From 9fa4cd11ba4923fa152216907cea0f59f0b4b0a1 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 14 Jun 2024 17:29:48 -0400 Subject: [PATCH 1/7] Started updating NodeNorm Jupyter Notebook. --- documentation/NodeNormalization.ipynb | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/documentation/NodeNormalization.ipynb b/documentation/NodeNormalization.ipynb index e0d6936..68f2a11 100644 --- a/documentation/NodeNormalization.ipynb +++ b/documentation/NodeNormalization.ipynb @@ -21,13 +21,13 @@ "source": [ "## Introduction\n", "\n", - "[Node normalization](https://nodenormalization-sri.renci.org/apidocs) takes a CURIE, and returns:\n", + "The [Node Normalization Service](https://nodenormalization-sri.renci.org/docs) takes an input [CURIE](https://en.wikipedia.org/wiki/CURIE), and returns:\n", "\n", "* The preferred CURIE for this entity\n", "* All other known equivalent identifiers for the entity\n", "* Semantic types for the entity as defined by the [Biolink Model](https://biolink.github.io/biolink-model/)\n", "\n", - "The data currently served by Node Normalization is created by the prototype project [Babel](https://github.com/TranslatorIIPrototypes/Babel), which attempts to find identifier equivalences, and makes sure that CURIE prefixes are Biolink Model compliant. NodeNormalization, however, is independent of Babel and as improved identifier equivalence tools are developed, their results can be easily incorporated." + "The data currently served by the Node Normalization Service is created by [Babel](https://github.com/TranslatorSRI/Babel), a pipeline for combining identifiers from hundreds of data sources including ontologies and publicly accessible databases into a series of _cliques_ -- sets of identifiers ordered as per the preferred prefix list for that semantic type." ] }, { @@ -580,9 +580,7 @@ { "cell_type": "code", "execution_count": 13, - "metadata": { - "scrolled": false - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -728,7 +726,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -742,7 +740,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.1" + "version": "3.12.4" } }, "nbformat": 4, From 6cedf64c75ddc593bbda3175001441cb6986244d Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 14 Jun 2024 17:38:55 -0400 Subject: [PATCH 2/7] Updated further. --- documentation/NodeNormalization.ipynb | 1167 +++++++++++++++++++++++-- 1 file changed, 1106 insertions(+), 61 deletions(-) diff --git a/documentation/NodeNormalization.ipynb b/documentation/NodeNormalization.ipynb index 68f2a11..b2160cd 100644 --- a/documentation/NodeNormalization.ipynb +++ b/documentation/NodeNormalization.ipynb @@ -8,7 +8,7 @@ } }, "source": [ - "# NodeNormalization" + "# Introduction to the Node Normalization Service (NodeNorm)" ] }, { @@ -21,7 +21,7 @@ "source": [ "## Introduction\n", "\n", - "The [Node Normalization Service](https://nodenormalization-sri.renci.org/docs) takes an input [CURIE](https://en.wikipedia.org/wiki/CURIE), and returns:\n", + "The [Node Normalization Service](https://nodenormalization-sri.renci.org/docs) (NodeNorm) takes an input [CURIE](https://en.wikipedia.org/wiki/CURIE), and returns:\n", "\n", "* The preferred CURIE for this entity\n", "* All other known equivalent identifiers for the entity\n", @@ -30,6 +30,17 @@ "The data currently served by the Node Normalization Service is created by [Babel](https://github.com/TranslatorSRI/Babel), a pipeline for combining identifiers from hundreds of data sources including ontologies and publicly accessible databases into a series of _cliques_ -- sets of identifiers ordered as per the preferred prefix list for that semantic type." ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Instances of NodeNorm\n", + "\n", + "For the examples in this document, we will use the _development_ version of the Node Normalization Service, hosted at https://nodenormalization-sri.renci.org/ by the Renaissance Computing Institute (RENCI) at the University of North Carolina. This version is updated more frequently than the production instance listed below.\n", + "\n", + "The production instance of NodeNorm is hosted by the NCATS Translator project at https://nodenorm.transltr.io/docs, and may be older than the development version hosted below. As with other NCATS Translator tools, a [CI instance](https://nodenorm.ci.transltr.io/docs) and a [Test instance](https://nodenorm.test.transltr.io/docs) have also been deployed, but are not likely to be useful for non-Translator users." + ] + }, { "cell_type": "markdown", "metadata": { @@ -40,7 +51,7 @@ "source": [ "## Metadata\n", "\n", - "There are two metadata services that can be used to find out what sorts of results have been incorporated into NodeNormalization. These return the semantic types that are included, and the prefixes included for each type." + "There are two metadata services that can be used to find out what sorts of results have been incorporated into the Node Normalization service. These return the semantic types that are included, and the prefixes included for each type." ] }, { @@ -51,7 +62,7 @@ } }, "source": [ - "Which types have been normalized?" + "#### Which types have been normalized?" ] }, { @@ -70,26 +81,72 @@ "{\n", " \"semantic_types\": {\n", " \"types\": [\n", - " \"biolink:GenomicEntity\",\n", - " \"biolink:BiologicalProcessOrActivity\",\n", - " \"biolink:MolecularActivity\",\n", - " \"biolink:DiseaseOrPhenotypicFeature\",\n", - " \"biolink:GeneFamily\",\n", - " \"biolink:Cell\",\n", - " \"biolink:OrganismalEntity\",\n", + " \"biolink:Protein\",\n", " \"biolink:Pathway\",\n", + " \"biolink:Behavior\",\n", + " \"biolink:BiologicalProcess\",\n", + " \"biolink:GeneGroupingMixin\",\n", + " \"biolink:AdministrativeEntity\",\n", + " \"biolink:Attribute\",\n", " \"biolink:MolecularEntity\",\n", - " \"biolink:Gene\",\n", + " \"biolink:Entity\",\n", + " \"biolink:GeneFamily\",\n", " \"biolink:BiologicalEntity\",\n", - " \"biolink:BiologicalProcess\",\n", - " \"biolink:AnatomicalEntity\",\n", + " \"biolink:DiseaseOrPhenotypicFeature\",\n", + " \"biolink:MolecularActivity\",\n", " \"biolink:OrganismTaxon\",\n", - " \"biolink:Entity\",\n", - " \"biolink:Disease\",\n", + " \"biolink:MolecularMixture\",\n", + " \"biolink:GenomicEntity\",\n", + " \"biolink:GeographicLocation\",\n", + " \"biolink:ActivityAndBehavior\",\n", + " \"biolink:MacromolecularComplex\",\n", + " \"biolink:GeneProductMixin\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\",\n", + " \"biolink:StudyPopulation\",\n", + " \"biolink:MacromolecularMachineMixin\",\n", + " \"biolink:InformationContentEntity\",\n", + " \"biolink:SubjectOfInvestigation\",\n", + " \"biolink:Device\",\n", + " \"biolink:OrganismalEntity\",\n", + " \"biolink:Polypeptide\",\n", + " \"biolink:NamedThing\",\n", + " \"biolink:ChemicalMixture\",\n", + " \"biolink:ClinicalAttribute\",\n", + " \"biolink:Event\",\n", + " \"biolink:OntologyClass\",\n", + " \"biolink:ComplexMolecularMixture\",\n", + " \"biolink:NucleicAcidEntity\",\n", + " \"biolink:Occurrent\",\n", + " \"biolink:ChemicalEntity\",\n", + " \"biolink:GrossAnatomicalStructure\",\n", + " \"biolink:Activity\",\n", + " \"biolink:PopulationOfIndividualOrganisms\",\n", + " \"biolink:OrganismAttribute\",\n", + " \"biolink:Phenomenon\",\n", + " \"biolink:AnatomicalEntity\",\n", + " \"biolink:GeneOrGeneProduct\",\n", + " \"biolink:SmallMolecule\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:Human\",\n", + " \"biolink:Food\",\n", " \"biolink:CellularComponent\",\n", - " \"biolink:ChemicalSubstance\",\n", + " \"biolink:BiologicalProcessOrActivity\",\n", + " \"biolink:Drug\",\n", + " \"biolink:PlanetaryEntity\",\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:Publication\",\n", + " \"biolink:Disease\",\n", + " \"biolink:Cohort\",\n", + " \"biolink:Agent\",\n", + " \"biolink:PhysiologicalProcess\",\n", + " \"biolink:ChemicalOrDrugOrTreatment\",\n", + " \"biolink:Procedure\",\n", + " \"biolink:Gene\",\n", + " \"biolink:PhysicalEntity\",\n", + " \"biolink:ThingWithTaxon\",\n", " \"biolink:PhenotypicFeature\",\n", - " \"biolink:NamedThing\"\n", + " \"biolink:Cell\"\n", " ]\n", " }\n", "}\n" @@ -112,12 +169,14 @@ } }, "source": [ - "Even if a semantic type has some identifier equivalence, not every vocabulary has been included. To see which vocabularies are likely to give useful results, call:" + "#### Which prefixes are supported?