diff --git a/pyproject.toml b/pyproject.toml index 965bbd4f..5498f384 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,13 +29,13 @@ dependencies = [ "uvicorn", "click", "boto3", - "ga4gh.vrs~=2.0.0a8", + "ga4gh.vrs==2.0.0a13", ] dynamic = ["version"] [project.optional-dependencies] etl = [ - "disease-normalizer[etl]~=0.5.0", + "disease-normalizer[etl]~=0.7.0", "owlready2", "rdflib", "wikibaseintegrator>=0.12.0", diff --git a/src/therapy/etl/base.py b/src/therapy/etl/base.py index 70d2c9df..45bb5c55 100644 --- a/src/therapy/etl/base.py +++ b/src/therapy/etl/base.py @@ -286,7 +286,7 @@ def _normalize_disease(self, query: str) -> str | None: if term in self._disease_cache: return self._disease_cache[term] response = self.disease_normalizer.normalize(term) - normalized_id = response.normalized_id + normalized_id = response.disease.primaryCode.root if response.disease else None self._disease_cache[term] = normalized_id if normalized_id is None: _logger.warning("Failed to normalize disease term: %s", query) diff --git a/src/therapy/main.py b/src/therapy/main.py index 8a006a06..c29c722d 100644 --- a/src/therapy/main.py +++ b/src/therapy/main.py @@ -74,7 +74,7 @@ def custom_openapi() -> dict: "Return merged strongest-match concept for query string " "provided by user." ) merged_matches_summary = ( - "Given query, provide merged normalized record as a " "Therapeutic Agent." + "Given query, provide merged normalized record as a Therapy Mappable Concept." ) merged_response_descr = "A response to a validly-formed query." normalize_q_descr = "Therapy to normalize." @@ -148,7 +148,7 @@ def normalize( :param q: therapy search term :param bool infer_namespace: if True, try to infer namespace from query term. :returns: JSON response with matching normalized record provided as a - Therapeutic Agent, and source metadata + Therapy Mappable Concept, and source metadata """ try: response = query_handler.normalize(html.unescape(q), infer_namespace) diff --git a/src/therapy/query.py b/src/therapy/query.py index a85aca95..51362dcd 100644 --- a/src/therapy/query.py +++ b/src/therapy/query.py @@ -7,12 +7,23 @@ from typing import Any, TypeVar from botocore.exceptions import ClientError -from ga4gh.core import domain_models, entity_models +from disease.schemas import NAMESPACE_TO_SYSTEM_URI as DISEASE_NAMESPACE_TO_SYSTEM_URI +from disease.schemas import NamespacePrefix as DiseaseNamespacePrefix +from ga4gh.core.models import ( + Coding, + ConceptMapping, + Extension, + MappableConcept, + Relation, + code, +) from uvicorn.config import logger from therapy import NAMESPACE_LUIS, PREFIX_LOOKUP, SOURCES from therapy.database import AbstractDatabase from therapy.schemas import ( + NAMESPACE_TO_SYSTEM_URI, + SYSTEM_URI_TO_NAMESPACE, BaseNormalizationService, HasIndication, MatchesNormalized, @@ -350,20 +361,17 @@ def _add_merged_meta(self, response: NormalizationService) -> NormalizationServi :return: completed response object. """ sources_meta = {} - therapeutic_agent = response.therapeutic_agent - sources = [response.normalized_id.split(":")[0]] # type: ignore[union-attr] - if therapeutic_agent.mappings: # type: ignore[union-attr] - sources += [m.coding.system for m in therapeutic_agent.mappings] # type: ignore[union-attr] + therapy = response.therapy + + sources = [] + for m in therapy.mappings or []: + ns = SYSTEM_URI_TO_NAMESPACE.get(m.coding.system) + if ns in PREFIX_LOOKUP: + sources.append(PREFIX_LOOKUP[ns]) for src in sources: - try: - src_name = SourceName(PREFIX_LOOKUP[src]) - except KeyError: - # not an imported source - continue - else: - if src_name not in sources_meta: - sources_meta[src_name] = self.db.get_source_metadata(src_name) + if src not in sources_meta: + sources_meta[src] = self.db.get_source_metadata(src) response.source_meta_ = sources_meta # type: ignore[assignment] return response @@ -377,42 +385,88 @@ def _record_order(self, record: dict) -> tuple[int, str]: source_rank = SourcePriority[src] return source_rank, record["concept_id"] - def _add_therapeutic_agent( + def _add_therapy( self, response: NormalizationService, record: dict, match_type: MatchType, ) -> NormalizationService: - """Format received DB record as therapeutic agent and update response object. + """Format received DB record as Mappable Concept and update response object. :param NormalizationService response: in-progress response object :param Dict record: record as stored in DB :param str query: query string from user request :param MatchType match_type: type of match achieved :return: completed response object ready to return to user """ - therapeutic_agent_obj = domain_models.TherapeuticAgent( - id=f"normalize.therapy.{record['concept_id']}", label=record.get("label") + + def _create_concept_mapping( + concept_id: str, + relation: Relation, + ns_to_system_uri: dict[str, str], + ns_prefix: NamespacePrefix | DiseaseNamespacePrefix, + ) -> ConceptMapping: + """Create concept mapping for therapy or disease identifier + + ``system`` will use OBO Foundry persistent URL (PURL), source homepage, or + namespace prefix, in that order of preference, if available. + + :param concept_id: Concept identifier represented as a curie + :param relation: SKOS mapping relationship, default is relatedMatch + :param ns_to_system_uri: Dictionary containing mapping from namespace to + system URI + :param ns_prefix: Namespace prefix enum + :return: Concept mapping for therapy or disease identifier + """ + source = concept_id.split(":")[0] + + try: + source = ns_prefix(source) + except ValueError: + try: + source = ns_prefix(source.upper()) + except ValueError as e: + err_msg = f"Namespace prefix not supported: {source}" + raise ValueError(err_msg) from e + + system = ns_to_system_uri.get(source, source) + + return ConceptMapping( + coding=Coding(code=code(concept_id), system=system), relation=relation + ) + + therapy_obj = MappableConcept( + id=f"normalize.therapy.{record['concept_id']}", + primaryCode=code(root=record["concept_id"]), + conceptType="Therapy", + label=record.get("label"), ) + # mappings + mappings = [ + _create_concept_mapping( + concept_id=record["concept_id"], + relation=Relation.EXACT_MATCH, + ns_to_system_uri=NAMESPACE_TO_SYSTEM_URI, + ns_prefix=NamespacePrefix, + ) + ] source_ids = record.get("xrefs", []) + record.get("associated_with", []) - mappings = [] - for source_id in source_ids: - system, code = source_id.split(":") - mappings.append( - entity_models.ConceptMapping( - coding=entity_models.Coding( - code=entity_models.Code(code), system=system.lower() - ), - relation=entity_models.Relation.RELATED_MATCH, - ) + mappings.extend( + _create_concept_mapping( + concept_id=source_id, + relation=Relation.RELATED_MATCH, + ns_to_system_uri=NAMESPACE_TO_SYSTEM_URI, + ns_prefix=NamespacePrefix, ) + for source_id in source_ids + ) if mappings: - therapeutic_agent_obj.mappings = mappings + therapy_obj.mappings = mappings + extensions = [] if "aliases" in record: - therapeutic_agent_obj.alternativeLabels = record["aliases"] + extensions.append(Extension(name="aliases", value=record["aliases"])) - extensions = [] if any( filter( lambda f: f in record, @@ -435,49 +489,44 @@ def _add_therapeutic_agent( indication = self._get_indication(ind_db) if indication.normalized_disease_id: - system, code = indication.normalized_disease_id.split(":") mappings = [ - entity_models.ConceptMapping( - coding=entity_models.Coding( - code=entity_models.Code(code), system=system.lower() - ), - relation=entity_models.Relation.RELATED_MATCH, + _create_concept_mapping( + concept_id=indication.normalized_disease_id, + relation=Relation.RELATED_MATCH, + ns_to_system_uri=DISEASE_NAMESPACE_TO_SYSTEM_URI, + ns_prefix=DiseaseNamespacePrefix, ) ] else: mappings = [] - ind_disease_obj = domain_models.Disease( + ind_disease_obj = MappableConcept( id=indication.disease_id, + conceptType="Disease", label=indication.disease_label, mappings=mappings or None, ) if indication.supplemental_info: ind_disease_obj.extensions = [ - entity_models.Extension(name=k, value=v) + Extension(name=k, value=v) for k, v in indication.supplemental_info.items() ] inds_list.append(ind_disease_obj.model_dump(exclude_none=True)) if inds_list: approv_value["has_indication"] = inds_list - approv = entity_models.Extension( - name="regulatory_approval", value=approv_value - ) + approv = Extension(name="regulatory_approval", value=approv_value) extensions.append(approv) trade_names = record.get("trade_names") if trade_names: - extensions.append( - entity_models.Extension(name="trade_names", value=trade_names) - ) + extensions.append(Extension(name="trade_names", value=trade_names)) if extensions: - therapeutic_agent_obj.extensions = extensions + therapy_obj.extensions = extensions response.match_type = match_type - response.normalized_id = record["concept_id"] - response.therapeutic_agent = therapeutic_agent_obj + response.therapy = therapy_obj return self._add_merged_meta(response) def _resolve_merge( @@ -537,7 +586,7 @@ def normalize(self, query: str, infer: bool = True) -> NormalizationService: response = NormalizationService(**self._prepare_normalized_response(query)) return self._perform_normalized_lookup( - response, query, infer, self._add_therapeutic_agent + response, query, infer, self._add_therapy ) def _construct_drug_match(self, record: dict) -> Therapy: diff --git a/src/therapy/schemas.py b/src/therapy/schemas.py index 26df31ef..12d2490a 100644 --- a/src/therapy/schemas.py +++ b/src/therapy/schemas.py @@ -4,7 +4,7 @@ from enum import Enum, IntEnum from typing import Any, Literal -from ga4gh.core import domain_models +from ga4gh.core.models import MappableConcept from pydantic import BaseModel, ConfigDict, StrictBool, constr from therapy import __version__ @@ -258,6 +258,44 @@ class NamespacePrefix(Enum): WIKIDATA = "wikidata" +# Source to URI. Will use OBO Foundry persistent URL (PURL) or source homepage +NAMESPACE_TO_SYSTEM_URI: dict[NamespacePrefix, str] = { + NamespacePrefix.ATC: "https://www.who.int/tools/atc-ddd-toolkit/atc-classification/", + NamespacePrefix.CHEBI: "http://purl.obolibrary.org/obo/chebi.owl", + NamespacePrefix.CHEMBL: "https://www.ebi.ac.uk/chembl/", + NamespacePrefix.CHEMIDPLUS: "https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus", + NamespacePrefix.CASREGISTRY: "https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus", + NamespacePrefix.CVX: "https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx", + NamespacePrefix.DRUGBANK: "https://go.drugbank.com", + NamespacePrefix.DRUGCENTRAL: "https://drugcentral.org", + NamespacePrefix.DRUGSATFDA_ANDA: "https://www.fda.gov/drugs/types-applications/abbreviated-new-drug-application-anda", + NamespacePrefix.DRUGSATFDA_NDA: "https://www.fda.gov/drugs/types-applications/new-drug-application-nda", + NamespacePrefix.HEMONC: "https://hemonc.org", + NamespacePrefix.INCHIKEY: "https://www.chemspider.com", + NamespacePrefix.IUPHAR_LIGAND: "https://www.guidetopharmacology.org/GRAC/LigandListForward", + NamespacePrefix.GUIDETOPHARMACOLOGY: "https://www.guidetopharmacology.org/GRAC/LigandListForward", + NamespacePrefix.MMSL: "https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html", + NamespacePrefix.MSH: "https://id.nlm.nih.gov/mesh/", + NamespacePrefix.NCIT: "http://purl.obolibrary.org/obo/ncit.owl", + NamespacePrefix.NDC: "https://dps.fda.gov/ndc", + NamespacePrefix.PUBCHEMCOMPOUND: "https://pubchem.ncbi.nlm.nih.gov/docs/compounds", + NamespacePrefix.PUBCHEMSUBSTANCE: "https://pubchem.ncbi.nlm.nih.gov/docs/substances", + NamespacePrefix.RXNORM: "https://www.nlm.nih.gov/research/umls/rxnorm/index.html", + NamespacePrefix.SPL: "https://www.fda.gov/industry/fda-data-standards-advisory-board/structured-product-labeling-resources", + NamespacePrefix.UMLS: "https://www.nlm.nih.gov/research/umls/index.html", + NamespacePrefix.UNII: "https://precision.fda.gov/uniisearch", + NamespacePrefix.UNIPROT: "https://www.uniprot.org", + NamespacePrefix.USP: "https://www.usp.org/health-quality-safety/compendial-nomenclature", + NamespacePrefix.VANDF: "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF", + NamespacePrefix.WIKIDATA: "https://www.wikidata.org", +} + +# URI to source +SYSTEM_URI_TO_NAMESPACE = { + system_uri: ns.value for ns, system_uri in NAMESPACE_TO_SYSTEM_URI.items() +} + + class DataLicenseAttributes(BaseModel): """Define constraints for data license attributes.""" @@ -484,8 +522,7 @@ class UnmergedNormalizationService(BaseNormalizationService): class NormalizationService(BaseNormalizationService): """Response containing one or more merged records and source data.""" - normalized_id: str | None = None - therapeutic_agent: domain_models.TherapeuticAgent | None = None + therapy: MappableConcept | None = None source_meta_: dict[SourceName, SourceMeta] | None = None model_config = ConfigDict( @@ -494,18 +531,31 @@ class NormalizationService(BaseNormalizationService): "query": "cisplatin", "warnings": None, "match_type": 80, - "normalized_id": "rxcui:2555", - "therapeutic_agent": { - "type": "TherapeuticAgent", + "therapy": { + "conceptType": "Therapy", + "primaryCode": "rxcui:2555", "id": "normalize.therapy.rxcui:2555", "label": "cisplatin", "mappings": [ { - "coding": {"code": "C376", "system": "ncit"}, + "coding": { + "code": "2555", + "system": "https://www.nlm.nih.gov/research/umls/rxnorm/index.html", + }, + "relation": "exactMatch", + }, + { + "coding": { + "code": "C376", + "system": "http://purl.obolibrary.org/obo/ncit.owl", + }, "relation": "relatedMatch", }, { - "coding": {"code": "15663-27-1", "system": "chemidplus"}, + "coding": { + "code": "15663-27-1", + "system": "https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus", + }, "relation": "relatedMatch", }, { diff --git a/tests/data/fixtures/query_fixtures.json b/tests/data/fixtures/query_fixtures.json index 2bb93081..94d0d240 100644 --- a/tests/data/fixtures/query_fixtures.json +++ b/tests/data/fixtures/query_fixtures.json @@ -1,49 +1,53 @@ { "normalize_cisplatin": { - "type": "TherapeuticAgent", + "conceptType": "Therapy", "label": "cisplatin", "description": null, "id": "normalize.therapy.rxcui:2555", - "alternativeLabels": [ - "Liplacis", - "cis-diamminedichloroplatinum III", - "APRD00359", - "(sp-4-2)-diamminedichloroplatinum", - "cis-Diaminedichloroplatinum", - "CDDP", - "1,2-Diaminocyclohexaneplatinum II citrate", - "Platinol", - "Platinol-AQ", - "DDP", - "cis-platinum", - "cisplatino", - "PLATINUM, DIAMMINEDICHLORO-, (SP-4-2)-", - "Cis-diamminedichloroplatinum ii", - "INT230-6 COMPONENT CISPLATIN", - "Cis-diamminedichloroplatinum", - "DACP", - "Cis-DDP", - "cisplatinum", - "NSC 119875", - "cis-diamminedichloroplatinum(II)", - "Cis-platin", - "(SP-4-2)-DIAMMINEDICHLOROPLATINUM", - "NSC119875", - "CIS-DIAMMINEDICHLOROPLATINUM", - "NSC-119875", - "Cisplatinum", - "CIS-DIAMMINEDICHLOROPLATINUM II", - "INT-230-6 COMPONENT CISPLATIN", - "CIS-DDP", - "Peyrone's salt", - "Cis-platinum ii", - "CISplatin", - "Fauldiscipla", - "CISPLATIN", - "Cisplatin", - "Mitometh" - ], + "primaryCode": "rxcui:2555", "extensions": [ + { + "name": "aliases", + "value": [ + "Liplacis", + "cis-diamminedichloroplatinum III", + "APRD00359", + "(sp-4-2)-diamminedichloroplatinum", + "cis-Diaminedichloroplatinum", + "CDDP", + "1,2-Diaminocyclohexaneplatinum II citrate", + "Platinol", + "Platinol-AQ", + "DDP", + "cis-platinum", + "cisplatino", + "PLATINUM, DIAMMINEDICHLORO-, (SP-4-2)-", + "Cis-diamminedichloroplatinum ii", + "INT230-6 COMPONENT CISPLATIN", + "Cis-diamminedichloroplatinum", + "DACP", + "Cis-DDP", + "cisplatinum", + "NSC 