (>=0.2)"]
 name = "h11"
 version = "0.14.0"
 description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -895,6 +1010,7 @@ files = [
 name = "habanero"
 version = "1.2.3"
 description = "Low Level Client for Crossref Search API"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -914,6 +1030,7 @@ test = ["pytest"]
 name = "hbreader"
 version = "0.9.1"
 description = "Honey Badger reader - a generic file/url/string open and read tool"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -925,6 +1042,7 @@ files = [
 name = "httpcore"
 version = "0.17.3"
 description = "A minimal low-level HTTP client."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -936,16 +1054,17 @@ files = [
 anyio = ">=3.0,<5.0"
 certifi = "*"
 h11 = ">=0.13,<0.15"
-sniffio = "==1.*"
+sniffio = ">=1.0.0,<2.0.0"
 
 [package.extras]
 http2 = ["h2 (>=3,<5)"]
-socks = ["socksio (==1.*)"]
+socks = ["socksio (>=1.0.0,<2.0.0)"]
 
 [[package]]
 name = "httptools"
 version = "0.6.0"
 description = "A collection of framework independent HTTP protocol utils."
+category = "dev"
 optional = false
 python-versions = ">=3.5.0"
 files = [
@@ -993,6 +1112,7 @@ test = ["Cython (>=0.29.24,<0.30.0)"]
 name = "httpx"
 version = "0.24.1"
 description = "The next generation HTTP client."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1008,14 +1128,15 @@ sniffio = "*"
 
 [package.extras]
 brotli = ["brotli", "brotlicffi"]
-cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"]
+cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10,<14)"]
 http2 = ["h2 (>=3,<5)"]
-socks = ["socksio (==1.*)"]
+socks = ["socksio (>=1.0.0,<2.0.0)"]
 