\n", + "\n", + "Even if a semantic type has some identifier equivalence, not every vocabulary has been included. To see which vocabularies are likely to give useful results for a specific Biolink class, call:" ] }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 3, "metadata": { "slideshow": { "slide_type": "subslide" @@ -129,18 +188,22 @@ "output_type": "stream", "text": [ "{\n", - " \"biolink:ChemicalSubstance\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"96566919\",\n", - " \"INCHIKEY\": \"96349470\",\n", - " \"CHEMBL.COMPOUND\": \"1889978\",\n", - " \"MESH\": \"274298\",\n", - " \"CHEBI\": \"135769\",\n", - " \"KEGG.COMPOUND\": \"18744\",\n", - " \"HMDB\": \"113979\",\n", - " \"UNII\": \"82937\",\n", - " \"DRUGBANK\": \"10742\",\n", - " \"GTOPDB\": \"8895\"\n", + " \"biolink:ChemicalEntity\": {\n", + " \"curie_prefix\": {\n", + " \"PUBCHEM.COMPOUND\": \"124460882\",\n", + " \"INCHIKEY\": \"110336273\",\n", + " \"CHEMBL.COMPOUND\": \"2399641\",\n", + " \"CHEBI\": \"196937\",\n", + " \"CAS\": \"3556698\",\n", + " \"HMDB\": \"217920\",\n", + " \"UNII\": \"126327\",\n", + " \"MESH\": \"258102\",\n", + " \"KEGG.COMPOUND\": \"16020\",\n", + " \"UMLS\": \"549120\",\n", + " \"DRUGBANK\": \"15179\",\n", + " \"DrugCentral\": \"4995\",\n", + " \"GTOPDB\": \"12347\",\n", + " \"RXCUI\": \"123395\"\n", " }\n", " }\n", "}\n" @@ -149,7 +212,7 @@ ], "source": [ "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes/',\n", - " params={'semantic_type':\"biolink:ChemicalSubstance\"})\n", + " params={'semantic_type':\"biolink:ChemicalEntity\"})\n", "print( json.dumps( result.json(), indent = 2))" ] }, @@ -166,8 +229,9 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 4, "metadata": { + "scrolled": true, "slideshow": { "slide_type": "skip" } @@ -178,37 +242,42 @@ "output_type": "stream", "text": [ "{\n", - " \"biolink:ChemicalSubstance\": {\n", + " \"biolink:ChemicalEntity\": {\n", " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"96566919\",\n", - " \"INCHIKEY\": \"96349470\",\n", - " \"CHEMBL.COMPOUND\": \"1889978\",\n", - " \"MESH\": \"274298\",\n", - " \"CHEBI\": \"135769\",\n", - " \"KEGG.COMPOUND\": \"18744\",\n", - " \"HMDB\": \"113979\",\n", - " \"UNII\": \"82937\",\n", - " \"DRUGBANK\": \"10742\",\n", - " \"GTOPDB\": \"8895\"\n", + " \"PUBCHEM.COMPOUND\": \"124460882\",\n", + " \"INCHIKEY\": \"110336273\",\n", + " \"CHEMBL.COMPOUND\": \"2399641\",\n", + " \"CHEBI\": \"196937\",\n", + " \"CAS\": \"3556698\",\n", + " \"HMDB\": \"217920\",\n", + " \"UNII\": \"126327\",\n", + " \"MESH\": \"258102\",\n", + " \"KEGG.COMPOUND\": \"16020\",\n", + " \"UMLS\": \"549120\",\n", + " \"DRUGBANK\": \"15179\",\n", + " \"DrugCentral\": \"4995\",\n", + " \"GTOPDB\": \"12347\",\n", + " \"RXCUI\": \"123395\"\n", " }\n", " },\n", " \"biolink:Disease\": {\n", " \"curie_prefix\": {\n", - " \"UMLS\": \"225822\",\n", - " \"SNOMEDCT\": \"152614\",\n", - " \"MEDDRA\": \"23228\",\n", - " \"NCIT\": \"39158\",\n", - " \"MONDO\": \"44526\",\n", - " \"ORPHANET\": \"18282\",\n", - " \"MESH\": \"21066\",\n", - " \"HP\": \"3478\",\n", - " \"DOID\": \"19624\",\n", - " \"OMIM\": \"28954\",\n", - " \"EFO\": \"3820\",\n", - " \"ICD10\": \"24\",\n", - " \"ICD9\": \"12\",\n", - " \"MP\": \"4\",\n", - " \"medgen\": \"4\"\n", + " \"UMLS\": \"336767\",\n", + " \"SNOMEDCT\": \"94514\",\n", + " \"MEDDRA\": \"46033\",\n", + " \"MONDO\": \"24012\",\n", + " \"DOID\": \"11498\",\n", + " \"NCIT\": \"25540\",\n", + " \"HP\": \"2182\",\n", + " \"EFO\": \"3711\",\n", + " \"orphanet\": \"10780\",\n", + " \"MESH\": \"11238\",\n", + " \"OMIM\": \"10314\",\n", + " \"ICD10\": \"2429\",\n", + " \"ICD9\": \"2218\",\n", + " \"OMIM.PS\": \"556\",\n", + " \"KEGG.DISEASE\": \"40\",\n", + " \"MP\": \"1\"\n", " }\n", " }\n", "}\n" @@ -217,7 +286,983 @@ ], "source": [ "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes/',\n", - " params={'semantic_type':[\"biolink:ChemicalSubstance\",\"biolink:Disease\"]})\n", + " params={'semantic_type':[\"biolink:ChemicalEntity\",\"biolink:Disease\"]})\n", + "print( json.dumps( result.json(), indent = 2))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Or you can just ask for all the prefix counts for every type:" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"biolink:Pathway\": {\n", + " \"curie_prefix\": {\n", + " \"REACT\": \"21784\",\n", + " \"SMPDB\": \"30248\",\n", + " \"GO\": \"642\",\n", + " \"PANTHER.PATHWAY\": \"175\"\n", + " }\n", + " },\n", + " \"biolink:OrganismTaxon\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"749649\",\n", + " \"NCBITaxon\": \"2546095\",\n", + " \"MESH\": \"70628\"\n", + " }\n", + " },\n", + " \"biolink:GeneFamily\": {\n", + " \"curie_prefix\": {\n", + " \"PANTHER.FAMILY\": \"26138\",\n", + " \"HGNC.FAMILY\": \"1807\"\n", + " }\n", + " },\n", + " \"biolink:GeneGroupingMixin\": {\n", + " \"curie_prefix\": {\n", + " \"PANTHER.FAMILY\": \"26138\",\n", + " \"HGNC.FAMILY\": \"1807\"\n", + " }\n", + " },\n", + " \"biolink:Cell\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"6059\",\n", + " \"NCIT\": \"2371\",\n", + " \"CL\": \"2732\",\n", + " \"SNOMEDCT\": \"876\",\n", + " \"MESH\": \"324\"\n", + " }\n", + " },\n", + " \"biolink:MacromolecularComplex\": {\n", + " \"curie_prefix\": {\n", + " \"ComplexPortal\": \"1256\"\n", + " }\n", + " },\n", + " \"biolink:GrossAnatomicalStructure\": {\n", + " \"curie_prefix\": {\n", + " \"UBERON\": \"10327\",\n", + " \"UMLS\": \"2383\",\n", + " \"MESH\": \"783\",\n", + " \"NCIT\": \"2083\"\n", + " }\n", + " },\n", + " \"biolink:Disease\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"336767\",\n", + " \"SNOMEDCT\": \"94514\",\n", + " \"MEDDRA\": \"46033\",\n", + " \"MONDO\": \"24012\",\n", + " \"DOID\": \"11498\",\n", + " \"NCIT\": \"25540\",\n", + " \"HP\": \"2182\",\n", + " \"EFO\": \"3711\",\n", + " \"orphanet\": \"10780\",\n", + " \"MESH\": \"11238\",\n", + " \"OMIM\": \"10314\",\n", + " \"ICD10\": \"2429\",\n", + " \"ICD9\": \"2218\",\n", + " \"OMIM.PS\": \"556\",\n", + " \"KEGG.DISEASE\": \"40\",\n", + " \"MP\": \"1\"\n", + " }\n", + " },\n", + " \"biolink:PhenotypicFeature\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"349701\",\n", + " \"MEDDRA\": \"22184\",\n", + " \"HP\": \"15600\",\n", + " \"SNOMEDCT\": \"46683\",\n", + " \"NCIT\": \"20731\",\n", + " \"EFO\": \"8509\",\n", + " \"MESH\": \"885\",\n", + " \"MP\": \"9\"\n", + " }\n", + " },\n", + " \"biolink:CellularComponent\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"7927\",\n", + " \"MESH\": \"273\",\n", + " \"GO\": \"4058\",\n", + " \"SNOMEDCT\": \"539\",\n", + " \"NCIT\": \"1446\",\n", + " \"UBERON\": \"4\"\n", + " }\n", + " },\n", + " \"biolink:ComplexMolecularMixture\": {\n", + " \"curie_prefix\": {\n", + " \"MESH\": \"177\",\n", + " \"UMLS\": \"101\",\n", + " \"DRUGBANK\": \"6\",\n", + " \"CAS\": \"6\"\n", + " }\n", + " },\n", + " \"biolink:Human\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"39\"\n", + " }\n", + " },\n", + " \"biolink:DiseaseOrPhenotypicFeature\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"686497\",\n", + " \"MEDDRA\": \"68217\",\n", + " \"HP\": \"17782\",\n", + " \"SNOMEDCT\": \"141197\",\n", + " \"NCIT\": \"46271\",\n", + " \"EFO\": \"12220\",\n", + " \"MESH\": \"12123\",\n", + " \"MP\": \"10\",\n", + " \"MONDO\": \"24012\",\n", + " \"DOID\": \"11498\",\n", + " \"orphanet\": \"10780\",\n", + " \"OMIM\": \"10314\",\n", + " \"ICD10\": \"2429\",\n", + " \"ICD9\": \"2218\",\n", + " \"OMIM.PS\": \"556\",\n", + " \"KEGG.DISEASE\": \"40\"\n", + " }\n", + " },\n", + " \"biolink:NucleicAcidEntity\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"449\"\n", + " }\n", + " },\n", + " \"biolink:ClinicalAttribute\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"107356\"\n", + " }\n", + " },\n", + " \"biolink:Food\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"8468\"\n", + " }\n", + " },\n", + " \"biolink:OrganismAttribute\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"983\"\n", + " }\n", + " },\n", + " \"biolink:Attribute\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"108339\"\n", + " }\n", + " },\n", + " \"biolink:PhysiologicalProcess\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"31047\"\n", + " }\n", + " },\n", + " \"biolink:Event\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"235\"\n", + " }\n", + " },\n", + " \"biolink:Device\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"77193\"\n", + " }\n", + " },\n", + " \"biolink:GeographicLocation\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"4667\"\n", + " }\n", + " },\n", + " \"biolink:PlanetaryEntity\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"4667\"\n", + " }\n", + " },\n", + " \"biolink:Phenomenon\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"4666\"\n", + " }\n", + " },\n", + " \"biolink:Behavior\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"4156\"\n", + " }\n", + " },\n", + " \"biolink:BiologicalProcess\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"35203\",\n", + " \"REACT\": \"21789\",\n", + " \"SMPDB\": \"30248\",\n", + " \"GO\": \"27186\",\n", + " \"PANTHER.PATHWAY\": \"175\"\n", + " }\n", + " },\n", + " \"biolink:Activity\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"41367\"\n", + " }\n", + " },\n", + " \"biolink:Procedure\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"426906\"\n", + " }\n", + " },\n", + " \"biolink:ActivityAndBehavior\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"472429\"\n", + " }\n", + " },\n", + " \"biolink:Agent\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"4222\"\n", + " }\n", + " },\n", + " \"biolink:AdministrativeEntity\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"4222\"\n", + " }\n", + " },\n", + " \"biolink:Cohort\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"7353\"\n", + " }\n", + " },\n", + " \"biolink:PopulationOfIndividualOrganisms\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"11427\"\n", + " }\n", + " },\n", + " \"biolink:StudyPopulation\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"7353\"\n", + " }\n", + " },\n", + " \"biolink:Drug\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"165406\",\n", + " \"RXCUI\": \"101635\",\n", + " \"MESH\": \"56\",\n", + " \"CAS\": \"3\"\n", + " }\n", + " },\n", + " \"biolink:Publication\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"48564\",\n", + " \"PMID\": \"36980104\",\n", + " \"doi\": \"28069780\",\n", + " \"PMC\": \"9078478\"\n", + " }\n", + " },\n", + " \"biolink:InformationContentEntity\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"102266\",\n", + " \"PMID\": \"36980104\",\n", + " \"doi\": \"28069780\",\n", + " \"PMC\": \"9078478\"\n", + " }\n", + " },\n", + " \"biolink:PhysicalEntity\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"6328\"\n", + " }\n", + " },\n", + " \"biolink:MolecularActivity\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"31085\",\n", + " \"REACT\": \"85594\",\n", + " \"RHEA\": \"65080\",\n", + " \"EC\": \"8639\",\n", + " \"GO\": \"11198\",\n", + " \"TCDB\": \"22\",\n", + " \"KEGG.REACTION\": \"5\"\n", + " }\n", + " },\n", + " \"biolink:Occurrent\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"539227\",\n", + " \"REACT\": \"107383\",\n", + " \"SMPDB\": \"30248\",\n", + " \"GO\": \"38384\",\n", + " \"PANTHER.PATHWAY\": \"175\",\n", + " \"RHEA\": \"65080\",\n", + " \"EC\": \"8639\",\n", + " \"TCDB\": \"22\",\n", + " \"KEGG.REACTION\": \"5\"\n", + " }\n", + " },\n", + " \"biolink:BiologicalProcessOrActivity\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"66288\",\n", + " \"REACT\": \"107383\",\n", + " \"SMPDB\": \"30248\",\n", + " \"GO\": \"38384\",\n", + " \"PANTHER.PATHWAY\": \"175\",\n", + " \"RHEA\": \"65080\",\n", + " \"EC\": \"8639\",\n", + " \"TCDB\": \"22\",\n", + " \"KEGG.REACTION\": \"5\"\n", + " }\n", + " 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" \"DRUGBANK\": \"15179\",\n", + " \"DrugCentral\": \"4995\",\n", + " \"GTOPDB\": \"12347\",\n", + " \"RXCUI\": \"123395\",\n", + " \"NCBIGene\": \"51090837\",\n", + " \"ENSEMBL\": \"33596063\",\n", + " \"WormBase\": \"48780\",\n", + " \"ZFIN\": \"38025\",\n", + " \"RGD\": \"56689\",\n", + " \"MGI\": \"80229\",\n", + " \"dictyBase\": \"13892\",\n", + " \"HGNC\": \"43868\",\n", + " \"OMIM\": \"27613\",\n", + " \"FB\": \"30247\",\n", + " \"SGD\": \"7161\",\n", + " \"UBERON\": \"14411\",\n", + " \"NCIT\": \"56325\",\n", + " \"EMAPA\": \"946\",\n", + " \"FBbt\": \"118\",\n", + " \"ZFA\": \"610\",\n", + " \"WBbt\": \"18\",\n", + " \"PANTHER.FAMILY\": \"26138\",\n", + " \"HGNC.FAMILY\": \"1807\",\n", + " \"UniProtKB\": \"250393886\",\n", + " \"PR\": \"251709\",\n", + " \"MEDDRA\": \"68217\",\n", + " \"HP\": \"17782\",\n", + " \"SNOMEDCT\": \"142612\",\n", + " \"EFO\": \"12220\",\n", + " \"MP\": \"10\",\n", + " \"REACT\": \"107383\",\n", + " \"SMPDB\": \"30248\",\n", + " \"GO\": \"42442\",\n", + " \"PANTHER.PATHWAY\": \"175\",\n", + " \"CL\": \"2732\",\n", + " \"PMID\": \"36980104\",\n", + " \"doi\": \"28069780\",\n", + " \"PMC\": \"9078478\",\n", + " \"MONDO\": \"24012\",\n", + " \"DOID\": \"11498\",\n", + " \"orphanet\": \"10780\",\n", + " \"ICD10\": \"2429\",\n", + " \"ICD9\": \"2218\",\n", + " \"OMIM.PS\": \"556\",\n", + " \"KEGG.DISEASE\": \"40\",\n", + " \"RHEA\": \"65080\",\n", + " \"EC\": \"8639\",\n", + " \"TCDB\": \"22\",\n", + " \"KEGG.REACTION\": \"5\",\n", + " \"ComplexPortal\": \"1256\",\n", + " \"NCBITaxon\": \"2546095\"\n", + " }\n", + " },\n", + " \"biolink:NamedThing\": {\n", + " \"curie_prefix\": {\n", + " \"PUBCHEM.COMPOUND\": \"124460882\",\n", + " \"INCHIKEY\": \"110336300\",\n", + " \"CHEMBL.COMPOUND\": \"2399641\",\n", + " \"CHEBI\": \"197320\",\n", + " \"CAS\": \"3556712\",\n", + " \"HMDB\": \"217920\",\n", + " \"UNII\": \"126327\",\n", + " \"MESH\": \"343122\",\n", + " \"KEGG.COMPOUND\": \"16108\",\n", + " \"UMLS\": \"3206840\",\n", + " \"DRUGBANK\": \"15179\",\n", + " \"DrugCentral\": \"4995\",\n", + " \"GTOPDB\": \"12347\",\n", + " \"RXCUI\": \"123395\",\n", + " \"NCBIGene\": \"51090837\",\n", + " \"ENSEMBL\": \"33596063\",\n", + " \"WormBase\": \"48780\",\n", + " \"ZFIN\": \"38025\",\n", + " \"RGD\": \"56689\",\n", + " \"MGI\": \"80229\",\n", + " \"dictyBase\": \"13892\",\n", + " \"HGNC\": \"43868\",\n", + " \"OMIM\": \"27613\",\n", + " \"FB\": \"30247\",\n", + " \"SGD\": \"7161\",\n", + " \"UBERON\": \"14411\",\n", + " \"NCIT\": \"56325\",\n", + " \"EMAPA\": \"946\",\n", + " \"FBbt\": \"118\",\n", + " \"ZFA\": \"610\",\n", + " \"WBbt\": \"18\",\n", + " \"PANTHER.FAMILY\": \"26138\",\n", + " \"HGNC.FAMILY\": \"1807\",\n", + " \"UniProtKB\": \"250393886\",\n", + " \"PR\": \"251709\",\n", + " \"MEDDRA\": \"68217\",\n", + " \"HP\": \"17782\",\n", + " \"SNOMEDCT\": \"142612\",\n", + " \"EFO\": \"12220\",\n", + " \"MP\": \"10\",\n", + " \"REACT\": \"107383\",\n", + " \"SMPDB\": \"30248\",\n", + " \"GO\": \"42442\",\n", + " \"PANTHER.PATHWAY\": \"175\",\n", + " \"CL\": \"2732\",\n", + " \"PMID\": \"36980104\",\n", + " \"doi\": \"28069780\",\n", + " \"PMC\": \"9078478\",\n", + " \"MONDO\": \"24012\",\n", + " \"DOID\": \"11498\",\n", + " \"orphanet\": \"10780\",\n", + " \"ICD10\": \"2429\",\n", + " \"ICD9\": \"2218\",\n", + " \"OMIM.PS\": \"556\",\n", + " \"KEGG.DISEASE\": \"40\",\n", + " \"RHEA\": \"65080\",\n", + " \"EC\": \"8639\",\n", + " \"TCDB\": \"22\",\n", + " \"KEGG.REACTION\": \"5\",\n", + " \"ComplexPortal\": \"1256\",\n", + " \"NCBITaxon\": \"2546095\"\n", + " }\n", + " },\n", + " \"biolink:BiologicalEntity\": {\n", + " \"curie_prefix\": {\n", + " \"NCBIGene\": \"51090837\",\n", + " \"ENSEMBL\": \"33596063\",\n", + " \"WormBase\": \"48780\",\n", + " \"ZFIN\": \"38025\",\n", + " \"RGD\": \"56689\",\n", + " \"MGI\": \"80229\",\n", + " \"dictyBase\": \"13892\",\n", + " \"HGNC\": \"43868\",\n", + " \"OMIM\": \"27613\",\n", + " \"UMLS\": \"1131851\",\n", + " \"FB\": \"30247\",\n", + " \"SGD\": \"7161\",\n", + " \"UBERON\": \"14411\",\n", + " \"NCIT\": \"56325\",\n", + " \"MESH\": \"14392\",\n", + " \"EMAPA\": \"946\",\n", + " \"FBbt\": \"118\",\n", + " \"ZFA\": \"610\",\n", + " \"WBbt\": \"18\",\n", + " \"PANTHER.FAMILY\": \"26138\",\n", + " \"HGNC.FAMILY\": \"1807\",\n", + " \"UniProtKB\": \"250393886\",\n", + " \"PR\": \"251709\",\n", + " \"MEDDRA\": \"68217\",\n", + " \"HP\": \"17782\",\n", + " \"SNOMEDCT\": \"142612\",\n", + " \"EFO\": \"12220\",\n", + " \"MP\": \"10\",\n", + " \"REACT\": \"107383\",\n", + " \"SMPDB\": \"30248\",\n", + " \"GO\": \"42442\",\n", + " \"PANTHER.PATHWAY\": \"175\",\n", + " \"CL\": \"2732\",\n", + " \"CHEBI\": \"383\",\n", + " \"KEGG.COMPOUND\": \"88\",\n", + " \"CAS\": \"14\",\n", + " \"INCHIKEY\": \"27\",\n", + " \"MONDO\": \"24012\",\n", + " \"DOID\": \"11498\",\n", + " \"orphanet\": \"10780\",\n", + " \"ICD10\": \"2429\",\n", + " \"ICD9\": \"2218\",\n", + " \"OMIM.PS\": \"556\",\n", + " \"KEGG.DISEASE\": \"40\",\n", + " \"RHEA\": \"65080\",\n", + " \"EC\": \"8639\",\n", + " \"TCDB\": \"22\",\n", + " \"KEGG.REACTION\": \"5\",\n", + " \"ComplexPortal\": \"1256\"\n", + " }\n", + " },\n", + " \"biolink:Polypeptide\": {\n", + " \"curie_prefix\": {\n", + " \"UniProtKB\": \"250393886\",\n", + " \"ENSEMBL\": \"20797952\",\n", + " \"PR\": \"251709\",\n", + " \"UMLS\": \"164461\",\n", + " \"CHEBI\": \"383\",\n", + " \"MESH\": \"280\",\n", + " \"KEGG.COMPOUND\": \"88\",\n", + " \"CAS\": \"14\",\n", + " \"INCHIKEY\": \"27\"\n", + " }\n", + " }\n", + "}\n" + ] + } + ], + "source": [ + "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes')\n", "print( json.dumps( result.json(), indent = 2))" ] }, From 1d1f48c44e4670e08fbd02c74601457563f08601 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 14 Jun 2024 17:42:31 -0400 Subject: [PATCH 3/7] Reduced the length of one of the files. --- documentation/NodeNormalization.ipynb | 936 +------------------------- 1 file changed, 5 insertions(+), 931 deletions(-) diff --git a/documentation/NodeNormalization.ipynb b/documentation/NodeNormalization.ipynb index b2160cd..6419bec 100644 --- a/documentation/NodeNormalization.ipynb +++ b/documentation/NodeNormalization.ipynb @@ -299,7 +299,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 8, "metadata": {}, "outputs": [ { @@ -327,935 +327,6 @@ " \"PANTHER.FAMILY\": \"26138\",\n", " \"HGNC.FAMILY\": \"1807\"\n", " }\n", - " },\n", - " \"biolink:GeneGroupingMixin\": {\n", - " \"curie_prefix\": {\n", - " \"PANTHER.FAMILY\": \"26138\",\n", - " \"HGNC.FAMILY\": \"1807\"\n", - " }\n", - " },\n", - " \"biolink:Cell\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"6059\",\n", - " \"NCIT\": \"2371\",\n", - " \"CL\": \"2732\",\n", - " \"SNOMEDCT\": \"876\",\n", - " \"MESH\": \"324\"\n", - " }\n", - " },\n", - " \"biolink:MacromolecularComplex\": {\n", - " \"curie_prefix\": {\n", - " \"ComplexPortal\": \"1256\"\n", - " }\n", - " },\n", - " \"biolink:GrossAnatomicalStructure\": {\n", - " \"curie_prefix\": {\n", - " \"UBERON\": \"10327\",\n", - " \"UMLS\": \"2383\",\n", - " \"MESH\": \"783\",\n", - " \"NCIT\": \"2083\"\n", - " }\n", - " },\n", - " \"biolink:Disease\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"336767\",\n", - " \"SNOMEDCT\": \"94514\",\n", - " \"MEDDRA\": \"46033\",\n", - " \"MONDO\": \"24012\",\n", - " \"DOID\": \"11498\",\n", - " \"NCIT\": \"25540\",\n", - " \"HP\": \"2182\",\n", - " \"EFO\": \"3711\",\n", - " \"orphanet\": \"10780\",\n", - " \"MESH\": \"11238\",\n", - " \"OMIM\": \"10314\",\n", - " \"ICD10\": \"2429\",\n", - " \"ICD9\": \"2218\",\n", - " \"OMIM.PS\": \"556\",\n", - " \"KEGG.DISEASE\": \"40\",\n", - " \"MP\": \"1\"\n", - " }\n", - " },\n", - " \"biolink:PhenotypicFeature\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"349701\",\n", - " \"MEDDRA\": \"22184\",\n", - " \"HP\": \"15600\",\n", - " \"SNOMEDCT\": \"46683\",\n", - " \"NCIT\": \"20731\",\n", - " \"EFO\": \"8509\",\n", - " \"MESH\": \"885\",\n", - " \"MP\": \"9\"\n", - " }\n", - " },\n", - " \"biolink:CellularComponent\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"7927\",\n", - " \"MESH\": \"273\",\n", - " \"GO\": \"4058\",\n", - " \"SNOMEDCT\": \"539\",\n", - " \"NCIT\": \"1446\",\n", - " \"UBERON\": \"4\"\n", - " }\n", - " },\n", - " \"biolink:ComplexMolecularMixture\": {\n", - " \"curie_prefix\": {\n", - " \"MESH\": \"177\",\n", - " \"UMLS\": \"101\",\n", - " \"DRUGBANK\": \"6\",\n", - " \"CAS\": \"6\"\n", - " }\n", - " },\n", - " \"biolink:Human\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"39\"\n", - " }\n", - " },\n", - " \"biolink:DiseaseOrPhenotypicFeature\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"686497\",\n", - " \"MEDDRA\": \"68217\",\n", - " \"HP\": \"17782\",\n", - " \"SNOMEDCT\": \"141197\",\n", - " \"NCIT\": \"46271\",\n", - " \"EFO\": \"12220\",\n", - " \"MESH\": \"12123\",\n", - " \"MP\": \"10\",\n", - " \"MONDO\": \"24012\",\n", - " \"DOID\": \"11498\",\n", - " \"orphanet\": \"10780\",\n", - " \"OMIM\": \"10314\",\n", - " \"ICD10\": \"2429\",\n", - " \"ICD9\": \"2218\",\n", - " \"OMIM.PS\": \"556\",\n", - " \"KEGG.DISEASE\": \"40\"\n", - " }\n", - " },\n", - " \"biolink:NucleicAcidEntity\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"449\"\n", - " }\n", - " },\n", - " \"biolink:ClinicalAttribute\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"107356\"\n", - " }\n", - " },\n", - " \"biolink:Food\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"8468\"\n", - " }\n", - " },\n", - " \"biolink:OrganismAttribute\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"983\"\n", - " }\n", - " },\n", - " \"biolink:Attribute\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"108339\"\n", - " }\n", - " },\n", - " \"biolink:PhysiologicalProcess\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"31047\"\n", - " }\n", - " },\n", - " \"biolink:Event\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"235\"\n", - " }\n", - " },\n", - " \"biolink:Device\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"77193\"\n", - " }\n", - " },\n", - " \"biolink:GeographicLocation\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"4667\"\n", - " }\n", - " },\n", - " \"biolink:PlanetaryEntity\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"4667\"\n", - " }\n", - " },\n", - " \"biolink:Phenomenon\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"4666\"\n", - " }\n", - " },\n", - " \"biolink:Behavior\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"4156\"\n", - " }\n", - " },\n", - " \"biolink:BiologicalProcess\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"35203\",\n", - " \"REACT\": \"21789\",\n", - " \"SMPDB\": \"30248\",\n", - " \"GO\": \"27186\",\n", - " \"PANTHER.PATHWAY\": \"175\"\n", - " }\n", - " },\n", - " \"biolink:Activity\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"41367\"\n", - " }\n", - " },\n", - " \"biolink:Procedure\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"426906\"\n", - " }\n", - " },\n", - " \"biolink:ActivityAndBehavior\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"472429\"\n", - " }\n", - " },\n", - " \"biolink:Agent\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"4222\"\n", - " }\n", - " },\n", - " \"biolink:AdministrativeEntity\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"4222\"\n", - " }\n", - " },\n", - " \"biolink:Cohort\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"7353\"\n", - " }\n", - " },\n", - " \"biolink:PopulationOfIndividualOrganisms\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"11427\"\n", - " }\n", - " },\n", - " \"biolink:StudyPopulation\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"7353\"\n", - " }\n", - " },\n", - " \"biolink:Drug\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"165406\",\n", - " \"RXCUI\": \"101635\",\n", - " \"MESH\": \"56\",\n", - " \"CAS\": \"3\"\n", - " }\n", - " },\n", - " \"biolink:Publication\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"48564\",\n", - " \"PMID\": \"36980104\",\n", - " \"doi\": \"28069780\",\n", - " \"PMC\": \"9078478\"\n", - " }\n", - " },\n", - " \"biolink:InformationContentEntity\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"102266\",\n", - " \"PMID\": \"36980104\",\n", - " \"doi\": \"28069780\",\n", - " \"PMC\": \"9078478\"\n", - " }\n", - " },\n", - " \"biolink:PhysicalEntity\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"6328\"\n", - " }\n", - " },\n", - " \"biolink:MolecularActivity\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"31085\",\n", - " \"REACT\": \"85594\",\n", - " \"RHEA\": \"65080\",\n", - " \"EC\": \"8639\",\n", - " \"GO\": \"11198\",\n", - " \"TCDB\": \"22\",\n", - " \"KEGG.REACTION\": \"5\"\n", - " }\n", - " },\n", - " \"biolink:Occurrent\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"539227\",\n", - " \"REACT\": \"107383\",\n", - " \"SMPDB\": \"30248\",\n", - " \"GO\": \"38384\",\n", - " \"PANTHER.PATHWAY\": \"175\",\n", - " \"RHEA\": \"65080\",\n", - " \"EC\": \"8639\",\n", - " \"TCDB\": \"22\",\n", - " \"KEGG.REACTION\": \"5\"\n", - " }\n", - " },\n", - " \"biolink:BiologicalProcessOrActivity\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"66288\",\n", - " \"REACT\": \"107383\",\n", - " \"SMPDB\": \"30248\",\n", - " \"GO\": \"38384\",\n", - " \"PANTHER.PATHWAY\": \"175\",\n", - " \"RHEA\": \"65080\",\n", - " \"EC\": \"8639\",\n", - " \"TCDB\": \"22\",\n", - " \"KEGG.REACTION\": \"5\"\n", - " }\n", - " },\n", - " \"biolink:AnatomicalEntity\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"156584\",\n", - " \"UBERON\": \"14411\",\n", - " \"NCIT\": \"10054\",\n", - " \"MESH\": \"1989\",\n", - " \"EMAPA\": \"946\",\n", - " \"FBbt\": \"118\",\n", - " \"ZFA\": \"610\",\n", - " \"WBbt\": \"18\",\n", - " \"CL\": \"2732\",\n", - " \"SNOMEDCT\": \"1415\",\n", - " \"GO\": \"4058\"\n", - " }\n", - " },\n", - " \"biolink:SubjectOfInvestigation\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"168011\",\n", - " \"UBERON\": \"14411\",\n", - " \"NCIT\": \"10054\",\n", - " \"MESH\": \"1989\",\n", - " \"EMAPA\": \"946\",\n", - " \"FBbt\": \"118\",\n", - " \"ZFA\": \"610\",\n", - " \"WBbt\": \"18\",\n", - " \"CL\": \"2732\",\n", - " \"SNOMEDCT\": \"1415\",\n", - " \"GO\": \"4058\"\n", - " }\n", - " },\n", - " \"biolink:OrganismalEntity\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"168011\",\n", - " \"UBERON\": \"14411\",\n", - " \"NCIT\": \"10054\",\n", - " \"MESH\": \"1989\",\n", - " \"EMAPA\": \"946\",\n", - " \"FBbt\": \"118\",\n", - " \"ZFA\": \"610\",\n", - " \"WBbt\": \"18\",\n", - " \"CL\": \"2732\",\n", - " \"SNOMEDCT\": \"1415\",\n", - " \"GO\": \"4058\"\n", - " }\n", - " },\n", - " \"biolink:SmallMolecule\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"107145085\",\n", - " \"INCHIKEY\": \"97335417\",\n", - " \"CHEMBL.COMPOUND\": \"2259501\",\n", - " \"CHEBI\": \"181879\",\n", - " \"CAS\": \"3294326\",\n", - " \"HMDB\": \"217516\",\n", - " \"UNII\": \"66027\",\n", - " \"MESH\": \"79494\",\n", - " \"KEGG.COMPOUND\": \"14537\",\n", - " \"UMLS\": \"76720\",\n", - " \"DRUGBANK\": \"11162\",\n", - " \"DrugCentral\": \"4355\",\n", - " \"GTOPDB\": \"12107\",\n", - " \"RXCUI\": \"4192\"\n", - " }\n", - " },\n", - " \"biolink:MolecularEntity\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"107145085\",\n", - " \"INCHIKEY\": \"97335417\",\n", - " \"CHEMBL.COMPOUND\": \"2259501\",\n", - " \"CHEBI\": \"181879\",\n", - " \"CAS\": \"3294326\",\n", - " \"HMDB\": \"217516\",\n", - " \"UNII\": \"66027\",\n", - " \"MESH\": \"79494\",\n", - " \"KEGG.COMPOUND\": \"14537\",\n", - " \"UMLS\": \"77183\",\n", - " \"DRUGBANK\": \"11162\",\n", - " \"DrugCentral\": \"4355\",\n", - " \"GTOPDB\": \"12107\",\n", - " \"RXCUI\": \"4192\"\n", - " }\n", - " },\n", - " \"biolink:MolecularMixture\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"10351841\",\n", - " \"INCHIKEY\": \"6030497\",\n", - " \"CHEMBL.COMPOUND\": \"113226\",\n", - " \"CAS\": \"253943\",\n", - " \"UNII\": \"14462\",\n", - " \"MESH\": \"7354\",\n", - " \"UMLS\": \"172257\",\n", - " \"CHEBI\": \"3675\",\n", - " \"DRUGBANK\": \"467\",\n", - " \"RXCUI\": \"106125\",\n", - " \"DrugCentral\": \"306\",\n", - " \"HMDB\": \"354\",\n", - " \"KEGG.COMPOUND\": \"492\",\n", - " \"GTOPDB\": \"55\"\n", - " }\n", - " },\n", - " \"biolink:ChemicalOrDrugOrTreatment\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"124460882\",\n", - " \"INCHIKEY\": \"110336273\",\n", - " \"CHEMBL.COMPOUND\": \"2399641\",\n", - " \"CHEBI\": \"196937\",\n", - " \"CAS\": \"3556698\",\n", - " \"HMDB\": \"217920\",\n", - " \"UNII\": \"126327\",\n", - " \"MESH\": \"258102\",\n", - " \"KEGG.COMPOUND\": \"16020\",\n", - " \"UMLS\": \"549120\",\n", - " \"DRUGBANK\": \"15179\",\n", - " \"DrugCentral\": \"4995\",\n", - " \"GTOPDB\": \"12347\",\n", - " \"RXCUI\": \"123395\"\n", - " }\n", - " },\n", - " \"biolink:ChemicalEntity\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"124460882\",\n", - " \"INCHIKEY\": \"110336273\",\n", - " \"CHEMBL.COMPOUND\": \"2399641\",\n", - " \"CHEBI\": \"196937\",\n", - " \"CAS\": \"3556698\",\n", - " \"HMDB\": \"217920\",\n", - " \"UNII\": \"126327\",\n", - " \"MESH\": \"258102\",\n", - " \"KEGG.COMPOUND\": \"16020\",\n", - " \"UMLS\": \"549120\",\n", - " \"DRUGBANK\": \"15179\",\n", - " \"DrugCentral\": \"4995\",\n", - " \"GTOPDB\": \"12347\",\n", - " \"RXCUI\": \"123395\"\n", - " }\n", - " },\n", - " \"biolink:ChemicalMixture\": {\n", - " \"curie_prefix\": {\n", - " \"MESH\": \"7540\",\n", - " \"UMLS\": \"180833\",\n", - " \"DRUGBANK\": \"473\",\n", - " \"CAS\": \"253949\",\n", - " \"PUBCHEM.COMPOUND\": \"10351842\",\n", - " \"INCHIKEY\": \"6030498\",\n", - " \"CHEMBL.COMPOUND\": \"113226\",\n", - " \"UNII\": \"14463\",\n", - " \"CHEBI\": \"4173\",\n", - " \"RXCUI\": \"106125\",\n", - " \"DrugCentral\": \"306\",\n", - " \"HMDB\": \"354\",\n", - " \"KEGG.COMPOUND\": \"499\",\n", - " \"GTOPDB\": \"55\"\n", - " }\n", - " },\n", - " \"biolink:Gene\": {\n", - " \"curie_prefix\": {\n", - " \"NCBIGene\": \"51090837\",\n", - " \"ENSEMBL\": \"12798111\",\n", - " \"WormBase\": \"48780\",\n", - " \"ZFIN\": \"38025\",\n", - " \"RGD\": \"56689\",\n", - " \"MGI\": \"80229\",\n", - " \"dictyBase\": \"13892\",\n", - " \"HGNC\": \"43868\",\n", - " \"OMIM\": \"17299\",\n", - " \"UMLS\": \"46486\",\n", - " \"FB\": \"30247\",\n", - " \"SGD\": \"7161\"\n", - " }\n", - " },\n", - " \"biolink:PhysicalEssenceOrOccurrent\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"124460882\",\n", - " \"INCHIKEY\": \"110336273\",\n", - " \"CHEMBL.COMPOUND\": \"2399641\",\n", - " \"CHEBI\": \"196937\",\n", - " \"CAS\": \"3556698\",\n", - " \"HMDB\": \"217920\",\n", - " \"UNII\": \"126327\",\n", - " \"MESH\": \"260091\",\n", - " \"KEGG.COMPOUND\": \"16020\",\n", - " \"UMLS\": \"1297745\",\n", - " \"DRUGBANK\": \"15179\",\n", - " \"DrugCentral\": \"4995\",\n", - " \"GTOPDB\": \"12347\",\n", - " \"RXCUI\": \"123395\",\n", - " \"NCBIGene\": \"51090837\",\n", - " \"ENSEMBL\": \"12798111\",\n", - " \"WormBase\": \"48780\",\n", - " \"ZFIN\": \"38025\",\n", - " \"RGD\": \"56689\",\n", - " \"MGI\": \"80229\",\n", - " \"dictyBase\": \"13892\",\n", - " \"HGNC\": \"43868\",\n", - " \"OMIM\": \"17299\",\n", - " \"FB\": \"30247\",\n", - " \"SGD\": \"7161\",\n", - " \"UBERON\": \"14411\",\n", - " \"NCIT\": \"10054\",\n", - " \"EMAPA\": \"946\",\n", - " \"FBbt\": \"118\",\n", - " \"ZFA\": \"610\",\n", - " \"WBbt\": \"18\",\n", - " \"REACT\": \"107383\",\n", - " \"SMPDB\": \"30248\",\n", - " \"GO\": \"42442\",\n", - " \"PANTHER.PATHWAY\": \"175\",\n", - " \"CL\": \"2732\",\n", - " \"SNOMEDCT\": \"1415\",\n", - " \"RHEA\": \"65080\",\n", - " \"EC\": \"8639\",\n", - " \"TCDB\": \"22\",\n", - " \"KEGG.REACTION\": \"5\"\n", - " }\n", - " },\n", - " \"biolink:OntologyClass\": {\n", - " \"curie_prefix\": {\n", - " \"NCBIGene\": \"51090837\",\n", - " \"ENSEMBL\": \"12798111\",\n", - " \"WormBase\": \"48780\",\n", - " \"ZFIN\": \"38025\",\n", - " \"RGD\": \"56689\",\n", - " \"MGI\": \"80229\",\n", - " \"dictyBase\": \"13892\",\n", - " \"HGNC\": \"43868\",\n", - " \"OMIM\": \"17299\",\n", - " \"UMLS\": \"386968\",\n", - " \"FB\": \"30247\",\n", - " \"SGD\": \"7161\",\n", - " \"REACT\": \"107383\",\n", - " \"SMPDB\": \"30248\",\n", - " \"GO\": \"38384\",\n", - " \"PANTHER.PATHWAY\": \"175\",\n", - " \"RXCUI\": \"101635\",\n", - " \"MESH\": \"56\",\n", - " \"CAS\": \"3\",\n", - " \"RHEA\": \"65080\",\n", - " \"EC\": \"8639\",\n", - " \"TCDB\": \"22\",\n", - " \"KEGG.REACTION\": \"5\"\n", - " }\n", - " },\n", - " \"biolink:PhysicalEssence\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"124460882\",\n", - " \"INCHIKEY\": \"110336273\",\n", - " \"CHEMBL.COMPOUND\": \"2399641\",\n", - " \"CHEBI\": \"196937\",\n", - " \"CAS\": \"3556698\",\n", - " \"HMDB\": \"217920\",\n", - " \"UNII\": \"126327\",\n", - " \"MESH\": \"260091\",\n", - " \"KEGG.COMPOUND\": \"16020\",\n", - " \"UMLS\": \"758518\",\n", - " \"DRUGBANK\": \"15179\",\n", - " \"DrugCentral\": \"4995\",\n", - " \"GTOPDB\": \"12347\",\n", - " \"RXCUI\": \"123395\",\n", - " \"NCBIGene\": \"51090837\",\n", - " \"ENSEMBL\": \"12798111\",\n", - " \"WormBase\": \"48780\",\n", - " \"ZFIN\": \"38025\",\n", - " \"RGD\": \"56689\",\n", - " \"MGI\": \"80229\",\n", - " \"dictyBase\": \"13892\",\n", - " \"HGNC\": \"43868\",\n", - " \"OMIM\": \"17299\",\n", - " \"FB\": \"30247\",\n", - " \"SGD\": \"7161\",\n", - " \"UBERON\": \"14411\",\n", - " \"NCIT\": \"10054\",\n", - " \"EMAPA\": \"946\",\n", - " \"FBbt\": \"118\",\n", - " \"ZFA\": \"610\",\n", - " \"WBbt\": \"18\",\n", - " \"CL\": \"2732\",\n", - " \"SNOMEDCT\": \"1415\",\n", - " \"GO\": \"4058\"\n", - " }\n", - " },\n", - " \"biolink:GenomicEntity\": {\n", - " \"curie_prefix\": {\n", - " \"NCBIGene\": \"51090837\",\n", - " \"ENSEMBL\": \"12798111\",\n", - " \"WormBase\": \"48780\",\n", - " \"ZFIN\": \"38025\",\n", - " \"RGD\": \"56689\",\n", - " \"MGI\": \"80229\",\n", - " \"dictyBase\": \"13892\",\n", - " \"HGNC\": \"43868\",\n", - " \"OMIM\": \"17299\",\n", - " \"UMLS\": \"86728\",\n", - " \"FB\": \"30247\",\n", - " \"SGD\": \"7161\"\n", - " }\n", - " },\n", - " \"biolink:Protein\": {\n", - " \"curie_prefix\": {\n", - " \"UniProtKB\": \"250393886\",\n", - " \"ENSEMBL\": \"20797952\",\n", - " \"PR\": \"251709\",\n", - " \"UMLS\": \"164056\"\n", - " }\n", - " },\n", - " \"biolink:MacromolecularMachineMixin\": {\n", - " \"curie_prefix\": {\n", - " \"NCBIGene\": \"51090837\",\n", - " \"ENSEMBL\": \"33596063\",\n", - " \"WormBase\": \"48780\",\n", - " \"ZFIN\": \"38025\",\n", - " \"RGD\": \"56689\",\n", - " \"MGI\": \"80229\",\n", - " \"dictyBase\": \"13892\",\n", - " \"HGNC\": \"43868\",\n", - " \"OMIM\": \"17299\",\n", - " \"UMLS\": \"210542\",\n", - " \"FB\": \"30247\",\n", - " \"SGD\": \"7161\",\n", - " \"UniProtKB\": \"250393886\",\n", - " \"PR\": \"251709\",\n", - " \"ComplexPortal\": \"1256\"\n", - " }\n", - " },\n", - " \"biolink:GeneOrGeneProduct\": {\n", - " \"curie_prefix\": {\n", - " \"NCBIGene\": \"51090837\",\n", - " \"ENSEMBL\": \"33596063\",\n", - " \"WormBase\": \"48780\",\n", - " \"ZFIN\": \"38025\",\n", - " \"RGD\": \"56689\",\n", - " \"MGI\": \"80229\",\n", - " \"dictyBase\": \"13892\",\n", - " \"HGNC\": \"43868\",\n", - " \"OMIM\": \"17299\",\n", - " \"UMLS\": \"210542\",\n", - " \"FB\": \"30247\",\n", - " \"SGD\": \"7161\",\n", - " \"UniProtKB\": \"250393886\",\n", - " \"PR\": \"251709\"\n", - " }\n", - " },\n", - " \"biolink:ThingWithTaxon\": {\n", - " \"curie_prefix\": {\n", - " \"NCBIGene\": \"51090837\",\n", - " \"ENSEMBL\": \"33596063\",\n", - " \"WormBase\": \"48780\",\n", - " \"ZFIN\": \"38025\",\n", - " \"RGD\": \"56689\",\n", - " \"MGI\": \"80229\",\n", - " \"dictyBase\": \"13892\",\n", - " \"HGNC\": \"43868\",\n", - " \"OMIM\": \"27613\",\n", - " \"UMLS\": \"1132300\",\n", - " \"FB\": \"30247\",\n", - " \"SGD\": \"7161\",\n", - " \"UBERON\": \"14411\",\n", - " \"NCIT\": \"56325\",\n", - " \"MESH\": \"14392\",\n", - " \"EMAPA\": \"946\",\n", - " \"FBbt\": \"118\",\n", - " \"ZFA\": \"610\",\n", - " \"WBbt\": \"18\",\n", - " \"PANTHER.FAMILY\": \"26138\",\n", - " \"HGNC.FAMILY\": \"1807\",\n", - " \"UniProtKB\": \"250393886\",\n", - " \"PR\": \"251709\",\n", - " \"MEDDRA\": \"68217\",\n", - " \"HP\": \"17782\",\n", - " \"SNOMEDCT\": \"142612\",\n", - " \"EFO\": \"12220\",\n", - " \"MP\": \"10\",\n", - " \"REACT\": \"107383\",\n", - " \"SMPDB\": \"30248\",\n", - " \"GO\": \"42442\",\n", - " \"PANTHER.PATHWAY\": \"175\",\n", - " \"CL\": \"2732\",\n", - " \"CHEBI\": \"383\",\n", - " \"KEGG.COMPOUND\": \"88\",\n", - " \"CAS\": \"14\",\n", - " \"INCHIKEY\": \"27\",\n", - " \"MONDO\": \"24012\",\n", - " \"DOID\": \"11498\",\n", - " \"orphanet\": \"10780\",\n", - " \"ICD10\": \"2429\",\n", - " \"ICD9\": \"2218\",\n", - " \"OMIM.PS\": \"556\",\n", - " \"KEGG.DISEASE\": \"40\",\n", - " \"RHEA\": \"65080\",\n", - " \"EC\": \"8639\",\n", - " \"TCDB\": \"22\",\n", - " \"KEGG.REACTION\": \"5\",\n", - " \"ComplexPortal\": \"1256\"\n", - " }\n", - " },\n", - " \"biolink:ChemicalEntityOrProteinOrPolypeptide\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"124460882\",\n", - " \"INCHIKEY\": \"110336300\",\n", - " \"CHEMBL.COMPOUND\": \"2399641\",\n", - " \"CHEBI\": \"197320\",\n", - " \"CAS\": \"3556712\",\n", - " \"HMDB\": \"217920\",\n", - " \"UNII\": \"126327\",\n", - " \"MESH\": \"258382\",\n", - " \"KEGG.COMPOUND\": \"16108\",\n", - " \"UMLS\": \"713581\",\n", - " \"DRUGBANK\": \"15179\",\n", - " \"DrugCentral\": \"4995\",\n", - " \"GTOPDB\": \"12347\",\n", - " \"RXCUI\": \"123395\",\n", - " \"UniProtKB\": \"250393886\",\n", - " \"ENSEMBL\": \"20797952\",\n", - " \"PR\": \"251709\"\n", - " }\n", - " },\n", - " \"biolink:ChemicalEntityOrGeneOrGeneProduct\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"124460882\",\n", - " \"INCHIKEY\": \"110336300\",\n", - " \"CHEMBL.COMPOUND\": \"2399641\",\n", - " \"CHEBI\": \"197320\",\n", - " \"CAS\": \"3556712\",\n", - " \"HMDB\": \"217920\",\n", - " \"UNII\": \"126327\",\n", - " \"MESH\": \"258382\",\n", - " \"KEGG.COMPOUND\": \"16108\",\n", - " \"UMLS\": \"760067\",\n", - " \"DRUGBANK\": \"15179\",\n", - " \"DrugCentral\": \"4995\",\n", - " \"GTOPDB\": \"12347\",\n", - " \"RXCUI\": \"123395\",\n", - " \"NCBIGene\": \"51090837\",\n", - " \"ENSEMBL\": \"33596063\",\n", - " \"WormBase\": \"48780\",\n", - " \"ZFIN\": \"38025\",\n", - " \"RGD\": \"56689\",\n", - " \"MGI\": \"80229\",\n", - " \"dictyBase\": \"13892\",\n", - " \"HGNC\": \"43868\",\n", - " \"OMIM\": \"17299\",\n", - " \"FB\": \"30247\",\n", - " \"SGD\": \"7161\",\n", - " \"PANTHER.FAMILY\": \"26138\",\n", - " \"HGNC.FAMILY\": \"1807\",\n", - " \"UniProtKB\": \"250393886\",\n", - " \"PR\": \"251709\"\n", - " }\n", - " },\n", - " \"biolink:GeneProductMixin\": {\n", - " \"curie_prefix\": {\n", - " \"UniProtKB\": \"250393886\",\n", - " \"ENSEMBL\": \"20797952\",\n", - " \"PR\": \"251709\",\n", - " \"UMLS\": \"164056\"\n", - " }\n", - " },\n", - " \"biolink:Entity\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"124460882\",\n", - " \"INCHIKEY\": \"110336300\",\n", - " \"CHEMBL.COMPOUND\": \"2399641\",\n", - " \"CHEBI\": \"197320\",\n", - " \"CAS\": \"3556712\",\n", - " \"HMDB\": \"217920\",\n", - " \"UNII\": \"126327\",\n", - " \"MESH\": \"343122\",\n", - " \"KEGG.COMPOUND\": \"16108\",\n", - " \"UMLS\": \"3206840\",\n", - " \"DRUGBANK\": \"15179\",\n", - " \"DrugCentral\": \"4995\",\n", - " \"GTOPDB\": \"12347\",\n", - " \"RXCUI\": \"123395\",\n", - " \"NCBIGene\": \"51090837\",\n", - " \"ENSEMBL\": \"33596063\",\n", - " \"WormBase\": \"48780\",\n", - " \"ZFIN\": \"38025\",\n", - " \"RGD\": \"56689\",\n", - " \"MGI\": \"80229\",\n", - " \"dictyBase\": \"13892\",\n", - " \"HGNC\": \"43868\",\n", - " \"OMIM\": \"27613\",\n", - " \"FB\": \"30247\",\n", - " \"SGD\": \"7161\",\n", - " \"UBERON\": \"14411\",\n", - " \"NCIT\": \"56325\",\n", - " \"EMAPA\": \"946\",\n", - " \"FBbt\": \"118\",\n", - " \"ZFA\": \"610\",\n", - " \"WBbt\": \"18\",\n", - " \"PANTHER.FAMILY\": \"26138\",\n", - " \"HGNC.FAMILY\": \"1807\",\n", - " \"UniProtKB\": \"250393886\",\n", - " \"PR\": \"251709\",\n", - " \"MEDDRA\": \"68217\",\n", - " \"HP\": \"17782\",\n", - " \"SNOMEDCT\": \"142612\",\n", - " \"EFO\": \"12220\",\n", - " \"MP\": \"10\",\n", - " \"REACT\": \"107383\",\n", - " \"SMPDB\": \"30248\",\n", - " \"GO\": \"42442\",\n", - " \"PANTHER.PATHWAY\": \"175\",\n", - " \"CL\": \"2732\",\n", - " \"PMID\": \"36980104\",\n", - " \"doi\": \"28069780\",\n", - " \"PMC\": \"9078478\",\n", - " \"MONDO\": \"24012\",\n", - " \"DOID\": \"11498\",\n", - " \"orphanet\": \"10780\",\n", - " \"ICD10\": \"2429\",\n", - " \"ICD9\": \"2218\",\n", - " \"OMIM.PS\": \"556\",\n", - " \"KEGG.DISEASE\": \"40\",\n", - " \"RHEA\": \"65080\",\n", - " \"EC\": \"8639\",\n", - " \"TCDB\": \"22\",\n", - " \"KEGG.REACTION\": \"5\",\n", - " \"ComplexPortal\": \"1256\",\n", - " \"NCBITaxon\": \"2546095\"\n", - " }\n", - " },\n", - " \"biolink:NamedThing\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"124460882\",\n", - " \"INCHIKEY\": \"110336300\",\n", - " \"CHEMBL.COMPOUND\": \"2399641\",\n", - " \"CHEBI\": \"197320\",\n", - " \"CAS\": \"3556712\",\n", - " \"HMDB\": \"217920\",\n", - " \"UNII\": \"126327\",\n", - " \"MESH\": \"343122\",\n", - " \"KEGG.COMPOUND\": \"16108\",\n", - " \"UMLS\": \"3206840\",\n", - " \"DRUGBANK\": \"15179\",\n", - " \"DrugCentral\": \"4995\",\n", - " \"GTOPDB\": \"12347\",\n", - " \"RXCUI\": \"123395\",\n", - " \"NCBIGene\": \"51090837\",\n", - " \"ENSEMBL\": \"33596063\",\n", - " \"WormBase\": \"48780\",\n", - " \"ZFIN\": \"38025\",\n", - " \"RGD\": \"56689\",\n", - " \"MGI\": \"80229\",\n", - " \"dictyBase\": \"13892\",\n", - " \"HGNC\": \"43868\",\n", - " \"OMIM\": \"27613\",\n", - " \"FB\": \"30247\",\n", - " \"SGD\": \"7161\",\n", - " \"UBERON\": \"14411\",\n", - " \"NCIT\": \"56325\",\n", - " \"EMAPA\": \"946\",\n", - " \"FBbt\": \"118\",\n", - " \"ZFA\": \"610\",\n", - " \"WBbt\": \"18\",\n", - " \"PANTHER.FAMILY\": \"26138\",\n", - " \"HGNC.FAMILY\": \"1807\",\n", - " \"UniProtKB\": \"250393886\",\n", - " \"PR\": \"251709\",\n", - " \"MEDDRA\": \"68217\",\n", - " \"HP\": \"17782\",\n", - " \"SNOMEDCT\": \"142612\",\n", - " \"EFO\": \"12220\",\n", - " \"MP\": \"10\",\n", - " \"REACT\": \"107383\",\n", - " \"SMPDB\": \"30248\",\n", - " \"GO\": \"42442\",\n", - " \"PANTHER.PATHWAY\": \"175\",\n", - " \"CL\": \"2732\",\n", - " \"PMID\": \"36980104\",\n", - " \"doi\": \"28069780\",\n", - " \"PMC\": \"9078478\",\n", - " \"MONDO\": \"24012\",\n", - " \"DOID\": \"11498\",\n", - " \"orphanet\": \"10780\",\n", - " \"ICD10\": \"2429\",\n", - " \"ICD9\": \"2218\",\n", - " \"OMIM.PS\": \"556\",\n", - " \"KEGG.DISEASE\": \"40\",\n", - " \"RHEA\": \"65080\",\n", - " \"EC\": \"8639\",\n", - " \"TCDB\": \"22\",\n", - " \"KEGG.REACTION\": \"5\",\n", - " \"ComplexPortal\": \"1256\",\n", - " \"NCBITaxon\": \"2546095\"\n", - " }\n", - " },\n", - " \"biolink:BiologicalEntity\": {\n", - " \"curie_prefix\": {\n", - " \"NCBIGene\": \"51090837\",\n", - " \"ENSEMBL\": \"33596063\",\n", - " \"WormBase\": \"48780\",\n", - " \"ZFIN\": \"38025\",\n", - " \"RGD\": \"56689\",\n", - " \"MGI\": \"80229\",\n", - " \"dictyBase\": \"