119875", + "cis-diamminedichloroplatinum(II)", + "Cis-platin", + "(SP-4-2)-DIAMMINEDICHLOROPLATINUM", + "NSC119875", + "CIS-DIAMMINEDICHLOROPLATINUM", + "NSC-119875", + "Cisplatinum", + "CIS-DIAMMINEDICHLOROPLATINUM II", + "INT-230-6 COMPONENT CISPLATIN", + "CIS-DDP", + "Peyrone's salt", + "Cis-platinum ii", + "CISplatin", + "Fauldiscipla", + "CISPLATIN", + "Cisplatin", + "Mitometh" + ] + }, { "name": "regulatory_approval", "value": { @@ -54,7 +58,9 @@ "gtopdb_approved", "hemonc_approved" ], - "approval_year": ["1978"], + "approval_year": [ + "1978" + ], "has_indication": [ { "id": "hemonc:671", @@ -68,13 +74,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7251" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7251" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "hemonc:645", @@ -88,13 +94,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7431" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7431" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "hemonc:569", @@ -108,13 +114,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C9334" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C9334" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D013945", @@ -128,13 +134,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3411" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3411" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D064129", @@ -148,13 +154,13 @@ "mappings": [ { "coding": { - "system": "mondo", - "code": "0850353" + "system": "http://purl.obolibrary.org/obo/mondo.owl", + "code": "mondo:0850353" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D001661", @@ -168,13 +174,13 @@ "mappings": [ { "coding": { - "system": "mondo", - "code": "0003060" + "system": "http://purl.obolibrary.org/obo/mondo.owl", + "code": "mondo:0003060" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D009369", @@ -188,13 +194,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3262" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3262" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "EFO:0003868", @@ -208,13 +214,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7606" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7606" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D002294", @@ -228,13 +234,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C2929" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C2929" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018281", @@ -248,13 +254,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C4436" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C4436" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D004806", @@ -268,13 +274,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3017" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3017" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D004938", @@ -288,13 +294,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7478" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7478" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D055752", @@ -308,13 +314,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C4917" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C4917" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D007680", @@ -328,13 +334,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7548" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7548" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D002276", @@ -348,13 +354,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C2915" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C2915" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018242", @@ -368,13 +374,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3222" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3222" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D005185", @@ -388,13 +394,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3032" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3032" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D009190", @@ -408,13 +414,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3247" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3247" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D016403", @@ -428,13 +434,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C8851" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C8851" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D007674", @@ -448,13 +454,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3149" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3149" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D013274", @@ -468,13 +474,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3387" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3387" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D014565", @@ -485,7 +491,7 @@ "value": "chembl_phase_3" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D014523", @@ -499,13 +505,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3619" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3619" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D016411", @@ -519,13 +525,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3468" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3468" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D009373", @@ -539,13 +545,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3708" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3708" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D001005", @@ -559,13 +565,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C2877" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C2877" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D013953", @@ -579,13 +585,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C4962" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C4962" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D008107", @@ -599,13 +605,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3196" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3196" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D014846", @@ -619,13 +625,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7502" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7502" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D031901", @@ -639,13 +645,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C4699" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C4699" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D005706", @@ -659,13 +665,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3048" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3048" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D016545", @@ -679,13 +685,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C4533" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C4533" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D007012", @@ -699,13 +705,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7190" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7190" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D002292", @@ -719,13 +725,13 @@ "mappings": [ { "coding": { - "system": "mondo", - "code": "0005086" + "system": "http://purl.obolibrary.org/obo/mondo.owl", + "code": "mondo:0005086" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D004066", @@ -739,13 +745,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3959" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3959" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D008113", @@ -759,13 +765,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C34803" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C34803" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "EFO:1000043", @@ -779,13 +785,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7978" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7978" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D004067", @@ -799,13 +805,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C4890" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C4890" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D015179", @@ -819,13 +825,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C2956" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C2956" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D010190", @@ -839,13 +845,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3305" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3305" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D006258", @@ -859,13 +865,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C4013" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C4013" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D012208", @@ -879,13 +885,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3359" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3359" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D016483", @@ -899,13 +905,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3471" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3471" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D001932", @@ -919,13 +925,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3568" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3568" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D021441", @@ -939,13 +945,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C9120" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C9120" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D002822", @@ -959,13 +965,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C2948" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C2948" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D020250", @@ -976,7 +982,7 @@ "value": "chembl_phase_3" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D058922", @@ -990,13 +996,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C4001" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C4001" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D015266", @@ -1010,13 +1016,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C9231" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C9231" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D013736", @@ -1030,13 +1036,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7251" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7251" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D000077192", @@ -1050,13 +1056,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3512" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3512" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D014594", @@ -1070,13 +1076,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3552" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3552" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D005833", @@ -1090,13 +1096,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3053" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3053" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D052016", @@ -1110,13 +1116,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C115965" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C115965" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "EFO:0005570", @@ -1130,13 +1136,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C9314" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C9314" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D009101", @@ -1150,13 +1156,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3242" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3242" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D002280", @@ -1170,13 +1176,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C156767" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C156767" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D009959", @@ -1190,13 +1196,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7398" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7398" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D009447", @@ -1210,13 +1216,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3270" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3270" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D007938", @@ -1230,13 +1236,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3161" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3161" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D010610", @@ -1250,13 +1256,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7545" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7545" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D008545", @@ -1270,13 +1276,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3224" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3224" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D000306", @@ -1290,13 +1296,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C2858" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C2858" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D006689", @@ -1310,13 +1316,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C9357" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C9357" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D002583", @@ -1330,13 +1336,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C9311" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C9311" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D002289", @@ -1350,13 +1356,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C2926" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C2926" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D009325", @@ -1367,7 +1373,7 @@ "value": "chembl_phase_2" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018288", @@ -1381,13 +1387,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3915" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3915" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D000230", @@ -1401,13 +1407,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C2852" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C2852" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018287", @@ -1421,13 +1427,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3780" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3780" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018240", @@ -1441,13 +1447,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3011" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3011" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D001943", @@ -1461,13 +1467,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C2910" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C2910" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D010996", @@ -1478,7 +1484,7 @@ "value": "chembl_phase_3" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D016543", @@ -1492,13 +1498,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C4627" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C4627" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D012468", @@ -1512,13 +1518,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3811" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3811" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D006528", @@ -1532,13 +1538,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3099" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3099" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D008479", @@ -1552,13 +1558,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3549" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3549" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D013724", @@ -1572,13 +1578,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3403" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3403" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D010534", @@ -1592,13 +1598,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3322" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3322" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D010255", @@ -1612,13 +1618,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C6014" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C6014" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018285", @@ -1632,13 +1638,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C36077" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C36077" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018239", @@ -1652,13 +1658,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C9309" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C9309" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D010051", @@ -1672,13 +1678,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7431" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7431" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D008224", @@ -1692,13 +1698,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3209" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3209" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D000077195", @@ -1712,13 +1718,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C4044" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C4044" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D008654", @@ -1732,13 +1738,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3234" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3234" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018197", @@ -1752,13 +1758,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3728" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3728" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018236", @@ -1772,13 +1778,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3752" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3752" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D017728", @@ -1792,13 +1798,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3720" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3720" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D000740", @@ -1812,13 +1818,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C2869" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C2869" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D002277", @@ -1832,13 +1838,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C2916" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C2916" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D010412", @@ -1852,13 +1858,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3317" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3317" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D012878", @@ -1872,13 +1878,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3372" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3372" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D012175", @@ -1892,13 +1898,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7541" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7541" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D012509", @@ -1912,13 +1918,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C9118" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C9118" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018273", @@ -1932,13 +1938,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3770" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3770" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D008223", @@ -1952,13 +1958,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3208" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3208" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D008228", @@ -1972,13 +1978,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3211" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3211" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D008175", @@ -1992,13 +1998,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3200" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3200" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D001749", @@ -2012,13 +2018,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C9334" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C9334" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D015459", @@ -2032,13 +2038,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3184" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3184" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D008527", @@ -2052,13 +2058,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3222" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3222" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D016889", @@ -2072,13 +2078,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3012" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3012" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D013280", @@ -2092,13 +2098,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C26887" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C26887" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D020522", @@ -2112,13 +2118,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C4337" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C4337" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D014987", @@ -2129,7 +2135,7 @@ "value": "chembl_phase_1" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D012516", @@ -2143,13 +2149,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C9145" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C9145" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018312", @@ -2163,13 +2169,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3794" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3794" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D009303", @@ -2183,13 +2189,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3257" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3257" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D005910", @@ -2203,13 +2209,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3059" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3059" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018305", @@ -2223,13 +2229,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3790" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3790" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D009362", @@ -2240,7 +2246,7 @@ "value": "chembl_phase_2" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D006103", @@ -2254,13 +2260,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C8196" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C8196" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D007822", @@ -2274,13 +2280,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3156" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3156" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D055728", @@ -2294,13 +2300,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C2862" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C2862" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D007119", @@ -2314,13 +2320,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7528" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7528" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018278", @@ -2334,13 +2340,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3773" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3773" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D008288", @@ -2354,13 +2360,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C34797" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C34797" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D018269", @@ -2374,13 +2380,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7558" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7558" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D014062", @@ -2394,13 +2400,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C9345" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C9345" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D013964", @@ -2414,13 +2420,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C7510" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C7510" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D046152", @@ -2434,13 +2440,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3868" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3868" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D064726", @@ -2454,13 +2460,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C71732" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C71732" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" } ] } @@ -2479,400 +2485,407 @@ "mappings": [ { "coding": { - "code": "C376", - "system": "ncit" + "code": "rxcui:2555", + "system": "https://www.nlm.nih.gov/research/umls/rxnorm/index.html" + }, + "relation": "exactMatch" + }, + { + "coding": { + "code": "ncit:C376", + "system": "http://purl.obolibrary.org/obo/ncit.owl" }, "relation": "relatedMatch" }, { "coding": { - "code": "105", - "system": "hemonc" + "code": "hemonc:105", + "system": "https://hemonc.org" }, "relation": "relatedMatch" }, { "coding": { - "code": "DB00515", - "system": "drugbank" + "code": "drugbank:DB00515", + "system": "https://go.drugbank.com" }, "relation": "relatedMatch" }, { "coding": { - "code": "DB12117", - "system": "drugbank" + "code": "drugbank:DB12117", + "system": "https://go.drugbank.com" }, "relation": "relatedMatch" }, { "coding": { - "code": "074656", - "system": "drugsatfda.anda" + "code": "drugsatfda.anda:074656", + "system": "https://www.fda.gov/drugs/types-applications/abbreviated-new-drug-application-anda" }, "relation": "relatedMatch" }, { "coding": { - "code": "074735", - "system": "drugsatfda.anda" + "code": "drugsatfda.anda:074735", + "system": "https://www.fda.gov/drugs/types-applications/abbreviated-new-drug-application-anda" }, "relation": "relatedMatch" }, { "coding": { - "code": "075036", - "system": "drugsatfda.anda" + "code": "drugsatfda.anda:075036", + "system": "https://www.fda.gov/drugs/types-applications/abbreviated-new-drug-application-anda" }, "relation": "relatedMatch" }, { "coding": { - "code": "206774", - "system": "drugsatfda.anda" + "code": "drugsatfda.anda:206774", + "system": "https://www.fda.gov/drugs/types-applications/abbreviated-new-drug-application-anda" }, "relation": "relatedMatch" }, { "coding": { - "code": "207323", - "system": "drugsatfda.anda" + "code": "drugsatfda.anda:207323", + "system": "https://www.fda.gov/drugs/types-applications/abbreviated-new-drug-application-anda" }, "relation": "relatedMatch" }, { "coding": { - "code": "018057", - "system": "drugsatfda.nda" + "code": "drugsatfda.nda:018057", + "system": "https://www.fda.gov/drugs/types-applications/new-drug-application-nda" }, "relation": "relatedMatch" }, { "coding": { - "code": "5343", - "system": "iuphar.ligand" + "code": "iuphar.ligand:5343", + "system": "https://www.guidetopharmacology.org/GRAC/LigandListForward" }, "relation": "relatedMatch" }, { "coding": { - "code": "CHEMBL11359", - "system": "chembl" + "code": "chembl:CHEMBL11359", + "system": "https://www.ebi.ac.uk/chembl/" }, "relation": "relatedMatch" }, { "coding": { - "code": "15663-27-1", - "system": "chemidplus" + "code": "chemidplus:15663-27-1", + "system": "https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus" }, "relation": "relatedMatch" }, { "coding": { - "code": "Q412415", - "system": "wikidata" + "code": "wikidata:Q412415", + "system": "https://www.wikidata.org" }, "relation": "relatedMatch" }, { "coding": { - "code": "0703-5748", - "system": "ndc" + "code": "ndc:0703-5748", + "system": "https://dps.fda.gov/ndc" }, "relation": "relatedMatch" }, { "coding": { - "code": "63323-103", - "system": "ndc" + "code": "ndc:63323-103", + "system": "https://dps.fda.gov/ndc" }, "relation": "relatedMatch" }, { "coding": { - "code": "70860-206", - "system": "ndc" + "code": "ndc:70860-206", + "system": "https://dps.fda.gov/ndc" }, "relation": "relatedMatch" }, { "coding": { - "code": "44567-509", - "system": "ndc" + "code": "ndc:44567-509", + "system": "https://dps.fda.gov/ndc" }, "relation": "relatedMatch" }, { "coding": { - "code": "m17910", - "system": "usp" + "code": "usp:m17910", + "system": "https://www.usp.org/health-quality-safety/compendial-nomenclature" }, "relation": "relatedMatch" }, { "coding": { - "code": "44567-530", - "system": "ndc" + "code": "ndc:44567-530", + "system": "https://dps.fda.gov/ndc" }, "relation": "relatedMatch" }, { "coding": { - "code": "178102005", - "system": "pubchem.substance" + "code": "pubchem.substance:178102005", + "system": "https://pubchem.ncbi.nlm.nih.gov/docs/substances" }, "relation": "relatedMatch" }, { "coding": { - "code": "9b008181-ab66-db2f-e053-2995a90aad57", - "system": "spl" + "code": "spl:9b008181-ab66-db2f-e053-2995a90aad57", + "system": "https://www.fda.gov/industry/fda-data-standards-advisory-board/structured-product-labeling-resources" }, "relation": "relatedMatch" }, { "coding": { - "code": "16729-288", - "system": "ndc" + "code": "ndc:16729-288", + "system": "https://dps.fda.gov/ndc" }, "relation": "relatedMatch" }, { "coding": { - "code": "a66eda32-1164-439a-ac8e-73138365ec06", - "system": "spl" + "code": "spl:a66eda32-1164-439a-ac8e-73138365ec06", + "system": "https://www.fda.gov/industry/fda-data-standards-advisory-board/structured-product-labeling-resources" }, "relation": "relatedMatch" }, { "coding": { - "code": "dd45d777-d4c1-40ee-b4f0-c9e001a15a8c", - "system": "spl" + "code": "spl:dd45d777-d4c1-40ee-b4f0-c9e001a15a8c", + "system": "https://www.fda.gov/industry/fda-data-standards-advisory-board/structured-product-labeling-resources" }, "relation": "relatedMatch" }, { "coding": { - "code": "27899", - "system": "chebi" + "code": "CHEBI:27899", + "system": "http://purl.obolibrary.org/obo/chebi.owl" }, "relation": "relatedMatch" }, { "coding": { - "code": "44567-511", - "system": "ndc" + "code": "ndc:44567-511", + "system": "https://dps.fda.gov/ndc" }, "relation": "relatedMatch" }, { "coding": { - "code": "0703-5747", - "system": "ndc" + "code": "ndc:0703-5747", + "system": "https://dps.fda.gov/ndc" }, "relation": "relatedMatch" }, { "coding": { - "code": "68083-162", - "system": "ndc" + "code": "ndc:68083-162", + "system": "https://dps.fda.gov/ndc" }, "relation": "relatedMatch" }, { "coding": { - "code": "L01XA01", - "system": "atc" + "code": "atc:L01XA01", + "system": "https://www.who.int/tools/atc-ddd-toolkit/atc-classification/" }, "relation": "relatedMatch" }, { "coding": { - "code": "44567-510", - "system": "ndc" + "code": "ndc:44567-510", + "system": "https://dps.fda.gov/ndc" }, "relation": "relatedMatch" }, { "coding": { - "code": "31747", - "system": "mmsl" + "code": "mmsl:31747", + "system": "https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html" }, "relation": "relatedMatch" }, { "coding": { - "code": "2c569ef0-588f-4828-8b2d-03a2120c9b4c", - "system": "spl" + "code": "spl:2c569ef0-588f-4828-8b2d-03a2120c9b4c", + "system": "https://www.fda.gov/industry/fda-data-standards-advisory-board/structured-product-labeling-resources" }, "relation": "relatedMatch" }, { "coding": { - 