 [[package]]
 name = "idna"
 version = "3.4"
 description = "Internationalized Domain Names in Applications (IDNA)"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1027,6 +1148,7 @@ files = [
 name = "ijson"
 version = "3.2.3"
 description = "Iterative JSON parser with standard Python iterator interfaces"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1114,6 +1236,7 @@ files = [
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1125,6 +1248,7 @@ files = [
 name = "importlib-metadata"
 version = "6.8.0"
 description = "Read metadata from Python packages"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1144,6 +1268,7 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs
 name = "importlib-resources"
 version = "6.1.0"
 description = "Read resources from Python packages"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1162,6 +1287,7 @@ testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)",
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1173,6 +1299,7 @@ files = [
 name = "isbnlib"
 version = "3.10.14"
 description = "Extract, clean, transform, hyphenate and metadata for ISBNs (International Standard Book Number)."
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -1184,6 +1311,7 @@ files = [
 name = "isodate"
 version = "0.6.1"
 description = "An ISO 8601 date/time/duration parser and formatter"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1198,6 +1326,7 @@ six = "*"
 name = "isoduration"
 version = "20.11.0"
 description = "Operations with ISO 8601 durations"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1212,6 +1341,7 @@ arrow = ">=0.15.0"
 name = "jinja2"
 version = "3.1.2"
 description = "A very fast and expressive template engine."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1229,6 +1359,7 @@ i18n = ["Babel (>=2.7)"]
 name = "jsbeautifier"
 version = "1.14.9"
 description = "JavaScript unobfuscator and beautifier."
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1243,6 +1374,7 @@ six = ">=1.13.0"
 name = "json-flattener"
 version = "0.1.9"
 description = "Python library for denormalizing nested dicts or json objects to tables and back"
+category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -1258,6 +1390,7 @@ pyyaml = "*"
 name = "jsonasobj"
 version = "1.3.1"
 description = "JSON as python objects"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1269,6 +1402,7 @@ files = [
 name = "jsonasobj2"
 version = "1.0.4"
 description = "JSON as python objects - version 2"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1283,6 +1417,7 @@ hbreader = "*"
 name = "jsonpatch"
 version = "1.33"
 description = "Apply JSON-Patches (RFC 6902)"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
@@ -1297,6 +1432,7 @@ jsonpointer = ">=1.9"
 name = "jsonpath-ng"
 version = "1.6.0"
 description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming."
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1311,6 +1447,7 @@ ply = "*"
 name = "jsonpointer"
 version = "2.4"
 description = "Identify specific nodes in a JSON document (RFC 6901)"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
@@ -1322,6 +1459,7 @@ files = [
 name = "jsonschema"
 version = "4.19.1"
 description = "An implementation of JSON Schema validation for Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1351,6 +1489,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 name = "jsonschema-specifications"
 version = "2023.7.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1365,6 +1504,7 @@ referencing = ">=0.28.0"
 name = "kgcl-rdflib"
 version = "0.5.0"
 description = "Schema for the KGCL project."
+category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -1380,6 +1520,7 @@ linkml-runtime = ">=1.1.24"
 name = "kgcl-schema"
 version = "0.6.0"
 description = "Schema for the KGCL project."
+category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -1397,6 +1538,7 @@ prefixmaps = ">=0.1.5,<0.2.0"
 name = "lark"
 version = "1.1.7"
 description = "a modern parsing library"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1414,6 +1556,7 @@ regex = ["regex"]
 name = "linkml"
 version = "1.5.7"
 description = "Linked Open Data Modeling Language"
+category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
@@ -1451,6 +1594,7 @@ watchdog = ">=0.9.0"
 name = "linkml-dataops"
 version = "0.1.0"
 description = "LinkML Data Operations API"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1469,6 +1613,7 @@ linkml-runtime = ">=1.1.6"
 name = "linkml-renderer"
 version = "0.3.0"
 description = "linkml-renderer"
+category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -1486,6 +1631,7 @@ pydantic = "*"
 name = "linkml-runtime"
 version = "1.5.7"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
+category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
@@ -1512,6 +1658,7 @@ requests = "*"
 name = "loguru"
 version = "0.7.2"
 description = "Python logging made (stupidly) simple"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1530,6 +1677,7 @@ dev = ["Sphinx (==7.2.5)", "colorama (==0.4.5)", "colorama (==0.4.6)", "exceptio
 name = "lxml"
 version = "4.9.3"
 description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API."
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*"
 files = [
@@ -1637,6 +1785,7 @@ source = ["Cython (>=0.29.35)"]
 name = "manubot"
 version = "0.5.6"
 description = "\"Python utilities for Manubot: Manuscripts, open and automated\""
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1667,6 +1816,7 @@ webpage = ["opentimestamps-client"]
 name = "markdown"
 version = "3.4.4"
 description = "Python implementation of John Gruber's Markdown."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1685,6 +1835,7 @@ testing = ["coverage", "pyyaml"]
 name = "markdown-it-py"
 version = "3.0.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1709,6 +1860,7 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 name = "markupsafe"
 version = "2.1.3"
 description = "Safely add untrusted strings to HTML/XML markup."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1732,16 +1884,6 @@ files = [
     {file = "MarkupSafe-2.1.3-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:5bbe06f8eeafd38e5d0a4894ffec89378b6c6a625ff57e3028921f8ff59318ac"},
     {file = "MarkupSafe-2.1.3-cp311-cp311-win32.whl", hash = "sha256:dd15ff04ffd7e05ffcb7fe79f1b98041b8ea30ae9234aed2a9168b5797c3effb"},
     {file = "MarkupSafe-2.1.3-cp311-cp311-win_amd64.whl", hash = "sha256:134da1eca9ec0ae528110ccc9e48041e0828d79f24121a1a146161103c76e686"},
-    {file = "MarkupSafe-2.1.3-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:f698de3fd0c4e6972b92290a45bd9b1536bffe8c6759c62471efaa8acb4c37bc"},
-    {file = "MarkupSafe-2.1.3-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:aa57bd9cf8ae831a362185ee444e15a93ecb2e344c8e52e4d721ea3ab6ef1823"},
-    {file = "MarkupSafe-2.1.3-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ffcc3f7c66b5f5b7931a5aa68fc9cecc51e685ef90282f4a82f0f5e9b704ad11"},
-    {file = "MarkupSafe-2.1.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:47d4f1c5f80fc62fdd7777d0d40a2e9dda0a05883ab11374334f6c4de38adffd"},
-    {file = "MarkupSafe-2.1.3-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:1f67c7038d560d92149c060157d623c542173016c4babc0c1913cca0564b9939"},
-    {file = "MarkupSafe-2.1.3-cp312-cp312-musllinux_1_1_aarch64.whl", hash = "sha256:9aad3c1755095ce347e26488214ef77e0485a3c34a50c5a5e2471dff60b9dd9c"},
-    {file = "MarkupSafe-2.1.3-cp312-cp312-musllinux_1_1_i686.whl", hash = "sha256:14ff806850827afd6b07a5f32bd917fb7f45b046ba40c57abdb636674a8b559c"},
-    {file = "MarkupSafe-2.1.3-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:8f9293864fe09b8149f0cc42ce56e3f0e54de883a9de90cd427f191c346eb2e1"},
-    {file = "MarkupSafe-2.1.3-cp312-cp312-win32.whl", hash = "sha256:715d3562f79d540f251b99ebd6d8baa547118974341db04f5ad06d5ea3eb8007"},
-    {file = "MarkupSafe-2.1.3-cp312-cp312-win_amd64.whl", hash = "sha256:1b8dd8c3fd14349433c79fa8abeb573a55fc0fdd769133baac1f5e07abf54aeb"},
     {file = "MarkupSafe-2.1.3-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:8e254ae696c88d98da6555f5ace2279cf7cd5b3f52be2b5cf97feafe883b58d2"},
     {file = "MarkupSafe-2.1.3-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:cb0932dc158471523c9637e807d9bfb93e06a95cbf010f1a38b98623b929ef2b"},
     {file = "MarkupSafe-2.1.3-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9402b03f1a1b4dc4c19845e5c749e3ab82d5078d16a2a4c2cd2df62d57bb0707"},
@@ -1778,6 +1920,7 @@ files = [
 name = "mdurl"
 version = "0.1.2"
 description = "Markdown URL utilities"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1789,6 +1932,7 @@ files = [
 name = "mergedeep"
 version = "1.3.4"
 description = "A deep merge function for 🐍."
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1800,6 +1944,7 @@ files = [
 name = "mkdocs"
 version = "1.5.3"
 description = "Project documentation with Markdown."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1831,6 +1976,7 @@ min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-imp
 name = "mkdocs-autorefs"
 version = "0.5.0"
 description = "Automatically link across pages in MkDocs."
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1846,6 +1992,7 @@ mkdocs = ">=1.1"
 name = "mkdocs-material"
 version = "9.4.2"
 description = "Documentation that simply works"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1875,6 +2022,7 @@ recommended = ["mkdocs-minify-plugin (>=0.7,<1.0)", "mkdocs-redirects (>=1.2,<2.
 name = "mkdocs-material-extensions"
 version = "1.2"
 description = "Extension pack for Python Markdown and MkDocs Material."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1886,6 +2034,7 @@ files = [
 name = "mkdocs-mermaid2-plugin"
 version = "0.6.0"
 description = "A MkDocs plugin for including mermaid graphs in markdown sources"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1907,6 +2056,7 @@ setuptools = ">=18.5"
 name = "mkdocstrings"
 version = "0.23.0"
 description = "Automatic documentation from sources, for MkDocs."
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1934,6 +2084,7 @@ python-legacy = ["mkdocstrings-python-legacy (>=0.2.1)"]
 name = "mkdocstrings-python"
 version = "1.7.0"
 description = "A Python handler for mkdocstrings."
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1949,6 +2100,7 @@ mkdocstrings = ">=0.20"
 name = "more-click"
 version = "0.1.2"
 description = "More click."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1966,6 +2118,7 @@ tests = ["coverage", "pytest"]
 name = "mypy-extensions"
 version = "1.0.0"
 description = "Type system extensions for programs checked with the mypy type checker."
+category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1977,6 +2130,7 @@ files = [
 name = "ndex2"
 version = "3.5.1"
 description = "Nice CX Python includes a client and a data model."
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1998,6 +2152,7 @@ urllib3 = ">=1.16"
 name = "networkx"
 version = "3.1"
 description = "Python package for creating and manipulating graphs and networks"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2016,6 +2171,7 @@ test = ["codecov (>=2.1)", "pytest (>=7.2)", "pytest-cov (>=4.0)"]
 name = "numpy"
 version = "1.25.2"
 description = "Fundamental package for array computing in Python"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2050,6 +2206,7 @@ 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 = [
@@ -2096,6 +2253,7 @@ 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 = [
@@ -2118,6 +2276,7 @@ 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 = [
@@ -2137,6 +2296,7 @@ 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 = [
@@ -2151,6 +2311,7 @@ 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 = [
@@ -2165,6 +2326,7 @@ attrs = ">=19.2.0"
 name = "packaging"
 version = "23.1"
 description = "Core utilities for Python packages"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2176,6 +2338,7 @@ files = [
 name = "paginate"
 version = "0.5.6"
 description = "Divides large result sets into pages for easier browsing"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2186,6 +2349,7 @@ 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 = [
@@ -2244,6 +2408,7 @@ xml = ["lxml (>=4.8.0)"]
 name = "pandas"
 version = "2.1.1"
 description = "Powerful data structures for data analysis, time series, and statistics"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2311,6 +2476,7 @@ xml = ["lxml (>=4.8.0)"]
 name = "panflute"
 version = "2.3.0"
 description = "Pythonic Pandoc filters"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2331,6 +2497,7 @@ pypi = ["Pygments", "docutils", "twine", "wheel"]
 name = "pansql"
 version = "0.0.1"
 description = "sqldf for pandas"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2347,6 +2514,7 @@ sqlalchemy = "*"
 name = "parse"
 version = "1.19.1"
 description = "parse() is the opposite of format()"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2358,6 +2526,7 @@ files = [
 name = "pathspec"
 version = "0.11.2"
 description = "Utility library for gitignore style pattern matching of file paths."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2369,6 +2538,7 @@ files = [
 name = "platformdirs"
 version = "3.10.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2384,6 +2554,7 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co
 name = "pluggy"
 version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2399,6 +2570,7 @@ testing = ["pytest", "pytest-benchmark"]
 name = "ply"
 version = "3.11"
 description = "Python Lex & Yacc"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2410,6 +2582,7 @@ files = [
 name = "prefixcommons"
 version = "0.1.12"
 description = "A python API for working with ID prefixes"
+category = "main"
 optional = false
 python-versions = ">=3.7,<4.0"
 files = [
@@ -2425,30 +2598,36 @@ requests = ">=2.28.1,<3.0.0"
 
 [[package]]
 name = "prefixmaps"
-version = "0.1.5"
+version = "0.1.6"
 description = "A python library for retrieving semantic prefix maps"
+category = "main"
 optional = false
-python-versions = ">=3.7.6,<4.0.0"
-files = [
-    {file = "prefixmaps-0.1.5-py3-none-any.whl", hash = "sha256:afe679efa0fa62ae69939771956a76e2958505743b40755c8bae85732622b5b2"},
-    {file = "prefixmaps-0.1.5.tar.gz", hash = "sha256:0073f69477f7e9e2359409c0e9d2f853c958600825d9ed859c4c6c71134010a1"},
-]
+python-versions = "^3.8.0"
+files = []
+develop = false
 
 [package.dependencies]
-click = ">=8.1.3,<9.0.0"
-greenlet = "2.0.1"
-importlib-metadata = ">=1.0.0"
+click = ">=8.1.3"
+curies = ">=0.5.3"
+pydantic = "^1.8.2"
 pyyaml = ">=5.3.1"
-typing-extensions = ">=4.4.0,<5.0.0"
+tox = "^4.11.3"
 
 [package.extras]
 docs = ["Sphinx[docs] (>=5.3.0,<6.0.0)", "myst-parser[docs] (>=0.18.1,<0.19.0)", "sphinx-autodoc-typehints[docs] (>=1.19.4,<2.0.0)", "sphinx-click[docs] (>=4.3.0,<5.0.0)", "sphinx-rtd-theme[docs] (>=1.0.0,<2.0.0)"]
-refresh = ["bioregistry[refresh] (>=0.8.0,<0.9.0)", "rdflib[refresh] (>=6.2.0,<7.0.0)", "requests[refresh] (>=2.28.1,<3.0.0)"]
+refresh = ["bioregistry[refresh] (>=0.10.0,<0.11.0)", "rdflib[refresh] (>=6.2.0,<7.0.0)", "requests[refresh] (>=2.28.1,<3.0.0)"]
+
+[package.source]
+type = "git"
+url = "https://github.com/linkml/prefixmaps.git"
+reference = "update_bioregistry"
+resolved_reference = "73def82a3a17b9e131f6c8429d117c7f90af81c6"
 
 [[package]]
 name = "pronto"
 version = "2.5.5"
 description = "Python frontend to ontologies."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2466,6 +2645,7 @@ python-dateutil = ">=2.8,<3.0"
 name = "pybase62"
 version = "1.0.0"
 description = "Python module for base62 encoding"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -2476,6 +2656,7 @@ files = [
 name = "pycparser"
 version = "2.21"
 description = "C parser in Python"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -2487,6 +2668,7 @@ files = [
 name = "pydantic"
 version = "1.10.12"
 description = "Data validation and settings management using python type hints"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2539,6 +2721,7 @@ 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 = [
@@ -2553,6 +2736,7 @@ plugins = ["importlib-metadata"]
 name = "pyjsg"
 version = "0.11.10"
 description = "Python JSON Schema Grammar interpreter"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2568,6 +2752,7 @@ 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 = [
@@ -2586,6 +2771,7 @@ 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 = [
@@ -2596,10 +2782,31 @@ files = [
 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
 
+[[package]]
+name = "pyproject-api"
+version = "1.6.1"
+description = "API to interact with the python pyproject.toml based projects"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pyproject_api-1.6.1-py3-none-any.whl", hash = "sha256:4c0116d60476b0786c88692cf4e325a9814965e2469c5998b830bba16b183675"},
+    {file = "pyproject_api-1.6.1.tar.gz", hash = "sha256:1817dc018adc0d1ff9ca1ed8c60e1623d5aaca40814b953af14a9cf9a5cae538"},
+]
+
+[package.dependencies]
+packaging = ">=23.1"
+tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
+
+[package.extras]
+docs = ["furo (>=2023.8.19)", "sphinx (<7.2)", "sphinx-autodoc-typehints (>=1.24)"]
+testing = ["covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "setuptools (>=68.1.2)", "wheel (>=0.41.2)"]
+
 [[package]]
 name = "pyrate-limiter"
 version = "3.1.0"
 description = "Python Rate-Limiter using Leaky-Bucket Algorithm"
+category = "dev"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -2615,6 +2822,7 @@ docs = ["furo (>=2022.3.4,<2023.0.0)", "myst-parser (>=0.17)", "sphinx (>=4.3.0,
 name = "pyshex"
 version = "0.8.1"
 description = "Python ShEx Implementation"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2637,6 +2845,7 @@ urllib3 = "*"
 name = "pyshexc"
 version = "0.9.1"
 description = "PyShExC - Python ShEx compiler"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2656,6 +2865,7 @@ shexjsg = ">=0.8.1"
 name = "pysocks"
 version = "1.7.1"
 description = "A Python SOCKS client module. See https://github.com/Anorov/PySocks for more information."
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -2668,6 +2878,7 @@ files = [
 name = "pysolr"
 version = "3.9.0"
 description = "Lightweight Python client for Apache Solr"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2684,6 +2895,7 @@ solrcloud = ["kazoo (>=2.5.0)"]
 name = "pystow"
 version = "0.5.0"
 description = "Easily pick a place to store data for your python package."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2708,6 +2920,7 @@ xml = ["lxml"]
 name = "pytest"
 version = "7.4.2"
 description = "pytest: simple powerful testing with Python"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2730,6 +2943,7 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no
 name = "pytest-logging"
 version = "2015.11.4"
 description = "Configures logging and allows tweaking the log level with a py.test flag"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2743,6 +2957,7 @@ pytest = ">=2.8.1"
 name = "python-dateutil"
 version = "2.8.2"
 description = "Extensions to the standard Python datetime module"
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -2757,6 +2972,7 @@ six = ">=1.5"
 name = "python-dotenv"
 version = "1.0.0"
 description = "Read key-value pairs from a .env file and set them as environment variables"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2771,6 +2987,7 @@ cli = ["click (>=5.0)"]
 name = "pytrie"
 version = "0.4.0"
 description = "A pure Python implementation of the trie data structure."
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2784,6 +3001,7 @@ sortedcontainers = "*"
 name = "pytz"
 version = "2023.3.post1"
 description = "World timezone definitions, modern and historical"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2795,6 +3013,7 @@ files = [
 name = "pywin32"
 version = "306"
 description = "Python for Window Extensions"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2818,6 +3037,7 @@ files = [
 name = "pyyaml"
 version = "6.0.1"
 description = "YAML parser and emitter for Python"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2826,7 +3046,6 @@ files = [
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@@ -2859,7 +3071,6 @@ files = [
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-    {file = "PyYAML-6.0.1-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:49a183be227561de579b4a36efbb21b3eab9651dd81b1858589f796549873dd6"},
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@@ -2867,7 +3078,6 @@ files = [
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     {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
@@ -2877,6 +3087,7 @@ files = [
 name = "pyyaml-env-tag"
 version = "0.1"
 description = "A custom YAML tag for referencing environment variables in YAML files. "
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2891,6 +3102,7 @@ pyyaml = "*"
 name = "ratelimit"
 version = "2.2.1"
 description = "API rate limit decorator"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2901,6 +3113,7 @@ files = [
 name = "rdflib"
 version = "7.0.0"
 description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
+category = "main"
 optional = false
 python-versions = ">=3.8.1,<4.0.0"
 files = [
@@ -2922,6 +3135,7 @@ networkx = ["networkx (>=2.0.0,<3.0.0)"]
 name = "rdflib-jsonld"
 version = "0.6.1"
 description = "rdflib extension adding JSON-LD parser and serializer"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2936,6 +3150,7 @@ rdflib = ">=5.0.0"
 name = "rdflib-shim"
 version = "1.0.3"
 description = "Shim for rdflib 5 and 6 incompatibilities"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2951,6 +3166,7 @@ rdflib-jsonld = "0.6.1"
 name = "referencing"
 version = "0.30.2"
 description = "JSON Referencing + Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2966,6 +3182,7 @@ rpds-py = ">=0.7.0"
 name = "regex"
 version = "2023.8.8"
 description = "Alternative regular expression module, to replace re."
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -3063,6 +3280,7 @@ files = [
 name = "requests"
 version = "2.31.0"
 description = "Python HTTP for Humans."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3085,6 +3303,7 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 name = "requests-cache"
 version = "1.1.0"
 description = "A persistent cache for python requests"
+category = "main"
 optional = false
 python-versions = ">=3.7,<4.0"
 files = [
@@ -3115,6 +3334,7 @@ yaml = ["pyyaml (>=5.4)"]
 name = "requests-toolbelt"
 version = "1.0.0"
 description = "A utility belt for advanced users of python-requests"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -3129,6 +3349,7 @@ requests = ">=2.0.1,<3.0.0"
 name = "rfc3339-validator"
 version = "0.1.4"
 description = "A pure python RFC3339 validator"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -3143,6 +3364,7 @@ six = "*"
 name = "rfc3987"
 version = "1.3.8"
 description = "Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3154,6 +3376,7 @@ files = [
 name = "rich"
 version = "13.5.3"
 description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
+category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -3172,6 +3395,7 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 name = "rpds-py"
 version = "0.10.3"
 description = "Python bindings to Rust's persistent data structures (rpds)"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3278,6 +3502,7 @@ files = [
 name = "ruamel-yaml"
 version = "0.17.32"
 description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
+category = "main"
 optional = false
 python-versions = ">=3"
 files = [
@@ -3296,6 +3521,7 @@ jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"]
 name = "ruamel-yaml-clib"
 version = "0.2.7"
 description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -3342,6 +3568,7 @@ files = [
 name = "ruff"
 version = "0.0.291"
 description = "An extremely fast Python linter, written in Rust."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3368,6 +3595,7 @@ files = [
 name = "scholarly"
 version = "1.7.11"
 description = "Simple access to Google Scholar authors and citations"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -3396,6 +3624,7 @@ tor = ["stem"]
 name = "scipy"
 version = "1.9.3"
 description = "Fundamental algorithms for scientific computing in Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3434,6 +3663,7 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 name = "selenium"
 version = "4.13.0"
 description = ""
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3451,6 +3681,7 @@ urllib3 = {version = ">=1.26,<3", extras = ["socks"]}
 name = "semsimian"
 version = "0.2.1"
 description = ""
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3495,6 +3726,7 @@ files = [
 name = "semsql"
 version = "0.3.2"
 description = ""
+category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -3511,6 +3743,7 @@ SQLAlchemy-Utils = ">=0.38.2,<0.39.0"
 name = "setuptools"
 version = "68.2.2"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3527,6 +3760,7 @@ testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jar
 name = "shellingham"
 version = "1.4.0"
 description = "Tool to Detect Surrounding Shell"
+category = "main"
 optional = false
 python-versions = "!=3.0,!=3.1,!=3.2,!=3.3,>=2.6"
 files = [
@@ -3538,6 +3772,7 @@ files = [
 name = "shexjsg"
 version = "0.8.2"
 description = "ShExJSG - Astract Syntax Tree for the ShEx 2.0 language"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3552,6 +3787,7 @@ pyjsg = ">=0.11.10"
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -3563,6 +3799,7 @@ files = [
 name = "sniffio"
 version = "1.3.0"
 description = "Sniff out which async library your code is running under"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3574,6 +3811,7 @@ files = [
 name = "snowballstemmer"
 version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -3585,6 +3823,7 @@ files = [
 name = "sortedcontainers"
 version = "2.4.0"
 description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3596,6 +3835,7 @@ files = [
 name = "soupsieve"
 version = "2.5"
 description = "A modern CSS selector implementation for Beautiful Soup."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3607,6 +3847,7 @@ files = [
 name = "sparqlslurper"
 version = "0.5.1"
 description = "SPARQL Slurper for rdflib"
+category = "main"
 optional = false
 python-versions = ">=3.7.4"
 files = [
@@ -3623,6 +3864,7 @@ sparqlwrapper = ">=1.8.2"
 name = "sparqlwrapper"
 version = "2.0.0"
 description = "SPARQL Endpoint interface to Python"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3643,6 +3885,7 @@ pandas = ["pandas (>=1.3.5)"]
 name = "sphinx"
 version = "7.2.6"
 description = "Python documentation generator"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -3678,6 +3921,7 @@ test = ["cython (>=3.0)", "filelock", "html5lib", "pytest (>=4.6)", "setuptools
 name = "sphinx-rtd-theme"
 version = "1.3.0"
 description = "Read the Docs theme for Sphinx"
+category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 files = [
@@ -3697,6 +3941,7 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 name = "sphinxcontrib-applehelp"
 version = "1.0.7"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -3715,6 +3960,7 @@ test = ["pytest"]
 name = "sphinxcontrib-devhelp"
 version = "1.0.5"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -3733,6 +3979,7 @@ test = ["pytest"]
 name = "sphinxcontrib-htmlhelp"
 version = "2.0.4"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -3751,6 +3998,7 @@ test = ["html5lib", "pytest"]
 name = "sphinxcontrib-jquery"
 version = "4.1"
 description = "Extension to include jQuery on newer Sphinx releases"
+category = "dev"
 optional = false
 python-versions = ">=2.7"
 files = [
@@ -3765,6 +4013,7 @@ Sphinx = ">=1.8"
 name = "sphinxcontrib-jsmath"
 version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
+category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -3779,6 +4028,7 @@ test = ["flake8", "mypy", "pytest"]
 name = "sphinxcontrib-qthelp"
 version = "1.0.6"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -3797,6 +4047,7 @@ test = ["pytest"]
 name = "sphinxcontrib-serializinghtml"
 version = "1.1.9"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -3815,6 +4066,7 @@ test = ["pytest"]
 name = "sqlalchemy"
 version = "2.0.21"
 description = "Database Abstraction Library"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3834,6 +4086,14 @@ files = [
     {file = "SQLAlchemy-2.0.21-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:b69f1f754d92eb1cc6b50938359dead36b96a1dcf11a8670bff65fd9b21a4b09"},
     {file = "SQLAlchemy-2.0.21-cp311-cp311-win32.whl", hash = "sha256:af520a730d523eab77d754f5cf44cc7dd7ad2d54907adeb3233177eeb22f271b"},
     {file = "SQLAlchemy-2.0.21-cp311-cp311-win_amd64.whl", hash = "sha256:141675dae56522126986fa4ca713739d00ed3a6f08f3c2eb92c39c6dfec463ce"},
+    {file = "SQLAlchemy-2.0.21-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:56628ca27aa17b5890391ded4e385bf0480209726f198799b7e980c6bd473bd7"},
+    {file = "SQLAlchemy-2.0.21-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:db726be58837fe5ac39859e0fa40baafe54c6d54c02aba1d47d25536170b690f"},
+    {file = "SQLAlchemy-2.0.21-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:e7421c1bfdbb7214313919472307be650bd45c4dc2fcb317d64d078993de045b"},
+    {file = "SQLAlchemy-2.0.21-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:632784f7a6f12cfa0e84bf2a5003b07660addccf5563c132cd23b7cc1d7371a9"},
+    {file = "SQLAlchemy-2.0.21-cp312-cp312-musllinux_1_1_aarch64.whl", hash = "sha256:f6f7276cf26145a888f2182a98f204541b519d9ea358a65d82095d9c9e22f917"},
+    {file = "SQLAlchemy-2.0.21-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:2a1f7ffac934bc0ea717fa1596f938483fb8c402233f9b26679b4f7b38d6ab6e"},
+    {file = "SQLAlchemy-2.0.21-cp312-cp312-win32.whl", hash = "sha256:bfece2f7cec502ec5f759bbc09ce711445372deeac3628f6fa1c16b7fb45b682"},
+    {file = "SQLAlchemy-2.0.21-cp312-cp312-win_amd64.whl", hash = "sha256:526b869a0f4f000d8d8ee3409d0becca30ae73f494cbb48801da0129601f72c6"},
     {file = "SQLAlchemy-2.0.21-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:7614f1eab4336df7dd6bee05bc974f2b02c38d3d0c78060c5faa4cd1ca2af3b8"},
     {file = "SQLAlchemy-2.0.21-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d59cb9e20d79686aa473e0302e4a82882d7118744d30bb1dfb62d3c47141b3ec"},
     {file = "SQLAlchemy-2.0.21-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a95aa0672e3065d43c8aa80080cdd5cc40fe92dc873749e6c1cf23914c4b83af"},
@@ -3893,6 +4153,7 @@ sqlcipher = ["sqlcipher3-binary"]
 name = "sqlalchemy-utils"
 version = "0.38.3"
 description = "Various utility functions for SQLAlchemy."
+category = "main"
 optional = false
 python-versions = "~=3.6"
 files = [
@@ -3921,6 +4182,7 @@ url = ["furl (>=0.4.1)"]
 name = "sssom"
 version = "0.3.41"
 description = "Operations on SSSOM mapping tables"
+category = "main"
 optional = false
 python-versions = ">=3.8,<4.0"
 files = [
@@ -3948,6 +4210,7 @@ validators = ">=0.20.0"
 name = "sssom-schema"
 version = "0.15.0"
 description = "SSSOM is a Simple Standard for Sharing Ontology Mappings."
+category = "main"
 optional = false
 python-versions = ">=3.7.6,<4.0.0"
 files = [
@@ -3963,6 +4226,7 @@ mkdocs-mermaid2-plugin = ">=0.6.0,<0.7.0"
 name = "starlette"
 version = "0.27.0"
 description = "The little ASGI library that shines."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3981,6 +4245,7 @@ full = ["httpx (>=0.22.0)", "itsdangerous", "jinja2", "python-multipart", "pyyam
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3988,10 +4253,39 @@ files = [
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
 ]
 