13892\",\n", - " \"HGNC\": \"43868\",\n", - " \"OMIM\": \"27613\",\n", - " \"UMLS\": \"1131851\",\n", - " \"FB\": \"30247\",\n", - " \"SGD\": \"7161\",\n", - " \"UBERON\": \"14411\",\n", - " \"NCIT\": \"56325\",\n", - " \"MESH\": \"14392\",\n", - " \"EMAPA\": \"946\",\n", - " \"FBbt\": \"118\",\n", - " \"ZFA\": \"610\",\n", - " \"WBbt\": \"18\",\n", - " \"PANTHER.FAMILY\": \"26138\",\n", - " \"HGNC.FAMILY\": \"1807\",\n", - " \"UniProtKB\": \"250393886\",\n", - " \"PR\": \"251709\",\n", - " \"MEDDRA\": \"68217\",\n", - " \"HP\": \"17782\",\n", - " \"SNOMEDCT\": \"142612\",\n", - " \"EFO\": \"12220\",\n", - " \"MP\": \"10\",\n", - " \"REACT\": \"107383\",\n", - " \"SMPDB\": \"30248\",\n", - " \"GO\": \"42442\",\n", - " \"PANTHER.PATHWAY\": \"175\",\n", - " \"CL\": \"2732\",\n", - " \"CHEBI\": \"383\",\n", - " \"KEGG.COMPOUND\": \"88\",\n", - " \"CAS\": \"14\",\n", - " \"INCHIKEY\": \"27\",\n", - " \"MONDO\": \"24012\",\n", - " \"DOID\": \"11498\",\n", - " \"orphanet\": \"10780\",\n", - " \"ICD10\": \"2429\",\n", - " \"ICD9\": \"2218\",\n", - " \"OMIM.PS\": \"556\",\n", - " \"KEGG.DISEASE\": \"40\",\n", - " \"RHEA\": \"65080\",\n", - " \"EC\": \"8639\",\n", - " \"TCDB\": \"22\",\n", - " \"KEGG.REACTION\": \"5\",\n", - " \"ComplexPortal\": \"1256\"\n", - " }\n", - " },\n", - " \"biolink:Polypeptide\": {\n", - " \"curie_prefix\": {\n", - " \"UniProtKB\": \"250393886\",\n", - " \"ENSEMBL\": \"20797952\",\n", - " \"PR\": \"251709\",\n", - " \"UMLS\": \"164461\",\n", - " \"CHEBI\": \"383\",\n", - " \"MESH\": \"280\",\n", - " \"KEGG.COMPOUND\": \"88\",\n", - " \"CAS\": \"14\",\n", - " \"INCHIKEY\": \"27\"\n", - " }\n", " }\n", "}\n" ] @@ -1263,7 +334,10 @@ ], "source": [ "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes')\n", - "print( json.dumps( result.json(), indent = 2))" + "responses = result.json()\n", + "\n", + "# Display only the first three responses. \n", + "print( json.dumps( dict(list(responses.items())[:3]), indent = 2))" ] }, { From 384998490b90e5cd258efe836df007835662366c Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 17 Jun 2024 18:32:07 -0400 Subject: [PATCH 4/7] Updated outputs. --- documentation/NodeNormalization.ipynb | 589 +++++++++++++++++++------- 1 file changed, 426 insertions(+), 163 deletions(-) diff --git a/documentation/NodeNormalization.ipynb b/documentation/NodeNormalization.ipynb index 6419bec..e786030 100644 --- a/documentation/NodeNormalization.ipynb +++ b/documentation/NodeNormalization.ipynb @@ -67,7 +67,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 2, "metadata": { "slideshow": { "slide_type": "subslide" @@ -81,72 +81,72 @@ "{\n", " \"semantic_types\": {\n", " \"types\": [\n", - " \"biolink:Protein\",\n", - " \"biolink:Pathway\",\n", - " \"biolink:Behavior\",\n", " \"biolink:BiologicalProcess\",\n", - " \"biolink:GeneGroupingMixin\",\n", - " \"biolink:AdministrativeEntity\",\n", - " \"biolink:Attribute\",\n", - " \"biolink:MolecularEntity\",\n", - " \"biolink:Entity\",\n", - " \"biolink:GeneFamily\",\n", " \"biolink:BiologicalEntity\",\n", - " \"biolink:DiseaseOrPhenotypicFeature\",\n", - " \"biolink:MolecularActivity\",\n", " \"biolink:OrganismTaxon\",\n", - " \"biolink:MolecularMixture\",\n", - " \"biolink:GenomicEntity\",\n", - " \"biolink:GeographicLocation\",\n", - " \"biolink:ActivityAndBehavior\",\n", - " \"biolink:MacromolecularComplex\",\n", - " \"biolink:GeneProductMixin\",\n", - " \"biolink:PhysicalEssenceOrOccurrent\",\n", - " \"biolink:StudyPopulation\",\n", - " \"biolink:MacromolecularMachineMixin\",\n", - " \"biolink:InformationContentEntity\",\n", - " \"biolink:SubjectOfInvestigation\",\n", " \"biolink:Device\",\n", - " \"biolink:OrganismalEntity\",\n", - " \"biolink:Polypeptide\",\n", - " \"biolink:NamedThing\",\n", + " \"biolink:PlanetaryEntity\",\n", + " \"biolink:GeneOrGeneProduct\",\n", " \"biolink:ChemicalMixture\",\n", - " \"biolink:ClinicalAttribute\",\n", - " \"biolink:Event\",\n", - " \"biolink:OntologyClass\",\n", " \"biolink:ComplexMolecularMixture\",\n", - " \"biolink:NucleicAcidEntity\",\n", - " \"biolink:Occurrent\",\n", - " \"biolink:ChemicalEntity\",\n", - " \"biolink:GrossAnatomicalStructure\",\n", - " \"biolink:Activity\",\n", - " \"biolink:PopulationOfIndividualOrganisms\",\n", - " \"biolink:OrganismAttribute\",\n", + " \"biolink:StudyPopulation\",\n", " \"biolink:Phenomenon\",\n", - " \"biolink:AnatomicalEntity\",\n", - " \"biolink:GeneOrGeneProduct\",\n", - " \"biolink:SmallMolecule\",\n", - " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", - " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", - " \"biolink:Human\",\n", + " \"biolink:ClinicalAttribute\",\n", + " \"biolink:MolecularActivity\",\n", " \"biolink:Food\",\n", - " \"biolink:CellularComponent\",\n", - " \"biolink:BiologicalProcessOrActivity\",\n", - " \"biolink:Drug\",\n", - " \"biolink:PlanetaryEntity\",\n", - " \"biolink:PhysicalEssence\",\n", " \"biolink:Publication\",\n", + " \"biolink:ChemicalEntity\",\n", + " \"biolink:NamedThing\",\n", + " \"biolink:MolecularMixture\",\n", + " \"biolink:GeneGroupingMixin\",\n", + " \"biolink:BiologicalProcessOrActivity\",\n", + " \"biolink:Gene\",\n", " \"biolink:Disease\",\n", + " \"biolink:OntologyClass\",\n", " \"biolink:Cohort\",\n", + " \"biolink:GrossAnatomicalStructure\",\n", + " \"biolink:Drug\",\n", + " \"biolink:SubjectOfInvestigation\",\n", + " \"biolink:PhenotypicFeature\",\n", + " \"biolink:MacromolecularComplex\",\n", + " \"biolink:Event\",\n", + " \"biolink:ActivityAndBehavior\",\n", + " \"biolink:PopulationOfIndividualOrganisms\",\n", + " \"biolink:NucleicAcidEntity\",\n", + " \"biolink:OrganismalEntity\",\n", + " \"biolink:Protein\",\n", + " \"biolink:Human\",\n", " \"biolink:Agent\",\n", - " \"biolink:PhysiologicalProcess\",\n", + " \"biolink:GeneFamily\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:Attribute\",\n", + " \"biolink:SmallMolecule\",\n", + " \"biolink:CellularComponent\",\n", " \"biolink:ChemicalOrDrugOrTreatment\",\n", + " \"biolink:MolecularEntity\",\n", + " \"biolink:InformationContentEntity\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\",\n", + " \"biolink:Cell\",\n", + " \"biolink:GenomicEntity\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", + " \"biolink:GeneProductMixin\",\n", + " \"biolink:Polypeptide\",\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:PhysiologicalProcess\",\n", + " \"biolink:Occurrent\",\n", " \"biolink:Procedure\",\n", - " \"biolink:Gene\",\n", " \"biolink:PhysicalEntity\",\n", + " \"biolink:Entity\",\n", + " \"biolink:OrganismAttribute\",\n", + " \"biolink:Behavior\",\n", + " \"biolink:Activity\",\n", + " \"biolink:AdministrativeEntity\",\n", + " \"biolink:GeographicLocation\",\n", + " \"biolink:AnatomicalEntity\",\n", + " \"biolink:MacromolecularMachineMixin\",\n", " \"biolink:ThingWithTaxon\",\n", - " \"biolink:PhenotypicFeature\",\n", - " \"biolink:Cell\"\n", + " \"biolink:DiseaseOrPhenotypicFeature\",\n", + " \"biolink:Pathway\"\n", " ]\n", " }\n", "}\n" @@ -375,7 +375,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 3, "metadata": { "scrolled": true, "slideshow": { @@ -390,13 +390,13 @@ "{\n", " \"MESH:D014867\": {\n", " \"id\": {\n", - " \"identifier\": \"PUBCHEM.COMPOUND:22247451\",\n", - " \"label\": \"Hydron;hydroxide\"\n", + " \"identifier\": \"CHEBI:15377\",\n", + " \"label\": \"WATER\"\n", " },\n", " \"equivalent_identifiers\": [\n", " {\n", - " \"identifier\": \"PUBCHEM.COMPOUND:22247451\",\n", - " \"label\": \"Hydron;hydroxide\"\n", + " \"identifier\": \"CHEBI:15377\",\n", + " \"label\": \"water\"\n", " },\n", " {\n", " \"identifier\": \"PUBCHEM.COMPOUND:962\",\n", @@ -407,11 +407,8 @@ " \"label\": \"WATER\"\n", " },\n", " {\n", - " \"identifier\": \"UNII:059QF0KO0R\"\n", - " },\n", - " {\n", - " \"identifier\": \"CHEBI:15377\",\n", - " \"label\": \"water\"\n", + " \"identifier\": \"UNII:059QF0KO0R\",\n", + " \"label\": \"WATER\"\n", " },\n", " {\n", " \"identifier\": \"DRUGBANK:DB09145\"\n", @@ -421,23 +418,39 @@ " \"label\": \"Water\"\n", " },\n", " {\n", - " \"identifier\": \"HMDB:HMDB0002111\"\n", + " \"identifier\": \"CAS:7732-18-5\"\n", + " },\n", + " {\n", + " \"identifier\": \"HMDB:HMDB0002111\",\n", + " \"label\": \"Water\"\n", " },\n", " {\n", " \"identifier\": \"KEGG.COMPOUND:C00001\",\n", " \"label\": \"H2O\"\n", " },\n", " {\n", - " \"identifier\": \"INCHIKEY:IKBQPNVYXHKVJS-LVZFUZTISA-N\"\n", + " \"identifier\": \"INCHIKEY:XLYOFNOQVPJJNP-UHFFFAOYSA-N\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0043047\",\n", + " \"label\": \"water\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:11295\"\n", " }\n", " ],\n", " \"type\": [\n", - " \"biolink:ChemicalSubstance\",\n", - " \"biolink:Entity\",\n", + " \"biolink:SmallMolecule\",\n", + " \"biolink:MolecularEntity\",\n", + " \"biolink:ChemicalEntity\",\n", " \"biolink:NamedThing\",\n", - " \"biolink:BiologicalEntity\",\n", - " \"biolink:MolecularEntity\"\n", - " ]\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:ChemicalOrDrugOrTreatment\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\"\n", + " ],\n", + " \"information_content\": 