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"system": "mondo", - "code": "0001475" + "system": "http://purl.obolibrary.org/obo/mondo.owl", + "code": "mondo:0001475" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D003866", @@ -2943,13 +2957,13 @@ "mappings": [ { "coding": { - "system": "mondo", - "code": "0002050" + "system": "http://purl.obolibrary.org/obo/mondo.owl", + "code": "mondo:0002050" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D008223", @@ -2963,13 +2977,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3208" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3208" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D012559", @@ -2983,13 +2997,13 @@ "mappings": [ { "coding": { - "system": "mondo", - "code": "0005090" + "system": "http://purl.obolibrary.org/obo/mondo.owl", + "code": "mondo:0005090" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D004827", @@ -3003,13 +3017,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3020" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3020" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D013226", @@ -3023,13 +3037,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C85079" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C85079" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D009357", @@ -3043,13 +3057,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C87101" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C87101" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D012640", @@ -3063,13 +3077,13 @@ "mappings": [ { "coding": { - "system": "ncit", - "code": "C3980" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C3980" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" }, { "id": "mesh:D001007", @@ -3083,13 +3097,13 @@ "mappings": [ { "coding": { - "system": "mondo", - "code": "0011918" + "system": "http://purl.obolibrary.org/obo/mondo.owl", + "code": "mondo:0011918" }, "relation": "relatedMatch" } ], - "type": "Disease" + "conceptType": "Disease" } ] } @@ -3104,304 +3118,340 @@ "Solfoton", "Phenobarbitone" ] + }, + { + "name": "aliases", + "value": [ + "PHENOBARBITAL", + "Phenemal", + "5-Ethyl-5-phenyl-2,4,6(1H,3H,5H)-pyrimidinetrione", + "phenobarbitone", + "Phenobarbitone", + "Phenobarbital civ", + "Phenylethylbarbituric Acid", + "phenobarb", + "PHENYLETHYLMALONYLUREA", + "Phenylethylbarbitursaeure", + "Phenylethylbarbitursäure", + "Phenobarbituric Acid", + "5-Ethyl-5-phenylbarbituric acid", + "PHENO", + "NSC-128143-", + "phenobarbital sodium", + "Phenylethylbarbiturate", + "Fenobarbital", + "phenobarbital", + "Phenobarbital", + "5-ethyl-5-phenyl-1,3-diazinane-2,4,6-trione", + "5-ethyl-5-phenylpyrimidine-2,4,6(1H,3H,5H)-trione", + "Luminal®", + "Phenylaethylbarbitursaeure", + "NSC-9848", + "5-ethyl-5-phenyl-2,4,6(1H,3H,5H)-pyrimidinetrione", + "5-Phenyl-5-ethylbarbituric acid", + "fenobarbital", + "NSC-128143", + "Luminal", + "Phenylethylmalonylurea", + "5-Ethyl-5-phenyl-pyrimidine-2,4,6-trione", + "Phenobarbitol", + "PHENobarbital", + "APRD00184", + "phenylethylbarbiturate", + "Phenyläthylbarbitursäure" + ] } ], "mappings": [ { "coding": { - 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"system": "inchikey", - "code": "ACTOXUHEUCPTEW-CEUOBAOPSA-N" + "system": "https://www.chemspider.com", + "code": "inchikey:ACTOXUHEUCPTEW-CEUOBAOPSA-N" }, "relation": "relatedMatch" }, { "coding": { - "system": "unii", - "code": "033ECH6IFG" + "system": "https://precision.fda.gov/uniisearch", + "code": "unii:033ECH6IFG" }, "relation": "relatedMatch" }, { "coding": { - "system": "umls", - "code": "C0037962" + "system": "https://www.nlm.nih.gov/research/umls/index.html", + "code": "umls:C0037962" }, "relation": "relatedMatch" } ], - "type": "TherapeuticAgent", - "alternativeLabels": [ - "Rovamycin", - "Spiramycin 1", - "Foromacidin A", - "SPIRAMYCIN", - "Spiramycin", - "Demycarosylturimycin H", - "Antibiotic 799", - "Rovamycine", - "(4R,5S,6R,7R,9R,10R,11E,13E,16R)-10-{[(2R,5S,6R)-5-(dimethylamino)-6-methyltetrahydro-2H-pyran-2-yl]oxy}-9,16-dimethyl-5-methoxy-2-oxo-7-(2-oxoethyl)oxacyclohexadeca-11,13-dien-6-yl 3,6-dideoxy-4-O-(2,6-dideoxy-3-C-methyl-alpha-L-ribo-hexopyranosyl)-3-(dimethylamino)-alpha-D-glucopyranoside", - "RP 5337", - "Provamycin", - "Spiramycin A", - "Spiramycin I", - "spiramycin I", - "Foromacidine A" + "conceptType": "Therapy", + "extensions": [ + { + "name": "aliases", + "value": [ + "Rovamycin", + "Spiramycin 1", + "Foromacidin A", + "SPIRAMYCIN", + "Spiramycin", + "Demycarosylturimycin H", + "Antibiotic 799", + "Rovamycine", + "(4R,5S,6R,7R,9R,10R,11E,13E,16R)-10-{[(2R,5S,6R)-5-(dimethylamino)-6-methyltetrahydro-2H-pyran-2-yl]oxy}-9,16-dimethyl-5-methoxy-2-oxo-7-(2-oxoethyl)oxacyclohexadeca-11,13-dien-6-yl 3,6-dideoxy-4-O-(2,6-dideoxy-3-C-methyl-alpha-L-ribo-hexopyranosyl)-3-(dimethylamino)-alpha-D-glucopyranoside", + "RP 5337", + "Provamycin", + "Spiramycin A", + "Spiramycin I", + "spiramycin I", + "Foromacidine A" + ] + } ] }, "normalize_therapeutic_procedure": { - "type": "TherapeuticAgent", + "conceptType": "Therapy", "label": "Therapeutic Procedure", "description": null, "id": "normalize.therapy.ncit:C49236", - "alternativeLabels": [ - "Therapeutic Interventions", - "any therapy", - "therapy", - "TX", - "TREAT", - "Therapeutic Method", - "Therapeutic", - "Treatment", - "Therapeutic Technique", - "Therapy", - "treatment_or_therapy", - "treatment or therapy", - "any_therapy", - "treatment" + "primaryCode": "ncit:C49236", + "extensions": [ + { + "name": "aliases", + "value": [ + "Therapeutic Interventions", + "any therapy", + "therapy", + "TX", + "TREAT", + "Therapeutic Method", + "Therapeutic", + "Treatment", + "Therapeutic Technique", + "Therapy", + "treatment_or_therapy", + "treatment or therapy", + "any_therapy", + "treatment" + ] + } ], "mappings": [ { "coding": { - "code": "C0087111", - "system": "umls" + "system": "http://purl.obolibrary.org/obo/ncit.owl", + "code": "ncit:C49236" + }, + "relation": "exactMatch" + }, + { + "coding": { + "code": "umls:C0087111", + "system": "https://www.nlm.nih.gov/research/umls/index.html" }, "relation": "relatedMatch" } @@ -3433,7 +3483,9 @@ ], "trade_names": [], "xrefs": [], - "associated_with": ["umls:C0087111"], + "associated_with": [ + "umls:C0087111" + ], "approval_ratings": null, "approval_year": [], "has_indication": [] @@ -3471,8 +3523,12 @@ "Spiramycin I" ], "trade_names": [], - "xrefs": ["drugbank:DB06145"], - "associated_with": ["atc:J01FA02"], + "xrefs": [ + "drugbank:DB06145" + ], + "associated_with": [ + "atc:J01FA02" + ], "approval_ratings": null, "approval_year": [], "has_indication": [] @@ -3506,8 +3562,13 @@ "RP 5337" ], "trade_names": [], - "xrefs": ["chemidplus:8025-81-8"], - "associated_with": ["umls:C0037962", "unii:71ODY0V87H"], + "xrefs": [ + "chemidplus:8025-81-8" + ], + "associated_with": [ + "umls:C0037962", + "unii:71ODY0V87H" + ], "approval_ratings": null, "approval_year": [], "has_indication": [] @@ -3540,7 +3601,9 @@ "Demycarosylturimycin H" ], "trade_names": [], - "xrefs": ["chemidplus:24916-50-5"], + "xrefs": [ + "chemidplus:24916-50-5" + ], "associated_with": [ "inchikey:ACTOXUHEUCPTEW-CEUOBAOPSA-N", "unii:033ECH6IFG" @@ -3571,7 +3634,9 @@ "aliases": [], "trade_names": [], "xrefs": [], - "associated_with": ["unii:71ODY0V87H"], + "associated_with": [ + "unii:71ODY0V87H" + ], "approval_ratings": null, "approval_year": [], "has_indication": [] @@ -3595,14 +3660,18 @@ { "concept_id": "wikidata:Q422265", "label": "spiramycin", - "aliases": ["spiramycin I"], + "aliases": [ + "spiramycin I" + ], "trade_names": [], "xrefs": [ "chemidplus:8025-81-8", "rxcui:9991", "chembl:CHEMBL1256397" ], - "associated_with": ["pubchem.compound:5356392"], + "associated_with": [ + "pubchem.compound:5356392" + ], "approval_ratings": null, "approval_year": [], "has_indication": [] @@ -3642,8 +3711,14 @@ "Cis-DDP", "PLATINUM, DIAMMINEDICHLORO-, (SP-4-2)-" ], - "trade_names": ["Platinol", "Cisplatin"], - "xrefs": ["drugbank:DB12117", "drugbank:DB00515"], + "trade_names": [ + "Platinol", + "Cisplatin" + ], + "xrefs": [ + "drugbank:DB12117", + "drugbank:DB00515" + ], "associated_with": [ "atc:L01XA01", "unii:Q20Q21Q62J", @@ -3653,7 +3728,9 @@ "vandf:4018139", "mmsl:d00195" ], - "approval_ratings": ["rxnorm_prescribable"], + "approval_ratings": [ + "rxnorm_prescribable" + ], "approval_year": [], "has_indication": [] } @@ -3678,7 +3755,9 @@ "label": "Cisplatin", "aliases": [], "trade_names": [], - "xrefs": ["chemidplus:15663-27-1"], + "xrefs": [ + "chemidplus:15663-27-1" + ], "associated_with": [ "CHEBI:27899", "unii:Q20Q21Q62J", @@ -3719,10 +3798,16 @@ "NSC119875" ], "trade_names": [], - "xrefs": ["rxcui:2555"], + "xrefs": [ + "rxcui:2555" + ], "associated_with": [], - "approval_ratings": ["hemonc_approved"], - "approval_year": ["1978"], + "approval_ratings": [ + "hemonc_approved" + ], + "approval_year": [ + "1978" + ], "has_indication": [ { "disease_id": "hemonc:671", @@ -3744,7 +3829,9 @@ "disease_id": "hemonc:645", "disease_label": "Ovarian cancer", "normalized_disease_id": "ncit:C7431", - "supplemental_info": { "regulatory_body": "FDA" } + "supplemental_info": { + "regulatory_body": "FDA" + } } ] } @@ -3775,7 +3862,9 @@ "APRD00359" ], "trade_names": [], - "xrefs": ["chemidplus:15663-27-1"], + "xrefs": [ + "chemidplus:15663-27-1" + ], "associated_with": [ "inchikey:LXZZYRPGZAFOLE-UHFFFAOYSA-L", "unii:Q20Q21Q62J" @@ -3787,9 +3876,13 @@ { "concept_id": "drugbank:DB12117", "label": "Mitometh", - "aliases": ["DDP"], + "aliases": [ + "DDP" + ], "trade_names": [], - "xrefs": ["chemidplus:107465-03-2"], + "xrefs": [ + "chemidplus:107465-03-2" + ], "associated_with": [ "unii:H8MTN7XVC2", "inchikey:MOTIYCLHZZLHHQ-UHFFFAOYSA-N" @@ -3819,14 +3912,18 @@ "label": "CISPLATIN", "aliases": [], "trade_names": [], - "xrefs": ["rxcui:309311"], + "xrefs": [ + "rxcui:309311" + ], "associated_with": [ "spl:adf5773e-9095-4cb4-a90f-72cbf82f4493", "ndc:0703-5748", "unii:Q20Q21Q62J", "ndc:0703-5747" ], - "approval_ratings": ["fda_prescription"], + "approval_ratings": [ + "fda_prescription" + ], "approval_year": [], "has_indication": [] }, @@ -3835,13 +3932,17 @@ "label": "CISPLATIN", "aliases": [], "trade_names": [], - "xrefs": ["rxcui:309311"], + "xrefs": [ + "rxcui:309311" + ], "associated_with": [ "ndc:63323-103", "unii:Q20Q21Q62J", "spl:9b008181-ab66-db2f-e053-2995a90aad57" ], - "approval_ratings": ["fda_prescription"], + "approval_ratings": [ + "fda_prescription" + ], "approval_year": [], "has_indication": [] }, @@ -3850,14 +3951,18 @@ "label": "CISPLATIN", "aliases": [], "trade_names": [], - "xrefs": ["rxcui:309311"], + "xrefs": [ + "rxcui:309311" + ], "associated_with": [ "ndc:0143-9505", "unii:Q20Q21Q62J", "ndc:0143-9504", "spl:2c569ef0-588f-4828-8b2d-03a2120c9b4c" ], - "approval_ratings": ["fda_prescription"], + "approval_ratings": [ + "fda_prescription" + ], "approval_year": [], "has_indication": [] }, @@ -3866,7 +3971,9 @@ "label": "CISPLATIN", "aliases": [], "trade_names": [], - "xrefs": ["rxcui:309311"], + "xrefs": [ + "rxcui:309311" + ], "associated_with": [ "ndc:16729-288", "spl:c43de769-d6d8-3bb9-e053-2995a90a5aa2", @@ -3874,7 +3981,9 @@ "spl:c3ddc4a5-9f1b-a8ee-e053-2a95a90a2265", "ndc:68001-283" ], - "approval_ratings": ["fda_prescription"], + "approval_ratings": [ + "fda_prescription" + ], "approval_year": [], "has_indication": [] }, @@ -3883,7 +3992,9 @@ "label": "CISPLATIN", "aliases": [], "trade_names": [], - "xrefs": ["rxcui:309311"], + "xrefs": [ + "rxcui:309311" + ], "associated_with": [ "ndc:72266-252", "spl:0219ee77-eb38-b81f-e063-6394a90a5ca4", @@ -3897,7 +4008,9 @@ "ndc:70860-206", "ndc:68083-163" ], - "approval_ratings": ["fda_prescription"], + "approval_ratings": [ + "fda_prescription" + ], "approval_year": [], "has_indication": [] }, @@ -3905,8 +4018,14 @@ "concept_id": "drugsatfda.nda:018057", "label": "CISPLATIN", "aliases": [], - "trade_names": ["PLATINOL-AQ", "PLATINOL"], - "xrefs": ["rxcui:309311", "rxcui:1736854"], + "trade_names": [ + "PLATINOL-AQ", + "PLATINOL" + ], + "xrefs": [ + "rxcui:309311", + "rxcui:1736854" + ], "associated_with": [ "unii:Q20Q21Q62J", "ndc:44567-509", @@ -3939,7 +4058,9 @@ { "concept_id": "iuphar.ligand:5343", "label": "cisplatin", - "aliases": ["Platinol"], + "aliases": [ + "Platinol" + ], "trade_names": [], "xrefs": [ "chemidplus:15663-27-1", @@ -3951,7 +4072,9 @@ "pubchem.substance:178102005", "CHEBI:27899" ], - "approval_ratings": ["gtopdb_approved"], + "approval_ratings": [ + "gtopdb_approved" + ], "approval_year": [], "has_indication": [] } @@ -3999,7 +4122,9 @@ ], "xrefs": [], "associated_with": [], - "approval_ratings": ["chembl_phase_4"], + "approval_ratings": [ + "chembl_phase_4" + ], "approval_year": [], "has_indication": [ { @@ -4988,8 +5113,12 @@ "1,2-Diaminocyclohexaneplatinum II citrate" ], "trade_names": [], - "xrefs": ["drugbank:DB00515"], - "associated_with": ["unii:Q20Q21Q62J"], + "xrefs": [ + "drugbank:DB00515" + ], + "associated_with": [ + "unii:Q20Q21Q62J" + ], "approval_ratings": null, "approval_year": [], "has_indication": [] @@ -5029,7 +5158,9 @@ "iuphar.ligand:5343", "drugbank:DB00515" ], - "associated_with": ["pubchem.compound:5702198"], + "associated_with": [ + "pubchem.compound:5702198" + ], "approval_ratings": null, "approval_year": [], "has_indication": [] diff --git a/tests/unit/test_query.py b/tests/unit/test_query.py index 11e6e43a..68416d08 100644 --- a/tests/unit/test_query.py +++ b/tests/unit/test_query.py @@ -5,7 +5,7 @@ from pathlib import Path import pytest -from ga4gh.core import domain_models +from ga4gh.core.models import MappableConcept from therapy.database.database import AbstractDatabase from therapy.query import InvalidParameterError, QueryHandler @@ -107,10 +107,10 @@ def unmerged_normalized_spiramycin(fixture_data): def compare_ta(response, fixture, query, match_type, warnings=None): - """Verify correctness of returned core therapeutic agent object against test fixture + """Verify correctness of returned core therapy object against test fixture :param Dict response: actual response - :param Dict fixture: expected therapeutic agent object + :param Dict fixture: expected therapy object :param str query: query used in search :param MatchType match_type: expected MatchType :param List warnings: expected warnings @@ -137,15 +137,17 @@ def compare_ta(response, fixture, query, match_type, warnings=None): assert response.match_type == match_type - fixture = domain_models.TherapeuticAgent(**fixture.copy()) - assert response.normalized_id == fixture.id.split("normalize.therapy.")[-1] - actual = response.therapeutic_agent + fixture = MappableConcept(**fixture.copy()) + assert ( + response.therapy.primaryCode.root == fixture.id.split("normalize.therapy.")[-1] + ) + actual = response.therapy actual_keys = actual.model_dump(exclude_none=True).keys() fixture_keys = fixture.model_dump(exclude_none=True).keys() assert actual_keys == fixture_keys assert actual.id == fixture.id - assert actual.type == fixture.type + assert actual.conceptType == fixture.conceptType assert actual.label == fixture.label assert bool(actual.mappings) == bool(fixture.mappings) @@ -162,10 +164,6 @@ def compare_ta(response, fixture, query, match_type, warnings=None): assert no_matches == [], no_matches assert len(actual.mappings) == len(fixture.mappings) - assert bool(actual.alternativeLabels) == bool(fixture.alternativeLabels) - if actual.alternativeLabels: - assert set(actual.alternativeLabels) == set(fixture.alternativeLabels) - def get_extension(extensions, name): matches = [e for e in extensions if e.name == name] if len(matches) > 1: