From 7c0ce2bfb55acc7713abd3f4d539ff655726e801 Mon Sep 17 00:00:00 2001 From: Vincent Rubinetti Date: Fri, 15 Dec 2023 13:13:43 -0500 Subject: [PATCH] Bring back oak and phenio (text annotator) (#497) Closes #234 --------- Co-authored-by: Kevin Schaper Co-authored-by: madanucd Co-authored-by: glass-ships --- Makefile | 2 +- backend/poetry.lock | 1255 +++--- backend/pyproject.toml | 2 +- .../src/monarch_py/api/additional_models.py | 4 + backend/src/monarch_py/api/config.py | 13 + backend/src/monarch_py/api/main.py | 7 +- backend/src/monarch_py/api/text_annotation.py | 19 + .../api/utils/get_text_annotations.py | 75 + .../implementations/oak/annotation_utils.py | 89 + .../implementations/oak/oak_implementation.py | 75 +- frontend/fixtures/index.ts | 2 +- frontend/fixtures/text-annotator.json | 3689 +++++++---------- frontend/public/mockServiceWorker.js | 13 +- frontend/src/api/index.ts | 4 +- frontend/src/api/text-annotator.ts | 82 +- frontend/src/components/AppNodeBadge.vue | 3 + frontend/src/global/styles.scss | 8 + frontend/src/main.ts | 4 +- .../src/pages/explore/TabTextAnnotator.vue | 22 +- frontend/src/pages/explore/tabs.json | 3 +- frontend/src/router/index.ts | 59 +- frontend/yarn.lock | 1108 ++--- 22 files changed, 2976 insertions(+), 3562 deletions(-) create mode 100644 backend/src/monarch_py/api/text_annotation.py create mode 100644 backend/src/monarch_py/api/utils/get_text_annotations.py create mode 100644 backend/src/monarch_py/implementations/oak/annotation_utils.py diff --git a/Makefile b/Makefile index ae8f0d919..96874e8d5 100644 --- a/Makefile +++ b/Makefile @@ -131,7 +131,7 @@ data: .PHONY: dev-frontend dev-frontend: frontend/src/api/model.ts cd frontend && \ - yarn dev + VITE_API=local yarn dev .PHONY: dev-api diff --git a/backend/poetry.lock b/backend/poetry.lock index b9e59d3cc..bd18534a5 100644 --- a/backend/poetry.lock +++ b/backend/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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content to annotate") diff --git a/backend/src/monarch_py/api/config.py b/backend/src/monarch_py/api/config.py index ef2112f85..fc9ca9ca9 100644 --- a/backend/src/monarch_py/api/config.py +++ b/backend/src/monarch_py/api/config.py @@ -6,6 +6,7 @@ from pydantic import BaseSettings from monarch_py.implementations.solr.solr_implementation import SolrImplementation +from monarch_py.implementations.oak.oak_implementation import OakImplementation from monarch_py.datamodels.model import TermSetPairwiseSimilarity, SemsimSearchResult @@ -43,6 +44,11 @@ def convert_nans(input_dict, to_value=None): class SemsimianHTTPRequester: """A class that makes HTTP requests to the semsimian_server.""" + def compare(self, subjects, objects): + host = f"http://{settings.semsimian_server_host}:{settings.semsimian_server_port}" + path = f"/compare/{','.join(subjects)}/{','.join(objects)}" + url = f"{host}/{path}" + def convert_tsps_data(self, data): """Convert to a format that can be coerced into a TermSetPairwiseSimilarity model @@ -104,3 +110,10 @@ def search(self, termset: List[str], prefix: str, limit: int): @lru_cache(maxsize=1) def semsimian(): return SemsimianHTTPRequester() + + +@lru_cache(maxsize=1) +def oak(): + oak_implementation = OakImplementation() + oak_implementation.init_phenio_adapter(force_update=False) + return oak_implementation diff --git a/backend/src/monarch_py/api/main.py b/backend/src/monarch_py/api/main.py index f24e38b4f..fc27f3f2f 100644 --- a/backend/src/monarch_py/api/main.py +++ b/backend/src/monarch_py/api/main.py @@ -2,8 +2,8 @@ from fastapi import FastAPI from fastapi.middleware.cors import CORSMiddleware from fastapi.responses import RedirectResponse -from monarch_py.api import association, entity, histopheno, search, semsim -from monarch_py.api.config import semsimian +from monarch_py.api import association, entity, histopheno, search, semsim, text_annotation +from monarch_py.api.config import semsimian, oak from monarch_py.api.middleware.logging_middleware import LoggingMiddleware from monarch_py.service.curie_service import CurieService @@ -18,7 +18,7 @@ @app.on_event("startup") async def initialize_app(): semsimian() - # Let the curie service singleton initialize itself + oak() CurieService() @@ -27,6 +27,7 @@ async def initialize_app(): app.include_router(histopheno.router, prefix=f"{PREFIX}/histopheno") app.include_router(search.router, prefix=PREFIX) app.include_router(semsim.router, prefix=f"{PREFIX}/semsim") +app.include_router(text_annotation.router, prefix=PREFIX) # Allow CORS app.add_middleware( diff --git a/backend/src/monarch_py/api/text_annotation.py b/backend/src/monarch_py/api/text_annotation.py new file mode 100644 index 000000000..78f732a56 --- /dev/null +++ b/backend/src/monarch_py/api/text_annotation.py @@ -0,0 +1,19 @@ +from fastapi import APIRouter, Path # , Depends, HTTPException, Query + +from monarch_py.api.additional_models import TextAnnotationRequest +from monarch_py.api.config import oak + +router = APIRouter(tags=["text_annotation"], responses={404: {"description": "Not Found"}}) + + +@router.get("/annotate/{content}") +def _annotate(content: str = Path(title="The text content to annotate")): + print(f"\n\nRunning oak annotate (GET):\n{content}\n") + return oak().annotate_text(content) + + +@router.post("/annotate") +def _post_annotate(request: TextAnnotationRequest): + print(f"\n\nRunning oak annotate (POST):\n{request.content}\n") + # print(request.content.split("\n")) + return oak().annotate_text(request.content) diff --git a/backend/src/monarch_py/api/utils/get_text_annotations.py b/backend/src/monarch_py/api/utils/get_text_annotations.py new file mode 100644 index 000000000..c279caf95 --- /dev/null +++ b/backend/src/monarch_py/api/utils/get_text_annotations.py @@ -0,0 +1,75 @@ +from monarch_py.api.config import oak +import re + +phenio_adapter = oak().phenio_adapter + + +def annotate_text(text): + sentences = re.split(r"(?= 4: + element = [ann.subject_start, ann.subject_end, str(ann.object_label) + "," + str(ann.object_id)] + if (get_word_length(sentence, ann.subject_start - 1) - len(ann.object_label)) < 2: + entities.append(element) + try: + # Trying to access an element that doesn't exist in the list + entities.sort() + entities = concatenate_same_entities(entities) + entities = concatenate_ngram_entities(entities) + replaced_text = replace_entities(sentence, entities) + result += replaced_text + " " + except IndexError as error: + # Handling the list index out of range error + result += sentence + " " + print("Error occurred:", error) + return result + + +def get_word_length(text, start): + word = "" + index = start + while index < len(text) and text[index].isalpha(): + word += text[index] + index += 1 + return len(word) + + +def concatenate_same_entities(lst): + result = {} + for elem in lst: + key = (elem[0], elem[1]) + if key in result: + result[key] += "|" + elem[2] + else: + result[key] = elem[2] + concatenated_list = [[key[0], key[1], value] for key, value in result.items()] + return concatenated_list + + +def concatenate_ngram_entities(lst): + merged_list = [] + start, end, text = lst[0] + for element in lst[1:]: + if element[0] <= end: # Check if range overlaps + end = max(end, element[1]) # Merge the range + text += "|" + element[2] # Concatenate the texts + else: + merged_list.append([start, end, text]) # Add the merged element to the result + start, end, text = element # Move to the next element + merged_list.append([start, end, text]) # Add the last merged element + return merged_list + + +def replace_entities(text, entities): + replaced_text = text + # Sort the entities in descending order of start character indices + entities = sorted(entities, key=lambda x: x[0], reverse=True) + for entity in entities: + start, end = entity[0] - 1, entity[1] + # entity_value = entity[2] + entity_value = f'{text[start:end]}' + replaced_text = replaced_text[:start] + entity_value + replaced_text[end:] + return replaced_text diff --git a/backend/src/monarch_py/implementations/oak/annotation_utils.py b/backend/src/monarch_py/implementations/oak/annotation_utils.py new file mode 100644 index 000000000..9c7942579 --- /dev/null +++ b/backend/src/monarch_py/implementations/oak/annotation_utils.py @@ -0,0 +1,89 @@ +""" +Utility functions for annotating text with OAK. +""" + +import re +import json +from typing import List + + +def get_word_length(text, start): + word = "" + index = start + while index < len(text) and text[index].isalpha(): + word += text[index] + index += 1 + return len(word) + + +def concatenate_same_entities(lst): + result = {} + for elem in lst: + key = (elem[0], elem[1]) + if key in result: + result[key] += "|" + elem[2] + else: + result[key] = elem[2] + concatenated_list = [[key[0], key[1], value] for key, value in result.items()] + return concatenated_list + + +def concatenate_ngram_entities(lst): + merged_list = [] + start, end, text = lst[0] + for element in lst[1:]: + if element[0] <= end: # Check if range overlaps + end = max(end, element[1]) # Merge the range + text += "|" + element[2] # Concatenate the texts + else: + merged_list.append([start, end, text]) # Add the merged element to the result + start, end, text = element # Move to the next element + merged_list.append([start, end, text]) # Add the last merged element + return merged_list + + +def replace_entities(text, entities): + replaced_text = text + # Sort the entities in descending order of start character indices + entities = sorted(entities, key=lambda x: x[0], reverse=True) + for entity in entities: + start, end = entity[0] - 1, entity[1] + # entity_value = entity[2] + entity_value = f'{text[start:end]}' + replaced_text = replaced_text[:start] + entity_value + replaced_text[end:] + return replaced_text + + +def convert_to_json(paragraphs: List[str]): + result = [] + span_pattern = re.compile(r'([^<]+)') + + for paragraph in paragraphs: + start_index = 0 + for match in span_pattern.finditer(paragraph): + span_data = match.group(1) + span_text = match.group(2) + + if start_index < match.start(): + non_span_text = paragraph[start_index : match.start()] + result.append({"text": non_span_text}) + + tokens = [] + for token_data in span_data.split("|"): + token_parts = token_data.split(",") + tokens.append({"id": token_parts[1], "name": token_parts[0]}) + + result.append({"text": span_text, "tokens": tokens}) + start_index = match.end() + + if start_index < len(paragraph): + non_span_text = paragraph[start_index:] + result.append({"text": non_span_text}) + + result.append({"text": "\n"}) + + api_response = json.dumps(result) + # Load the JSON + data = json.loads(api_response) + + return data diff --git a/backend/src/monarch_py/implementations/oak/oak_implementation.py b/backend/src/monarch_py/implementations/oak/oak_implementation.py index 513fc5c93..8f8460268 100644 --- a/backend/src/monarch_py/implementations/oak/oak_implementation.py +++ b/backend/src/monarch_py/implementations/oak/oak_implementation.py @@ -1,15 +1,23 @@ +import re import time from dataclasses import dataclass from typing import List -from loguru import logger - -from monarch_py.datamodels.model import TermSetPairwiseSimilarity from oaklib.interfaces.semsim_interface import SemanticSimilarityInterface from oaklib.selector import get_adapter from linkml_runtime.dumpers.json_dumper import JSONDumper +from loguru import logger import pystow +from monarch_py.datamodels.model import TermSetPairwiseSimilarity +from monarch_py.implementations.oak.annotation_utils import ( + get_word_length, + concatenate_same_entities, + concatenate_ngram_entities, + replace_entities, + convert_to_json, +) + @dataclass class OakImplementation(SemanticSimilarityInterface): @@ -20,6 +28,36 @@ class OakImplementation(SemanticSimilarityInterface): default_predicates = ["rdfs:subClassOf", "BFO:0000050", "UPHENO:0000001"] default_phenio_db_url = "https://data.monarchinitiative.org/monarch-kg-dev/latest/phenio.db.gz" + phenio_adapter = None + + def init_phenio_adapter(self, phenio_path: str = None, force_update: bool = False): + if self.phenio_adapter is None: + logger.info("Warming up semsimian") + start = time.time() + # self.phenio_adapter = get_adapter(f"sqlite:obo:phenio") + + if phenio_path: + logger.debug(f"Creating phenio adapter using phenio_path at {phenio_path}") + self.phenio_adapter = get_adapter(f"sqlite:{phenio_path}") + else: + monarchstow = pystow.module("monarch") + + with monarchstow.ensure_gunzip( + "phenio", url=self.default_phenio_db_url, force=force_update + ) as stowed_phenio_path: + logger.debug(f"Creating phenio adapter using pystow at {stowed_phenio_path}") + self.phenio_adapter = get_adapter(f"sqlite:{stowed_phenio_path}") + + # run a query to get the adapter to initialize properly + logger.debug("Running query to initialize adapter") + + # TODO: run a little bit of text annotation here to get oak warmed up + print("Oaklib adapter warmup") + for ann in self.phenio_adapter.annotate_text("Nystagmus, strabismus and fundus."): + print(ann.subject_start, ann.subject_end, ann.object_id, ann.object_label) + + logger.info(f"Phenio adapter ready, warmup time: {time.time() - start} sec") + return self def init_semsim(self, phenio_path: str = None, force_update: bool = False): if self.semsim is None: @@ -57,7 +95,7 @@ def compare( predicates = predicates or self.default_predicates logger.debug(f"Comparing {subjects} to {objects} using {predicates}") compare_time = time.time() - response = self.semsim.termset_pairwise_similarity( + response = self.semsim.termset_pairwise_similarity( # type: ignore subjects=subjects, objects=objects, predicates=predicates, @@ -67,3 +105,32 @@ def compare( response_dict = self.json_dumper.to_dict(response) return TermSetPairwiseSimilarity(**response_dict) + + def annotate_text(self, text): + """Annotate text using OAK""" + paragraphs = text.split("\n") + paragraphs_annotated = [] + for paragraph in paragraphs: + result = "" + sentences = re.split(r"(?= 4: + element = [ann.subject_start, ann.subject_end, str(ann.object_label) + "," + str(ann.object_id)] + if (get_word_length(sentence, ann.subject_start - 1) - len(ann.object_label)) < 2: + entities.append(element) + try: + entities.sort() + entities = concatenate_same_entities(entities) + entities = concatenate_ngram_entities(entities) + replaced_text = replace_entities(sentence, entities) + result += replaced_text + " " + except IndexError as error: + # Handling the list index out of range error + result += sentence + " " + print("Error occurred:", error) + + paragraphs_annotated.append(result) + result = convert_to_json(paragraphs_annotated) + return result diff --git a/frontend/fixtures/index.ts b/frontend/fixtures/index.ts index 276e14aba..2b9a61052 100644 --- a/frontend/fixtures/index.ts +++ b/frontend/fixtures/index.ts @@ -33,7 +33,7 @@ export const handlers = [ http.get("*/autocomplete", () => HttpResponse.json(autocomplete)), /** text annotator */ - http.post("*/nlp/annotate", () => HttpResponse.json(textAnnotator)), + http.post("*/annotate", () => HttpResponse.json(textAnnotator)), /** phenotype explorer */ http.get("*/sim/search", () => HttpResponse.json(phenotypeExplorerSearch)), diff --git a/frontend/fixtures/text-annotator.json b/frontend/fixtures/text-annotator.json index 72a142fe8..12b6cd6ca 100644 --- a/frontend/fixtures/text-annotator.json +++ b/frontend/fixtures/text-annotator.json @@ -1,2261 +1,1428 @@ -{ - "content": "Lewis (1978) found 7 affected males and 5 affected females in 3 consecutive generations of a Caucasian kindred. As in the X-linked Nettleship-Falls form of ocular albinism (300500), the patients showed reduced visual acuity, photophobia, nystagmus, translucent irides, strabismus, hypermetropic refractive errors, and albinotic fundus with foveal hypoplasia. The skin lesions showed macromelanosomes as in X-linked ocular albinism. Deafness, which was accompanied by vestibular hypofunction, lentigines even in unexposed areas, optic nerve dysplasia, and dominant inheritance distinguished this form of ocular albinism. (In the LEOPARD syndrome (151100) vestibular function is normal.)\n\nBard (1978) described a kindred that was atypical of Waardenburg syndrome (see 193510) in several ways. Although the nasal root was prominent, one affected person had dystopia of the inner canthi or lower puncta. The face in some showed striking freckling of pale skin. Symptomatic vestibular disturbance was another unusual feature. Lewis (1989) expressed the opinion that the family reported by Bard (1978) as an instance of Waardenburg syndrome in fact had this disorder. Lewis (1989) had also been told of 2 other small families with the syndrome. Goldberg (1966) described a Waardenburg syndrome family with apparent ocular albinism.\n\nMorell et al. (1997) presented an update of the clinical findings in the family of Bard (1978). The deafness was sensorineural and congenital. Heterochromia iridis was a prominent feature in 1 sibship in which both segmental iris bicolor and complete heterochromia occurred. Most of the affected individuals showed transillumination defects of the iris. Hypopigmentation of the fundus was mild in some, moderate in others, and severe in yet others. Almost all affected individuals had strabismus and visual acuity defects. One individual with a prominent white forelock, characteristic of Waardenburg syndrome, was pictured.", - "spans": [ - { - "start": 21, - "end": 29, - "text": "affected", - "token": [ - { - "id": "HP:0032320", - "category": [], - "terms": ["Affected"] - } - ] - }, - { - "start": 21, - "end": 29, - "text": "affected", - "token": [ - { - "id": "RO:0002418", - "category": [], - "terms": ["causally upstream of or within"] - } - ] - }, - { - "start": 21, - "end": 29, - "text": "affected", - "token": [ - { - "id": "RO:0002264", - "category": [], - "terms": ["acts upstream of or within"] - } - ] - }, - { - "start": 30, - "end": 35, - "text": "males", - "token": [ - { - "id": "UBERON:0003101", - "category": [], - "terms": ["male organism"] - } - ] - }, - { - "start": 30, - "end": 35, - "text": "males", - "token": [ - { - "id": "PATO:0000384", - "category": [], - "terms": ["male"] - } - ] - }, - { - "start": 30, - "end": 35, - "text": "males", - "token": [ - { - "id": "WBbt:0007850", - "category": [], - "terms": ["male"] - } - ] - }, - { - "start": 42, - "end": 50, - "text": "affected", - "token": [ - { - "id": "HP:0032320", - "category": [], - "terms": ["Affected"] - } - ] - }, - { - "start": 42, - "end": 50, - "text": "affected", - "token": [ - { - "id": "RO:0002418", - "category": [], - "terms": ["causally upstream of or within"] - } - ] - }, - { - "start": 42, - "end": 50, - "text": "affected", - "token": [ - { - "id": "RO:0002264", - "category": [], - "terms": ["acts upstream of or within"] - } - ] - }, - { - "start": 51, - "end": 58, - "text": "females", - "token": [ - { - "id": "UBERON:0003100", - "category": [], - "terms": ["female organism"] - } - ] - }, - { - "start": 51, - "end": 58, - "text": "females", - "token": [ - { - "id": "PATO:0000383", - "category": [], - "terms": ["female"] - } - ] - }, - { - "start": 122, - "end": 130, - "text": "X-linked", - "token": [ - { - "id": "HP:0001417", - "category": [], - "terms": ["X-linked inheritance"] - } - ] - }, - { - "start": 163, - "end": 171, - "text": "albinism", - "token": [ - { - "id": "MONDO:0043209", - "category": [], - "terms": ["albinism"] - } - ] - }, - { - "start": 163, - "end": 171, - "text": "albinism", - "token": [ - { - "id": "HP:0001022", - "category": [], - "terms": ["Albinism"] - } - ] - }, - { - "start": 156, - "end": 171, - "text": "ocular albinism", - "token": [ - { - "id": "MP:0006159", - "category": [], - "terms": ["ocular albinism"] - } - ] - }, - { - "start": 156, - "end": 171, - "text": "ocular albinism", - "token": [ - { - "id": "MONDO:0017304", - "category": [], - "terms": ["ocular albinism (disease)"] - } - ] - }, - { - "start": 156, - "end": 171, - "text": "ocular albinism", - "token": [ - { - "id": "HP:0001107", - "category": [], - "terms": ["Ocular albinism"] - } - ] - }, - { - "start": 202, - "end": 209, - "text": "reduced", - "token": [ - { - "id": "PATO:0000587", - "category": [], - "terms": ["decreased size"] - } - ] - }, - { - "start": 202, - "end": 209, - "text": "reduced", - "token": [ - { - "id": "PATO:0001997", - "category": [], - "terms": ["decreased amount"] - } - ] - }, - { - "start": 202, - "end": 224, - "text": "reduced visual acuity,", - "token": [ - { - "id": "HP:0007663", - "category": [], - "terms": ["Reduced visual acuity"] - } - ] - }, - { - "start": 225, - "end": 237, - "text": "photophobia,", - "token": [ - { - "id": "HP:0000613", - "category": [], - "terms": ["Photophobia"] - } - ] - }, - { - "start": 225, - "end": 237, - "text": "photophobia,", - "token": [ - { - "id": "MP:0013787", - "category": [], - "terms": ["photophobia"] - } - ] - }, - { - "start": 238, - "end": 248, - "text": "nystagmus,", - "token": [ - { - "id": "HP:0000639", - "category": [], - "terms": ["Nystagmus"] - } - ] - }, - { - "start": 238, - "end": 248, - "text": "nystagmus,", - "token": [ - { - "id": "MONDO:0005712", - "category": [], - "terms": ["congenital nystagmus"] - } - ] - }, - { - "start": 249, - "end": 260, - "text": "translucent", - "token": [ - { - "id": "WBPhenotype:0000162", - "category": [], - "terms": ["pale larva"] - } - ] - }, - { - "start": 249, - "end": 260, - "text": "translucent", - "token": [ - { - "id": "PATO:0001354", - "category": [], - "terms": ["translucent"] - } - ] - }, - { - "start": 261, - "end": 268, - "text": "irides,", - "token": [ - { - "id": "ZFA:0001238", - "category": [], - "terms": ["iris"] - } - ] - }, - { - "start": 261, - "end": 268, - "text": "irides,", - "token": [ - { - "id": "UBERON:0001769", - "category": [], - "terms": ["iris"] - } - ] - }, - { - "start": 261, - "end": 268, - "text": "irides,", - "token": [ - { - "id": "ECO:0005520", - "category": [], - "terms": ["interferometric reflectance imaging sensor evidence"] - } - ] - }, - { - "start": 261, - "end": 268, - "text": "irides,", - "token": [ - { - "id": "MONDO:0100185", - "category": [], - "terms": ["immune reconstitution inflammatory syndrome"] - } - ] - }, - { - "start": 269, - "end": 280, - "text": "strabismus,", - "token": [ - { - "id": "MP:0005254", - "category": [], - "terms": ["strabismus"] - } - ] - }, - { - "start": 269, - "end": 280, - "text": "strabismus,", - "token": [ - { - "id": "MONDO:0003432", - "category": [], - "terms": ["strabismus"] - } - ] - }, - { - "start": 269, - "end": 280, - "text": "strabismus,", - "token": [ - { - "id": "HP:0000486", - "category": [], - "terms": ["Strabismus"] - } - ] - }, - { - "start": 328, - "end": 334, - "text": "fundus", - "token": [ - { - "id": "UBERON:0003951", - "category": [], - "terms": ["ocular fundus"] - } - ] - }, - { - "start": 340, - "end": 346, - "text": "foveal", - "token": [ - { - "id": "UBERON:0001786", - "category": [], - "terms": ["fovea centralis"] - } - ] - }, - { - "start": 347, - "end": 358, - "text": "hypoplasia.", - "token": [ - { - "id": "PATO:0000587", - "category": [], - "terms": ["decreased size"] - } - ] - }, - { - "start": 347, - "end": 358, - "text": "hypoplasia.", - "token": [ - { - "id": "FBcv:0000724", - "category": [], - "terms": ["hypoplasia"] - } - ] - }, - { - "start": 347, - "end": 358, - "text": "hypoplasia.", - "token": [ - { - "id": "PATO:0000645", - "category": [], - "terms": ["hypoplastic"] - } - ] - }, - { - "start": 340, - "end": 358, - "text": "foveal hypoplasia.", - "token": [ - { - "id": "HP:0007750", - "category": [], - "terms": ["Hypoplasia of the fovea"] - } - ] - }, - { - "start": 340, - "end": 358, - "text": "foveal hypoplasia.", - "token": [ - { - "id": "MONDO:0044203", - "category": [], - "terms": ["foveal hypoplasia"] - } - ] - }, - { - "start": 363, - "end": 367, - "text": "skin", - "token": [ - { - "id": "ZFA:0000368", - "category": [], - "terms": ["integument"] - } - ] - }, - { - "start": 363, - "end": 367, - "text": "skin", - "token": [ - { - "id": "MONDO:0002531", - "category": [], - "terms": ["skin neoplasm"] - } - ] - }, - { - "start": 363, - "end": 367, - "text": "skin", - "token": [ - { - "id": "UBERON:0000014", - "category": [], - "terms": ["zone of skin"] - } - ] - }, - { - "start": 363, - "end": 367, - "text": "skin", - "token": [ - { - "id": "UBERON:0002097", - "category": [], - "terms": ["skin of body"] - } - ] - }, - { - "start": 363, - "end": 367, - "text": "skin", - "token": [ - { - "id": "UBERON:0001003", - "category": [], - "terms": ["skin epidermis"] - } - ] - }, - { - "start": 363, - "end": 367, - "text": "skin", - "token": [ - { - "id": "UBERON:0002199", - "category": [], - "terms": ["integument"] - } - ] - }, - { - "start": 368, - "end": 375, - "text": "lesions", - "token": [ - { - "id": "PATO:0040025", - "category": [], - "terms": ["lesioned"] - } - ] - }, - { - "start": 363, - "end": 375, - "text": "skin lesions", - "token": [ - { - "id": "MP:0001212", - "category": [], - "terms": ["skin lesions"] - } - ] - }, - { - "start": 383, - "end": 399, - "text": "macromelanosomes", - "token": [ - { - "id": "MP:0030917", - "category": [], - "terms": ["enlarged melanosome"] - } - ] - }, - { - "start": 383, - "end": 399, - "text": "macromelanosomes", - "token": [ - { - "id": "HP:0005592", - "category": [], - "terms": ["Giant melanosomes in melanocytes"] - } - ] - }, - { - "start": 406, - "end": 414, - "text": "X-linked", - "token": [ - { - "id": "HP:0001417", - "category": [], - "terms": ["X-linked inheritance"] - } - ] - }, - { - "start": 422, - "end": 431, - "text": "albinism.", - "token": [ - { - "id": "MONDO:0043209", - "category": [], - "terms": ["albinism"] - } - ] - }, - { - "start": 422, - "end": 431, - "text": "albinism.", - "token": [ - { - "id": "HP:0001022", - "category": [], - "terms": ["Albinism"] - } - ] - }, - { - "start": 415, - "end": 431, - "text": "ocular albinism.", - "token": [ - { - "id": "MP:0006159", - "category": [], - "terms": ["ocular albinism"] - } - ] - }, - { - "start": 415, - "end": 431, - "text": "ocular albinism.", - "token": [ - { - "id": "MONDO:0017304", - "category": [], - "terms": ["ocular albinism (disease)"] - } - ] - }, - { - "start": 415, - "end": 431, - "text": "ocular albinism.", - "token": [ - { - "id": "HP:0001107", - "category": [], - "terms": ["Ocular albinism"] - } - ] - }, - { - "start": 406, - "end": 431, - "text": "X-linked ocular albinism.", - "token": [ - { - "id": "MONDO:0021019", - "category": [], - "terms": ["X-linked recessive ocular albinism"] - } - ] - }, - { - "start": 432, - "end": 441, - "text": "Deafness,", - "token": [ - { - "id": "MP:0001967", - "category": [], - "terms": ["deafness"] - } - ] - }, - { - "start": 432, - "end": 441, - "text": "Deafness,", - "token": [ - { - "id": "HP:0000365", - "category": [], - "terms": ["Hearing impairment"] - } - ] - }, - { - "start": 432, - "end": 441, - "text": "Deafness,", - "token": [ - { - "id": "MONDO:0005365", - "category": [], - "terms": ["hearing loss disorder"] - } - ] - }, - { - "start": 467, - "end": 491, - "text": "vestibular hypofunction,", - "token": [ - { - "id": "HP:0001756", - "category": [], - "terms": ["Vestibular hypofunction"] - } - ] - }, - { - "start": 492, - "end": 502, - "text": "lentigines", - "token": [ - { - "id": "MONDO:0007889", - "category": [], - "terms": ["lentigines"] - } - ] - }, - { - "start": 492, - "end": 502, - "text": "lentigines", - "token": [ - { - "id": "MONDO:0021582", - "category": [], - "terms": ["lentigo"] - } - ] - }, - { - "start": 521, - "end": 527, - "text": "areas,", - "token": [ - { - "id": "PATO:0001323", - "category": [], - "terms": ["area"] - } - ] - }, - { - "start": 534, - "end": 539, - "text": "nerve", - "token": [ - { - "id": "UBERON:0001021", - "category": [], - "terms": ["nerve"] - } - ] - }, - { - "start": 534, - "end": 539, - "text": "nerve", - "token": [ - { - "id": "ZFA:0007009", - "category": [], - "terms": ["nerve"] - } - ] - }, - { - "start": 528, - "end": 539, - "text": "optic nerve", - "token": [ - { - "id": "UBERON:0004904", - "category": [], - "terms": ["neuron projection bundle connecting eye with brain"] - } - ] - }, - { - "start": 528, - "end": 539, - "text": "optic nerve", - "token": [ - { - "id": "ZFA:0000435", - "category": [], - "terms": ["cranial nerve II"] - } - ] - }, - { - "start": 528, - "end": 539, - "text": "optic nerve", - "token": [ - { - "id": "UBERON:0000941", - "category": [], - "terms": ["cranial nerve II"] - } - ] - }, - { - "start": 540, - "end": 550, - "text": "dysplasia,", - "token": [ - { - "id": "PATO:0000640", - "category": [], - "terms": ["dysplastic"] - } - ] - }, - { - "start": 528, - "end": 550, - "text": "optic nerve dysplasia,", - "token": [ - { - "id": "MP:0001330", - "category": [], - "terms": ["abnormal optic nerve morphology"] - } - ] - }, - { - "start": 528, - "end": 550, - "text": "optic nerve dysplasia,", - "token": [ - { - "id": "HP:0001093", - "category": [], - "terms": ["Optic nerve dysplasia"] - } - ] - }, - { - "start": 564, - "end": 575, - "text": "inheritance", - "token": [ - { - "id": "HP:0000005", - "category": [], - "terms": ["Mode of inheritance"] - } - ] - }, - { - "start": 610, - "end": 619, - "text": "albinism.", - "token": [ - { - "id": "MONDO:0043209", - "category": [], - "terms": ["albinism"] - } - ] - }, - { - "start": 610, - "end": 619, - "text": "albinism.", - "token": [ - { - "id": "HP:0001022", - "category": [], - "terms": ["Albinism"] - } - ] - }, - { - "start": 603, - "end": 619, - "text": "ocular albinism.", - "token": [ - { - "id": "MP:0006159", - "category": [], - "terms": ["ocular albinism"] - } - ] - }, - { - "start": 603, - "end": 619, - "text": "ocular albinism.", - "token": [ - { - "id": "MONDO:0017304", - "category": [], - "terms": ["ocular albinism (disease)"] - } - ] - }, - { - "start": 603, - "end": 619, - "text": "ocular albinism.", - "token": [ - { - "id": "HP:0001107", - "category": [], - "terms": ["Ocular albinism"] - } - ] - }, - { - "start": 628, - "end": 635, - "text": "LEOPARD", - "token": [ - { - "id": "NCBITaxon:9691", - "category": [], - "terms": ["Panthera pardus"] - } - ] - }, - { - "start": 636, - "end": 644, - "text": "syndrome", - "token": [ - { - "id": "MONDO:0002254", - "category": [], - "terms": ["syndromic disease"] - } - ] - }, - { - "start": 636, - "end": 644, - "text": "syndrome", - "token": [ - { - "id": "MONDO:0024541", - "category": [], - "terms": ["trichohepatoenteric syndrome 1"] - } - ] - }, - { - "start": 628, - "end": 644, - "text": "LEOPARD syndrome", - "token": [ - { - "id": "MONDO:0007893", - "category": [], - "terms": ["Noonan syndrome with multiple lentigines"] - } - ] - }, - { - "start": 665, - "end": 673, - "text": "function", - "token": [ - { - "id": "BFO:0000034", - "category": [], - "terms": ["function"] - } - ] - }, - { - "start": 665, - "end": 673, - "text": "function", - "token": [ - { - "id": "RO:0000079", - "category": [], - "terms": ["function of"] - } - ] - }, - { - "start": 677, - "end": 685, - "text": "normal.)", - "token": [ - { - "id": "PATO:0000461", - "category": [], - "terms": ["normal"] - } - ] - }, - { - "start": 677, - "end": 685, - "text": "normal.)", - "token": [ - { - "id": "MP:0002169", - "category": [], - "terms": ["no abnormal phenotype detected"] - } - ] - }, - { - "start": 728, - "end": 736, - "text": "atypical", - "token": [ - { - "id": "PATO:0000460", - "category": [], - 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{ - "id": "UBERON:0002199", - "category": [], - "terms": ["integument"] - } - ] - }, - { - "start": 946, - "end": 956, - "text": "pale skin.", - "token": [ - { - "id": "MP:0003717", - "category": [], - "terms": ["pallor"] - } - ] - }, - { - "start": 946, - "end": 956, - "text": "pale skin.", - "token": [ - { - "id": "MP:0001633", - "category": [], - "terms": ["poor circulation"] - } - ] - }, - { - "start": 946, - "end": 956, - "text": "pale skin.", - "token": [ - { - "id": "MP:0001189", - "category": [], - "terms": ["absent skin pigmentation"] - } - ] - }, - { - "start": 1034, - "end": 1043, - "text": "expressed", - "token": [ - { - "id": "RO:0002206", - "category": [], - "terms": ["expressed in"] - } - ] - }, - { - "start": 1065, - "end": 1071, - "text": "family", - "token": [ - { - "id": "NCBITaxon:family", - "category": [], - "terms": ["family"] - } - ] - }, - { - "start": 1065, - "end": 1071, - "text": "family", - "token": [ - { - "id": "PCO:0000020", - "category": [], - "terms": ["family"] - 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"token": [ - { - "id": "MONDO:0017304", - "category": [], - "terms": ["ocular albinism (disease)"] - } - ] - }, - { - "start": 1309, - "end": 1325, - "text": "ocular albinism.", - "token": [ - { - "id": "HP:0001107", - "category": [], - "terms": ["Ocular albinism"] - } - ] - }, - { - "start": 1348, - "end": 1357, - "text": "presented", - "token": [ - { - "id": "PATO:0000467", - "category": [], - "terms": ["present"] - } - ] - }, - { - "start": 1400, - "end": 1406, - "text": "family", - "token": [ - { - "id": "NCBITaxon:family", - "category": [], - "terms": ["family"] - } - ] - }, - { - "start": 1400, - "end": 1406, - "text": "family", - "token": [ - { - "id": "PCO:0000020", - "category": [], - "terms": ["family"] - } - ] - }, - { - "start": 1427, - "end": 1435, - "text": "deafness", - "token": [ - { - "id": "MP:0001967", - "category": [], - "terms": ["deafness"] - } - ] - }, - { - "start": 1427, - "end": 1435, - "text": "deafness", - "token": [ - { - "id": "HP:0000365", - "category": [], - "terms": ["Hearing impairment"] - } - ] - }, - { - "start": 1427, - "end": 1435, - "text": "deafness", - "token": [ - { - "id": "MONDO:0005365", - "category": [], - "terms": ["hearing loss disorder"] - } - ] - }, - { - "start": 1458, - "end": 1469, - "text": "congenital.", - "token": [ - { - "id": "MONDO:0021140", - "category": [], - "terms": ["congenital"] - } - ] - }, - { - "start": 1484, - "end": 1490, - "text": "iridis", - "token": [ - { - "id": "UBERON:0005969", - "category": [], - "terms": ["eye trabecular meshwork"] - } - ] - }, - { - "start": 1470, - "end": 1490, - "text": "Heterochromia iridis", - "token": [ - { - "id": "MONDO:0007722", - "category": [], - "terms": ["heterochromia iridis (disease)"] - } - ] - }, - { - "start": 1470, - "end": 1490, - "text": "Heterochromia iridis", - "token": [ - { - "id": "HP:0001100", - "category": [], - "terms": ["Heterochromia iridis"] - } - ] - }, - { - "start": 1497, - "end": 1506, - "text": "prominent", - "token": [ - { - "id": "PATO:0001482", - "category": [], - "terms": ["prominent"] - } - ] - }, - { - "start": 1542, - "end": 1551, - "text": "segmental", - "token": [ - { - "id": "PATO:0002404", - "category": [], - "terms": ["segmental"] - } - ] - }, - { - "start": 1552, - "end": 1556, - "text": "iris", - "token": [ - { - "id": "ZFA:0001238", - "category": [], - "terms": ["iris"] - } - ] - }, - { - "start": 1552, - "end": 1556, - "text": "iris", - "token": [ - { - "id": "UBERON:0001769", - "category": [], - "terms": ["iris"] - } - ] - }, - { - "start": 1552, - "end": 1556, - "text": "iris", - "token": [ - { - "id": "ECO:0005520", - "category": [], - "terms": ["interferometric reflectance imaging sensor evidence"] - } - ] - }, - { - "start": 1552, - "end": 1556, - "text": "iris", - "token": [ - { - "id": "MONDO:0100185", - "category": [], - "terms": ["immune reconstitution inflammatory syndrome"] - } - ] - }, - { - "start": 1592, - "end": 1601, - "text": "occurred.", - "token": [ - { - "id": "BFO:0000066", - "category": [], - "terms": ["occurs in"] - } - ] - }, - { - "start": 1592, - "end": 1601, - "text": "occurred.", - "token": [ - { - "id": "OBO:mp/mp-equivalent-axioms-subq#occurs_in", - "category": [], - "terms": ["occurs in"] - } - ] - }, - { - "start": 1614, - "end": 1622, - "text": "affected", - "token": [ - { - "id": "HP:0032320", - "category": [], - "terms": ["Affected"] - } - ] - }, - { - "start": 1614, - "end": 1622, - "text": "affected", - "token": [ - { - "id": "RO:0002418", - "category": [], - "terms": ["causally upstream of or within"] - } - ] - }, - { - "start": 1614, - "end": 1622, - "text": "affected", - "token": [ - { - "id": "RO:0002264", - "category": [], - "terms": ["acts upstream of or within"] - } - ] - }, - { - "start": 1660, - "end": 1667, - "text": "defects", - "token": [ - { - "id": "MONDO:0008568", - "category": [], - "terms": ["thyroid hormone plasma membrane transport defect"] - } - ] - }, - { - "start": 1675, - "end": 1680, - "text": "iris.", - "token": [ - { - "id": "ZFA:0001238", - "category": [], - "terms": ["iris"] - } - ] - }, - { - "start": 1675, - "end": 1680, - "text": "iris.", - "token": [ - { - "id": "UBERON:0001769", - "category": [], - "terms": ["iris"] - } - ] - }, - { - "start": 1675, - "end": 1680, - "text": "iris.", - "token": [ - { - "id": "ECO:0005520", - "category": [], - "terms": ["interferometric reflectance imaging sensor evidence"] - } - ] - }, - { - "start": 1675, - "end": 1680, - "text": "iris.", - "token": [ - { - "id": "MONDO:0100185", - "category": [], - "terms": ["immune reconstitution inflammatory syndrome"] - } - ] - }, - { - "start": 1681, - "end": 1697, - "text": "Hypopigmentation", - "token": [ - { - "id": "MONDO:0007459", - "category": [], - "terms": ["dilution, pigmentary"] - } - ] - }, - { - "start": 1681, - "end": 1697, - "text": "Hypopigmentation", - "token": [ - { - "id": "MP:0005408", - "category": [], - "terms": ["hypopigmentation"] - } - ] - }, - { - "start": 1681, - "end": 1697, - "text": "Hypopigmentation", - "token": [ - { - "id": "HP:0001010", - "category": [], - "terms": ["Hypopigmentation of the skin"] - } - ] - }, - { - "start": 1675, - "end": 1697, - "text": "iris. Hypopigmentation", - "token": [ - { - "id": "HP:0007730", - "category": [], - "terms": ["Iris hypopigmentation"] - } - ] - }, - { - "start": 1705, - "end": 1711, - "text": "fundus", - "token": [ - { - "id": "UBERON:0003951", - "category": [], - "terms": ["ocular fundus"] - } - ] - }, - { - "start": 1681, - "end": 1711, - "text": "Hypopigmentation of the fundus", - "token": [ - { - "id": "HP:0007894", - "category": [], - "terms": ["Hypopigmentation of the fundus"] - } - ] - }, - { - "start": 1716, - "end": 1720, - "text": "mild", - "token": [ - { - "id": "HP:0012825", - "category": [], - "terms": ["Mild"] - } - ] - }, - { - "start": 1730, - "end": 1738, - "text": "moderate", - "token": [ - { - "id": "HP:0012826", - "category": [], - "terms": ["Moderate"] - } - ] - }, - { - "start": 1754, - "end": 1760, - "text": "severe", - "token": [ - { - "id": "HP:0012828", - "category": [], - "terms": ["Severe"] - } - ] - }, - { - "start": 1787, - "end": 1795, - "text": "affected", - "token": [ - { - "id": "HP:0032320", - "category": [], - "terms": ["Affected"] - } - ] - }, - { - "start": 1787, - "end": 1795, - "text": "affected", - "token": [ - { - "id": "RO:0002418", - "category": [], - "terms": ["causally upstream of or within"] - } - ] - }, - { - "start": 1787, - "end": 1795, - "text": "affected", - "token": [ - { - "id": "RO:0002264", - "category": [], - "terms": ["acts upstream of or within"] - } - ] - }, - { - "start": 1812, - "end": 1822, - "text": "strabismus", - "token": [ - { - "id": "MP:0005254", - "category": [], - "terms": ["strabismus"] - } - ] - }, - { - "start": 1812, - "end": 1822, - "text": "strabismus", - "token": [ - { - "id": "MONDO:0003432", - "category": [], - "terms": ["strabismus"] - } - ] - }, - { - "start": 1812, - "end": 1822, - "text": "strabismus", - "token": [ - { - "id": "HP:0000486", - "category": [], - "terms": ["Strabismus"] - } - ] - }, - { - "start": 1841, - "end": 1849, - "text": "defects.", - "token": [ - { - "id": "MONDO:0008568", - "category": [], - "terms": ["thyroid hormone plasma membrane transport defect"] - } - ] - }, - { - "start": 1872, - "end": 1881, - "text": "prominent", - "token": [ - { - "id": "PATO:0001482", - "category": [], - "terms": ["prominent"] - } - ] - }, - { - "start": 1882, - "end": 1887, - "text": "white", - "token": [ - { - "id": "PATO:0000323", - "category": [], - "terms": ["white"] - } - ] - }, - { - "start": 1888, - "end": 1897, - "text": "forelock,", - "token": [ - { - "id": "MONDO:0022109", - "category": [], - "terms": ["catatrichy"] - } - ] - }, - { - "start": 1882, - "end": 1897, - "text": "white forelock,", - "token": [ - { - "id": "HP:0002211", - "category": [], - "terms": ["White forelock"] - } - ] - }, - { - "start": 1928, - "end": 1937, - "text": "syndrome,", - "token": [ - { - "id": "MONDO:0002254", - "category": [], - "terms": ["syndromic disease"] - } - ] - }, - { - "start": 1928, - "end": 1937, - "text": "syndrome,", - "token": [ - { - "id": "MONDO:0024541", - "category": [], - "terms": ["trichohepatoenteric syndrome 1"] - } - ] - }, - { - "start": 1916, - "end": 1937, - "text": "Waardenburg syndrome,", - "token": [ - { - "id": "MONDO:0018094", - "category": [], - "terms": ["Waardenburg syndrome"] - } - ] - } - ] -} +[ + { + "text": "Lewis (1978) found 7 " + }, + { + "text": "affected", + "tokens": [ + { + "id": "HP:0032320", + "name": "Affected", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "RO:0002418", + "name": "causally upstream of or within", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "RO:0002264", + "name": "acts upstream of or within", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "males", + "tokens": [ + { + "id": "UBERON:0003101", + "name": "male organism", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "PATO:0000384", + "name": "male", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "WBbt:0007850", + "name": "male", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " and 5 " + }, + { + "text": "affected", + "tokens": [ + { + "id": "HP:0032320", + "name": "Affected", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "RO:0002418", + "name": "causally upstream of or within", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "RO:0002264", + "name": "acts upstream of or within", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "females", + "tokens": [ + { + "id": "UBERON:0003100", + "name": "female organism", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "PATO:0000383", + "name": "female", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " in 3 consecutive generations of a Caucasian kindred. As in the " + }, + { + "text": "X-linked", + "tokens": [ + { + "id": "HP:0001417", + "name": "X-linked inheritance", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " Nettleship-Falls form of " + }, + { + "text": "ocular " + }, + { + "text": "albinism", + "tokens": [ + { + "id": "MONDO:0043209", + "name": "albinism", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "HP:0001022", + "name": "Albinism", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " (300500), the patients showed " + }, + { + "text": "reduced", + "tokens": [ + { + "id": "PATO:0000587", + "name": "decreased size", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "PATO:0001997", + "name": "decreased amount", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " visual acuity," + }, + { + "text": " " + }, + { + "text": "photophobia,", + "tokens": [ + { + "id": "HP:0000613", + "name": "Photophobia", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MP:0013787", + "name": "photophobia", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "nystagmus,", + "tokens": [ + { + "id": "HP:0000639", + "name": "Nystagmus", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0005712", + "name": "congenital nystagmus", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "translucent", + "tokens": [ + { + "id": "WBPhenotype:0000162", + "name": "pale larva", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "PATO:0001354", + "name": "translucent", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "irides,", + "tokens": [ + { + "id": "ZFA:0001238", + "name": "iris", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "UBERON:0001769", + "name": "iris", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "ECO:0005520", + "name": "interferometric reflectance imaging sensor evidence", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0100185", + "name": "immune reconstitution inflammatory syndrome", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "strabismus,", + "tokens": [ + { + "id": "MP:0005254", + "name": "strabismus", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0003432", + "name": "strabismus", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "HP:0000486", + "name": "Strabismus", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " hypermetropic refractive errors, and albinotic " + }, + { + "text": "fundus", + "tokens": [ + { + "id": "UBERON:0003951", + "name": "ocular fundus", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " with " + }, + { + "text": "foveal", + "tokens": [ + { + "id": "UBERON:0001786", + "name": "fovea centralis", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "hypoplasia.", + "tokens": [ + { + "id": "PATO:0000587", + "name": "decreased size", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "FBcv:0000724", + "name": "hypoplasia", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "PATO:0000645", + "name": "hypoplastic", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " The " + }, + { + "text": "skin", + "tokens": [ + { + "id": "ZFA:0000368", + "name": "integument", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0002531", + "name": "skin neoplasm", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "UBERON:0000014", + "name": "zone of skin", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "UBERON:0002097", + "name": "skin of body", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "UBERON:0001003", + "name": "skin epidermis", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "UBERON:0002199", + "name": "integument", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "lesions", + "tokens": [ + { + "id": "PATO:0040025", + "name": "lesioned", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " showed " + }, + { + "text": "macromelanosomes", + "tokens": [ + { + "id": "MP:0030917", + "name": "enlarged melanosome", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "HP:0005592", + "name": "Giant melanosomes in melanocytes", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " as in " + }, + { + "text": "X-linked", + "tokens": [ + { + "id": "HP:0001417", + "name": "X-linked inheritance", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "ocular " + }, + { + "text": "albinism.", + "tokens": [ + { + "id": "MONDO:0043209", + "name": "albinism", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "HP:0001022", + "name": "Albinism", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "Deafness,", + "tokens": [ + { + "id": "MP:0001967", + "name": "deafness", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "HP:0000365", + "name": "Hearing impairment", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0005365", + "name": "hearing loss disorder", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " which was accompanied by " + }, + { + "text": "vestibular hypofunction,", + "tokens": [ + { + "id": "HP:0001756", + "name": "Vestibular hypofunction", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "lentigines", + "tokens": [ + { + "id": "MONDO:0007889", + "name": "lentigines", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0021582", + "name": "lentigo", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " even in unexposed " + }, + { + "text": "areas,", + "tokens": [ + { + "id": "PATO:0001323", + "name": "area", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "optic " + }, + { + "text": "nerve", + "tokens": [ + { + "id": "UBERON:0001021", + "name": "nerve", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "ZFA:0007009", + "name": "nerve", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "dysplasia,", + "tokens": [ + { + "id": "PATO:0000640", + "name": "dysplastic", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " and dominant " + }, + { + "text": "inheritance", + "tokens": [ + { + "id": "HP:0000005", + "name": "Mode of inheritance", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " distinguished this form of " + }, + { + "text": "ocular " + }, + { + "text": "albinism.", + "tokens": [ + { + "id": "MONDO:0043209", + "name": "albinism", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "HP:0001022", + "name": "Albinism", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " (In the " + }, + { + "text": "LEOPARD", + "tokens": [ + { + "id": "NCBITaxon:9691", + "name": "Panthera pardus", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "syndrome", + "tokens": [ + { + "id": "MONDO:0002254", + "name": "syndromic disease", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0024541", + "name": "trichohepatoenteric syndrome 1", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " (151100) vestibular " + }, + { + "text": "function", + "tokens": [ + { + "id": "BFO:0000034", + "name": "function", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "RO:0000079", + "name": "function of", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " is " + }, + { + "text": "normal.)", + "tokens": [ + { + "id": "PATO:0000461", + "name": "normal", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MP:0002169", + "name": "no abnormal phenotype detected", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": "\n\nBard (1978) described a kindred that was " + }, + { + "text": "atypical", + "tokens": [ + { + "id": "PATO:0000460", + "name": "abnormal", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " of " + }, + { + "text": "Waardenburg " + }, + { + "text": "syndrome", + "tokens": [ + { + "id": "MONDO:0002254", + "name": "syndromic disease", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0024541", + "name": "trichohepatoenteric syndrome 1", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " (see 193510) in several ways. Although the " + }, + { + "text": "nasal", + "tokens": [ + { + "id": "UBERON:0001681", + "name": "nasal bone", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "root", + "tokens": [ + { + "id": "OBO:PO_0009005", + "name": "root", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "NCBITaxon:1", + "name": "root", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " was " + }, + { + "text": "prominent,", + "tokens": [ + { + "id": "PATO:0001482", + "name": "prominent", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " one " + }, + { + "text": "affected", + "tokens": [ + { + "id": "HP:0032320", + "name": "Affected", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "RO:0002418", + "name": "causally upstream of or within", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "RO:0002264", + "name": "acts upstream of or within", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "person", + "tokens": [ + { + "id": "foaf:Person", + "name": "Person", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "schema:Person", + "name": "Person", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " had dystopia of the " + }, + { + "text": "inner " + }, + { + "text": "canthi", + "tokens": [ + { + "id": "UBERON:0006742", + "name": "canthus", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " or lower puncta. The " + }, + { + "text": "face", + "tokens": [ + { + "id": "UBERON:0001456", + "name": "face", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0010953", + "name": "Fanconi anemia complementation group E", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " in some showed striking " + }, + { + "text": "freckling", + "tokens": [ + { + "id": "HP:0001480", + "name": "Freckling", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " of " + }, + { + "text": "pale", + "tokens": [ + { + "id": "MONDO:0015595", + "name": "posttransplant acute limbic encephalitis", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "WBPhenotype:0001261", + "name": "pale", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "PATO:0000328", + "name": "low saturation", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "skin.", + "tokens": [ + { + "id": "ZFA:0000368", + "name": "integument", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0002531", + "name": "skin neoplasm", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "UBERON:0000014", + "name": "zone of skin", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "UBERON:0002097", + "name": "skin of body", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "UBERON:0001003", + "name": "skin epidermis", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "UBERON:0002199", + "name": "integument", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " Symptomatic vestibular disturbance was another unusual feature. Lewis (1989) " + }, + { + "text": "expressed", + "tokens": [ + { + "id": "RO:0002206", + "name": "expressed in", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " the opinion that the " + }, + { + "text": "family", + "tokens": [ + { + "id": "NCBITaxon:family", + "name": "family", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "PCO:0000020", + "name": "family", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " reported by Bard (1978) as an instance of " + }, + { + "text": "Waardenburg " + }, + { + "text": "syndrome", + "tokens": [ + { + "id": "MONDO:0002254", + "name": "syndromic disease", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0024541", + "name": "trichohepatoenteric syndrome 1", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " in fact had this " + }, + { + "text": "disorder.", + "tokens": [ + { + "id": "MONDO:0000001", + "name": "disease or disorder", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " Lewis (1989) had also been told of 2 other " + }, + { + "text": "small", + "tokens": [ + { + "id": "PATO:0000587", + "name": "decreased size", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "WBPhenotype:0000229", + "name": "small", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "families", + "tokens": [ + { + "id": "NCBITaxon:family", + "name": "family", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "PCO:0000020", + "name": "family", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " with the " + }, + { + "text": "syndrome.", + "tokens": [ + { + "id": "MONDO:0002254", + "name": "syndromic disease", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0024541", + "name": "trichohepatoenteric syndrome 1", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " Goldberg (1966) described a " + }, + { + "text": "Waardenburg " + }, + { + "text": "syndrome", + "tokens": [ + { + "id": "MONDO:0002254", + "name": "syndromic disease", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0024541", + "name": "trichohepatoenteric syndrome 1", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "family", + "tokens": [ + { + "id": "NCBITaxon:family", + "name": "family", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "PCO:0000020", + "name": "family", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " with apparent " + }, + { + "text": "ocular " + }, + { + "text": "albinism.", + "tokens": [ + { + "id": "MONDO:0043209", + "name": "albinism", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "HP:0001022", + "name": "Albinism", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": "\n\nMorell et al. (1997) " + }, + { + "text": "presented", + "tokens": [ + { + "id": "PATO:0000467", + "name": "present", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " an update of the clinical findings in the " + }, + { + "text": "family", + "tokens": [ + { + "id": "NCBITaxon:family", + "name": "family", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "PCO:0000020", + "name": "family", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " of Bard (1978). The " + }, + { + "text": "deafness", + "tokens": [ + { + "id": "MP:0001967", + "name": "deafness", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "HP:0000365", + "name": "Hearing impairment", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0005365", + "name": "hearing loss disorder", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " was sensorineural and " + }, + { + "text": "congenital.", + "tokens": [ + { + "id": "MONDO:0021140", + "name": "congenital", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "Heterochromia " + }, + { + "text": "iridis", + "tokens": [ + { + "id": "UBERON:0005969", + "name": "eye trabecular meshwork", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " was a " + }, + { + "text": "prominent", + "tokens": [ + { + "id": "PATO:0001482", + "name": "prominent", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " feature in 1 sibship in which both " + }, + { + "text": "segmental", + "tokens": [ + { + "id": "PATO:0002404", + "name": "segmental", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "iris", + "tokens": [ + { + "id": "ZFA:0001238", + "name": "iris", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "UBERON:0001769", + "name": "iris", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "ECO:0005520", + "name": "interferometric reflectance imaging sensor evidence", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0100185", + "name": "immune reconstitution inflammatory syndrome", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " bicolor and complete heterochromia " + }, + { + "text": "occurred.", + "tokens": [ + { + "id": "BFO:0000066", + "name": "occurs in", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "OBO:mp/mp-equivalent-axioms-subq#occurs_in", + "name": "occurs in", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " Most of the " + }, + { + "text": "affected", + "tokens": [ + { + "id": "HP:0032320", + "name": "Affected", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "RO:0002418", + "name": "causally upstream of or within", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "RO:0002264", + "name": "acts upstream of or within", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " individuals showed transillumination " + }, + { + "text": "defects", + "tokens": [ + { + "id": "MONDO:0008568", + "name": "thyroid hormone plasma membrane transport defect", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " of the " + }, + { + "text": "iris.", + "tokens": [ + { + "id": "ZFA:0001238", + "name": "iris", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "UBERON:0001769", + "name": "iris", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "ECO:0005520", + "name": "interferometric reflectance imaging sensor evidence", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0100185", + "name": "immune reconstitution inflammatory syndrome", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "Hypopigmentation", + "tokens": [ + { + "id": "MONDO:0007459", + "name": "dilution, pigmentary", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MP:0005408", + "name": "hypopigmentation", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "HP:0001010", + "name": "Hypopigmentation of the skin", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " of the " + }, + { + "text": "fundus", + "tokens": [ + { + "id": "UBERON:0003951", + "name": "ocular fundus", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " was " + }, + { + "text": "mild", + "tokens": [ + { + "id": "HP:0012825", + "name": "Mild", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " in some, " + }, + { + "text": "moderate", + "tokens": [ + { + "id": "HP:0012826", + "name": "Moderate", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " in others, and " + }, + { + "text": "severe", + "tokens": [ + { + "id": "HP:0012828", + "name": "Severe", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " in yet others. Almost all " + }, + { + "text": "affected", + "tokens": [ + { + "id": "HP:0032320", + "name": "Affected", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "RO:0002418", + "name": "causally upstream of or within", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "RO:0002264", + "name": "acts upstream of or within", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " individuals had " + }, + { + "text": "strabismus", + "tokens": [ + { + "id": "MP:0005254", + "name": "strabismus", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0003432", + "name": "strabismus", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "HP:0000486", + "name": "Strabismus", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " and visual acuity " + }, + { + "text": "defects.", + "tokens": [ + { + "id": "MONDO:0008568", + "name": "thyroid hormone plasma membrane transport defect", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " One individual with a " + }, + { + "text": "prominent", + "tokens": [ + { + "id": "PATO:0001482", + "name": "prominent", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "white", + "tokens": [ + { + "id": "PATO:0000323", + "name": "white", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " " + }, + { + "text": "forelock,", + "tokens": [ + { + "id": "MONDO:0022109", + "name": "catatrichy", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " characteristic of " + }, + { + "text": "Waardenburg " + }, + { + "text": "syndrome,", + "tokens": [ + { + "id": "MONDO:0002254", + "name": "syndromic disease", + "category": "biolink:PhenotypicQuality" + }, + { + "id": "MONDO:0024541", + "name": "trichohepatoenteric syndrome 1", + "category": "biolink:PhenotypicQuality" + } + ] + }, + { + "text": " was pictured" + }, + { + "text": "" + } +] diff --git a/frontend/public/mockServiceWorker.js b/frontend/public/mockServiceWorker.js index 81aef75a8..e369128ec 100644 --- a/frontend/public/mockServiceWorker.js +++ b/frontend/public/mockServiceWorker.js @@ -2,13 +2,13 @@ /* tslint:disable */ /** - * Mock Service Worker (2.0.9). + * Mock Service Worker (2.0.11). * @see https://github.com/mswjs/msw * - Please do NOT modify this file. * - Please do NOT serve this file on production. */ -const INTEGRITY_CHECKSUM = '0877fcdc026242810f5bfde0d7178db4' +const INTEGRITY_CHECKSUM = 'c5f7f8e188b673ea4e677df7ea3c5a39' const IS_MOCKED_RESPONSE = Symbol('isMockedResponse') const activeClientIds = new Set() @@ -121,11 +121,6 @@ async function handleRequest(event, requestId) { if (client && activeClientIds.has(client.id)) { ;(async function () { const responseClone = response.clone() - // When performing original requests, response body will - // always be a ReadableStream, even for 204 responses. - // But when creating a new Response instance on the client, - // the body for a 204 response must be null. - const responseBody = response.status === 204 ? null : responseClone.body sendToClient( client, @@ -137,11 +132,11 @@ async function handleRequest(event, requestId) { type: responseClone.type, status: responseClone.status, statusText: responseClone.statusText, - body: responseBody, + body: responseClone.body, headers: Object.fromEntries(responseClone.headers.entries()), }, }, - [responseBody], + [responseClone.body], ) })() } diff --git a/frontend/src/api/index.ts b/frontend/src/api/index.ts index 8a9e38fdc..3331dbcf2 100644 --- a/frontend/src/api/index.ts +++ b/frontend/src/api/index.ts @@ -5,7 +5,7 @@ import { getUrl } from "@/util/url"; export const biolink = "https://api.monarchinitiative.org/api"; /** served location of web app, from address bar or storage redirect */ -const url = new URL(window.sessionStorage.redirectHref || window.location.href); +const url = new URL(window.sessionStorage.redirect || window.location.href); /** get monarch api name/version to use */ @@ -21,7 +21,7 @@ if (url.hostname === "monarchinitiative.org") fromDomain = "prod"; const fromEnv = import.meta.env.VITE_API || ""; /** from param in url */ -const fromParam = new URLSearchParams(url.search).get("api") || ""; +const fromParam = url.searchParams.get("api") || ""; /** name of monarch api version to use. highest to lowest override priority. */ export const apiName = fromParam || fromEnv || fromDomain || "prod"; diff --git a/frontend/src/api/text-annotator.ts b/frontend/src/api/text-annotator.ts index 0f903d3ec..16bef7800 100644 --- a/frontend/src/api/text-annotator.ts +++ b/frontend/src/api/text-annotator.ts @@ -1,20 +1,16 @@ -import { getCategoryLabel } from "./categories"; -import { biolink, request } from "./index"; +import type { Node } from "@/api/model"; +import { stringify } from "@/util/object"; +import { apiUrl, request } from "./index"; /** annotations (from backend) */ -type _Annotations = { - content: string; - spans: { - start: number; - end: number; - text: string; - token: { - id: string; - category: string[]; - terms: string[]; - }[]; +export type _Annotations = { + text: string; + tokens?: { + id: string; + name: string; + category: string; }[]; -}; +}[]; /** get annotations from full text */ export const annotateText = async (content = ""): Promise => { @@ -22,60 +18,32 @@ export const annotateText = async (content = ""): Promise => { if (!content.trim()) return []; /** request params */ - const params = { longest_only: true }; + const params = {}; /** make request options */ const headers = new Headers(); - headers.append( - "Content-Type", - "application/x-www-form-urlencoded;charset=UTF-8", - ); - const body = "content=" + window.encodeURIComponent(content); - const options = { method: "POST", headers, body }; + headers.append("Content-Type", "application/json"); + headers.append("Accept", "application/json"); + const options = { + method: "POST", + headers, + body: stringify({ content }), + }; /** make query */ - const url = `${biolink}/nlp/annotate/entities`; + const url = `${apiUrl}/annotate`; const response = await request<_Annotations>(url, params, options); - const { spans } = response; - /** empty */ - if (!spans.length) return []; + const transformedResponse = response.map((item) => ({ + ...item, + tokens: item.tokens || [], + })); - /** get ordered, de-duped list of string indices, including start and end */ - const indices: [number, number][] = [ - 0, - ...new Set(spans.map(({ start, end }) => [start, end]).flat()), - content.length - 1, - ] - .sort((a, b) => a - b) - .map((index, i, array) => [index, array[i + 1] || index]); - - /** convert into desired result format */ - const annotations: Annotations = []; - for (const [start, end] of indices) { - annotations.push({ - text: content.slice(start, end), - tokens: spans - .filter((span) => span.start === start && span.end === end) - .map(({ token }) => token[0]) - .filter((token) => token) - .map((token) => ({ - id: token.id, - name: token.terms.join(", "), - category: getCategoryLabel(token.category), - })), - }); - } - - return annotations; + return transformedResponse; }; /** annotations (for frontend) */ export type Annotations = { text: string; - tokens: { - id: string; - name: string; - category: string; - }[]; + tokens: Partial[]; }[]; diff --git a/frontend/src/components/AppNodeBadge.vue b/frontend/src/components/AppNodeBadge.vue index 86799df03..85e9c6dbb 100644 --- a/frontend/src/components/AppNodeBadge.vue +++ b/frontend/src/components/AppNodeBadge.vue @@ -21,6 +21,7 @@ >{{ node.name || node.id }} {{ node.name }} + ({{ node.id }}) ({{ node.in_taxon_label }}) ({{ node.info }}) @@ -52,6 +53,8 @@ type Props = { state?: { [key: string]: unknown }; /** whether to use absolute link */ absolute?: boolean; + /** whether show id */ + showId?: boolean; }; const props = withDefaults(defineProps(), { diff --git a/frontend/src/global/styles.scss b/frontend/src/global/styles.scss index 9901cd63e..10cdfafc2 100644 --- a/frontend/src/global/styles.scss +++ b/frontend/src/global/styles.scss @@ -175,6 +175,14 @@ strong { opacity: 0.5; } +/** text with tooltip */ + +[data-tooltip] { + text-decoration: underline; + text-decoration-style: dashed; + text-underline-offset: 2px; +} + /** notification dot */ .notification { diff --git a/frontend/src/main.ts b/frontend/src/main.ts index b8fdbf521..90f4a84d8 100644 --- a/frontend/src/main.ts +++ b/frontend/src/main.ts @@ -53,7 +53,9 @@ if (new URL(window.location.href).hostname.endsWith("monarchinitiative.org")) { if ( import.meta.env.MODE === "test" || import.meta.env.VITE_MOCK === "true" || - new URLSearchParams(window.location.search).get("mock") === "true" + new URL( + window.sessionStorage.redirect || window.location.href, + ).searchParams.get("mock") === "true" ) { const { setupWorker } = await import("msw/browser"); const { handlers } = await import("../fixtures"); diff --git a/frontend/src/pages/explore/TabTextAnnotator.vue b/frontend/src/pages/explore/TabTextAnnotator.vue index 1cdab4ba8..ef9c4f8ec 100644 --- a/frontend/src/pages/explore/TabTextAnnotator.vue +++ b/frontend/src/pages/explore/TabTextAnnotator.vue @@ -43,15 +43,16 @@ :append-to="appendToBody" :tabindex="tokens.length ? 0 : -1" tag="span" - > - {{ text }} -