+[[package]]
+name = "tox"
+version = "4.11.3"
+description = "tox is a generic virtualenv management and test command line tool"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "tox-4.11.3-py3-none-any.whl", hash = "sha256:599af5e5bb0cad0148ac1558a0b66f8fff219ef88363483b8d92a81e4246f28f"},
+    {file = "tox-4.11.3.tar.gz", hash = "sha256:5039f68276461fae6a9452a3b2c7295798f00a0e92edcd9a3b78ba1a73577951"},
+]
+
+[package.dependencies]
+cachetools = ">=5.3.1"
+chardet = ">=5.2"
+colorama = ">=0.4.6"
+filelock = ">=3.12.3"
+packaging = ">=23.1"
+platformdirs = ">=3.10"
+pluggy = ">=1.3"
+pyproject-api = ">=1.6.1"
+tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
+virtualenv = ">=20.24.3"
+
+[package.extras]
+docs = ["furo (>=2023.8.19)", "sphinx (>=7.2.4)", "sphinx-argparse-cli (>=1.11.1)", "sphinx-autodoc-typehints (>=1.24)", "sphinx-copybutton (>=0.5.2)", "sphinx-inline-tabs (>=2023.4.21)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+testing = ["build[virtualenv] (>=0.10)", "covdefaults (>=2.3)", "detect-test-pollution (>=1.1.1)", "devpi-process (>=1)", "diff-cover (>=7.7)", "distlib (>=0.3.7)", "flaky (>=3.7)", "hatch-vcs (>=0.3)", "hatchling (>=1.18)", "psutil (>=5.9.5)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-xdist (>=3.3.1)", "re-assert (>=1.1)", "time-machine (>=2.12)", "wheel (>=0.41.2)"]
+
 [[package]]
 name = "tqdm"
 version = "4.66.1"
 description = "Fast, Extensible Progress Meter"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4012,6 +4306,7 @@ 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 = [
@@ -4032,6 +4327,7 @@ sortedcontainers = "*"
 name = "trio-websocket"
 version = "0.10.4"
 description = "WebSocket library for Trio"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4048,6 +4344,7 @@ 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 = [
@@ -4068,6 +4365,7 @@ 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 = [
@@ -4084,6 +4382,7 @@ 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 = [
@@ -4095,6 +4394,7 @@ files = [
 name = "tzdata"
 version = "2023.3"
 description = "Provider of IANA time zone data"
+category = "main"
 optional = false
 python-versions = ">=2"
 files = [
@@ -4106,6 +4406,7 @@ files = [
 name = "uri-template"
 version = "1.3.0"
 description = "RFC 6570 URI Template Processor"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4120,6 +4421,7 @@ 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 = [
@@ -4134,6 +4436,7 @@ 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 = [
@@ -4154,6 +4457,7 @@ 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 = [
@@ -4168,7 +4472,7 @@ 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\""}
 
@@ -4179,6 +4483,7 @@ 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 = [
@@ -4223,6 +4528,7 @@ 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 = [
@@ -4241,10 +4547,32 @@ testing = ["pytest (>=7.4.0)"]
 tooling = ["black (>=23.7.0)", "pyright (>=1.1.325)", "ruff (>=0.0.287)"]
 tooling-extras = ["pyaml (>=23.7.0)", "pypandoc-binary (>=1.11)", "pytest (>=7.4.0)"]
 
+[[package]]
+name = "virtualenv"
+version = "20.24.5"
+description = "Virtual Python Environment builder"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "virtualenv-20.24.5-py3-none-any.whl", hash = "sha256:b80039f280f4919c77b30f1c23294ae357c4c8701042086e3fc005963e4e537b"},
+    {file = "virtualenv-20.24.5.tar.gz", hash = "sha256:e8361967f6da6fbdf1426483bfe9fca8287c242ac0bc30429905721cefbff752"},
+]
+
+[package.dependencies]
+distlib = ">=0.3.7,<1"
+filelock = ">=3.12.2,<4"
+platformdirs = ">=3.9.1,<4"
+
+[package.extras]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
+
 [[package]]
 name = "watchdog"
 version = "3.0.0"
 description = "Filesystem events monitoring"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4284,6 +4612,7 @@ 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 = [
@@ -4318,6 +4647,7 @@ 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 = [
@@ -4333,6 +4663,7 @@ 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 = [
@@ -4349,6 +4680,7 @@ 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 = [
@@ -4428,6 +4760,7 @@ 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 = [
@@ -4442,6 +4775,7 @@ 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 = [
@@ -4526,6 +4860,7 @@ files = [
 name = "wsproto"
 version = "1.2.0"
 description = "WebSockets state-machine based protocol implementation"
+category = "dev"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -4540,6 +4875,7 @@ 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 = [
@@ -4554,4 +4890,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "b0b6ef6831375cd9f819ee81c28f246883022fe56d42719f3d168e07e998b056"
+content-hash = "c9e158f3706e78d180f43493639dcbe81de5f0ade1f3c2de615c651b372e7db0"
diff --git a/backend/pyproject.toml b/backend/pyproject.toml
index ee54f1e49..15be7e914 100644
--- a/backend/pyproject.toml
+++ b/backend/pyproject.toml
@@ -20,7 +20,8 @@ python = "^3.9"
 pydantic = "^1.10.2"
 curies = "<1"
 linkml = "^1.5.5"
-prefixmaps = "^0.1.5"
+prefixmaps = "^0.1.6"
+
 requests = "^2.28.1"
 typer = "^0.7.0"
 typer-cli = "^0.0.13"
@@ -29,8 +30,9 @@ docker = "^6.0.1"
 pystow = ">=0.5.0"
 loguru = "*"
 fastapi = "^0.103.1"
-oaklib = "^0.5.19"
+oaklib = ">=0.5.19"
 gunicorn = "^21.2.0"
+bioregistry = "^0.10.57"
 
 
 [tool.poetry.group.dev.dependencies]
diff --git a/backend/src/monarch_py/service/curie_service.py b/backend/src/monarch_py/service/curie_service.py
index 92c52b284..e82208aa3 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
 
-import curies
 from curies import Converter
+from prefixmaps.io.parser import load_multi_context, load_context
 
 
 class CurieService:
@@ -15,7 +15,11 @@ def __new__(cls):
         return cls._instance
 
     def initialize(self):
-        self.converter = curies.get_monarch_converter()
+        # this is a magic keyword that represents the "merged" context from Chris M's algorithm
+        # (https://github.com/linkml/prefixmaps/blob/main/src/prefixmaps/data/merged.csv)
+        context = load_multi_context(["merged"])
+        extended_prefix_map = context.as_extended_prefix_map()
+        self.converter = Converter.from_extended_prefix_map(extended_prefix_map)
 
     def expand(self, curie: str) -> str:
         return self.converter.expand(curie)
diff --git a/backend/tests/unit/test_curie_service.py b/backend/tests/unit/test_curie_service.py
new file mode 100644
index 000000000..925cd1f14
--- /dev/null
+++ b/backend/tests/unit/test_curie_service.py
@@ -0,0 +1,29 @@
+from monarch_py.service.curie_service import CurieService
+import pytest
+
+
+@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")]
+)
+def test_curie_expansion(curie, expanded_curie_part):
+    cs = CurieService()
+    expanded_curie = cs.expand(curie)
+    # print(expanded_curie, expanded_curie_part)
+    assert expanded_curie_part in expanded_curie