47.5\n", " }\n", "}\n" ] @@ -457,12 +470,14 @@ } }, "source": [ + "#### Batching\n", + "\n", "To improve performance, multiple CURIEs may be batched into a single function call as a POST:" ] }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 4, "metadata": { "scrolled": true, "slideshow": { @@ -486,28 +501,185 @@ " \"label\": \"amyotrophic lateral sclerosis\"\n", " },\n", " {\n", - " \"identifier\": \"DOID:332\"\n", + " \"identifier\": \"DOID:332\",\n", + " \"label\": \"amyotrophic lateral sclerosis\"\n", " },\n", " {\n", - " \"identifier\": \"OMIM:MTHU030638\"\n", + " \"identifier\": \"OMIM:PS105400\"\n", " },\n", " {\n", - " \"identifier\": \"OMIM:MTHU038375\"\n", + " \"identifier\": \"orphanet:803\"\n", " },\n", " {\n", - " \"identifier\": \"ORPHANET:803\"\n", + " \"identifier\": \"UMLS:C0002736\",\n", + " \"label\": \"Amyotrophic Lateral Sclerosis\"\n", " },\n", " {\n", - " \"identifier\": \"EFO:0000253\",\n", - " \"label\": \"amyotrophic lateral sclerosis\"\n", + " \"identifier\": \"MESH:D000690\",\n", + " \"label\": \"Amyotrophic Lateral Sclerosis\"\n", " },\n", " {\n", - " \"identifier\": \"UMLS:C0002736\",\n", + " \"identifier\": \"MEDDRA:10002026\"\n", + " },\n", + " {\n", + " \"identifier\": \"MEDDRA:10052889\"\n", + " },\n", + " {\n", + " \"identifier\": \"NCIT:C34373\",\n", " \"label\": \"Amyotrophic Lateral Sclerosis\"\n", " },\n", " {\n", - " \"identifier\": \"UMLS:C0393554\",\n", - " \"label\": \"Amyotrophic Lateral Sclerosis With Dementia\"\n", + " \"identifier\": \"SNOMEDCT:86044005\"\n", + " },\n", + " {\n", + " \"identifier\": \"ICD10:G12.21\"\n", + " },\n", + " {\n", + " \"identifier\": \"ICD9:335.20\"\n", + " },\n", + " {\n", + " \"identifier\": \"KEGG.DISEASE:05014\"\n", + " },\n", + " {\n", + " \"identifier\": \"HP:0007354\",\n", + " \"label\": \"Amyotrophic lateral sclerosis\"\n", + " }\n", + " ],\n", + " \"type\": [\n", + " \"biolink:Disease\",\n", + " \"biolink:DiseaseOrPhenotypicFeature\",\n", + " \"biolink:BiologicalEntity\",\n", + " \"biolink:NamedThing\",\n", + " \"biolink:ThingWithTaxon\"\n", + " ],\n", + " \"information_content\": 74.9\n", + " },\n", + " \"HGNC:613\": {\n", + " \"id\": {\n", + " \"identifier\": \"NCBIGene:348\",\n", + " \"label\": \"APOE\"\n", + " },\n", + " \"equivalent_identifiers\": [\n", + " {\n", + " \"identifier\": \"NCBIGene:348\",\n", + " \"label\": \"APOE\"\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSG00000130203\",\n", + " \"label\": \"APOE (Hsap)\"\n", + " },\n", + " {\n", + " \"identifier\": \"HGNC:613\",\n", + " \"label\": \"APOE\"\n", + " },\n", + " {\n", + " \"identifier\": \"OMIM:107741\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1412481\",\n", + " \"label\": \"APOE gene\"\n", + " },\n", + " {\n", + " \"identifier\": \"UniProtKB:A0A0S2Z3D5\",\n", + " \"label\": \"A0A0S2Z3D5_HUMAN Apolipoprotein E (Fragment) (trembl)\"\n", + " },\n", + " {\n", + " \"identifier\": \"UniProtKB:P02649\",\n", + " \"label\": \"APOE_HUMAN Apolipoprotein E (sprot)\"\n", + " },\n", + " {\n", + " \"identifier\": \"PR:P02649\",\n", + " \"label\": \"apolipoprotein E (human)\"\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSP00000252486\"\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSP00000252486.3\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C4308468\",\n", + " \"label\": \"ApoE protein, human\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C4721561\",\n", + " \"label\": \"Apolipoprotein E4, human\"\n", + " }\n", + " ],\n", + " \"type\": [\n", + " \"biolink:Gene\",\n", + " \"biolink:BiologicalEntity\",\n", + " \"biolink:NamedThing\",\n", + " \"biolink:GeneOrGeneProduct\",\n", + " \"biolink:GenomicEntity\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:OntologyClass\",\n", + " \"biolink:ThingWithTaxon\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\",\n", + " \"biolink:MacromolecularMachineMixin\",\n", + " \"biolink:Protein\",\n", + " \"biolink:Polypeptide\",\n", + " \"biolink:GeneProductMixin\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\"\n", + " ],\n", + " \"information_content\": 100.0\n", + " },\n", + " \"CURIE:NOTHING\": null\n", + "}\n" + ] + } + ], + "source": [ + "result = requests.post('https://nodenormalization-sri.renci.org/get_normalized_nodes',\n", + " json={\"curies\":[\"HP:0007354\", \"HGNC:613\", \"CURIE:NOTHING\"]})\n", + "print( json.dumps( result.json(), indent = 2))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### Descriptions\n", + "\n", + "Descriptions are included for concepts with descriptions in [UberGraph](https://github.com/INCATools/ubergraph/). You can use the `description` flag to include descriptions where available. Note that descriptions are included for each identifier, and the first description is included with the preferred identifier." + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"HP:0007354\": {\n", + " \"id\": {\n", + " \"identifier\": \"MONDO:0004976\",\n", + " \"label\": \"amyotrophic lateral sclerosis\",\n", + " \"description\": \"Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive muscular paralysis reflecting degeneration of motor neurons in the primary motor cortex, corticospinal tracts, brainstem and spinal cord.\"\n", + " },\n", + " \"equivalent_identifiers\": [\n", + " {\n", + " \"identifier\": \"MONDO:0004976\",\n", + " \"label\": \"amyotrophic lateral sclerosis\",\n", + " \"description\": \"Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive muscular paralysis reflecting degeneration of motor neurons in the primary motor cortex, corticospinal tracts, brainstem and spinal cord.\"\n", + " },\n", + " {\n", + " \"identifier\": \"DOID:332\",\n", + " \"label\": \"amyotrophic lateral sclerosis\"\n", + " },\n", + " {\n", + " \"identifier\": \"OMIM:PS105400\"\n", + " },\n", + " {\n", + " \"identifier\": \"orphanet:803\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0002736\",\n", + " \"label\": \"Amyotrophic Lateral Sclerosis\"\n", " },\n", " {\n", " \"identifier\": \"MESH:D000690\",\n", @@ -517,59 +689,111 @@ " \"identifier\": \"MEDDRA:10002026\"\n", " },\n", " {\n", - " \"identifier\": \"NCIT:C34373\",\n", - " \"label\": \"Amyotrophic Lateral Sclerosis\"\n", + " \"identifier\": \"MEDDRA:10052889\"\n", " },\n", " {\n", - " \"identifier\": \"SNOMEDCT:230258005\"\n", + " \"identifier\": \"NCIT:C34373\",\n", + " \"label\": \"Amyotrophic Lateral Sclerosis\",\n", + " \"description\": \"A neurodegenerative disorder characterized by progressive degeneration of the motor neurons of the central nervous system. It results in weakness and atrophy of the muscles which leads to an inability to initiate and control voluntary movements.\"\n", " },\n", " {\n", " \"identifier\": \"SNOMEDCT:86044005\"\n", " },\n", " {\n", + " \"identifier\": \"ICD10:G12.21\"\n", + " },\n", + " {\n", + " \"identifier\": \"ICD9:335.20\"\n", + " },\n", + " {\n", + " \"identifier\": \"KEGG.DISEASE:05014\"\n", + " },\n", + " {\n", " \"identifier\": \"HP:0007354\",\n", " \"label\": \"Amyotrophic lateral sclerosis\"\n", " }\n", " ],\n", " \"type\": [\n", " \"biolink:Disease\",\n", - " \"biolink:Disease\",\n", " \"biolink:DiseaseOrPhenotypicFeature\",\n", " \"biolink:BiologicalEntity\",\n", " \"biolink:NamedThing\",\n", - " \"biolink:Entity\"\n", - " ]\n", + " \"biolink:ThingWithTaxon\"\n", + " ],\n", + " \"information_content\": 74.9\n", " },\n", " \"HGNC:613\": {\n", " \"id\": {\n", " \"identifier\": \"NCBIGene:348\",\n", - " \"label\": \"APOE\"\n", + " \"label\": \"APOE\",\n", + " \"description\": \"An apolipoprotein E that is encoded in the genome of human.\"\n", " },\n", " \"equivalent_identifiers\": [\n", " {\n", - " \"identifier\": \"NCBIGene:348\"\n", + " \"identifier\": \"NCBIGene:348\",\n", + " \"label\": \"APOE\"\n", " },\n", " {\n", - " \"identifier\": \"ENSEMBL:ENSG00000130203\"\n", + " \"identifier\": \"ENSEMBL:ENSG00000130203\",\n", + " \"label\": \"APOE (Hsap)\"\n", " },\n", " {\n", " \"identifier\": \"HGNC:613\",\n", " \"label\": \"APOE\"\n", " },\n", " {\n", + " \"identifier\": \"OMIM:107741\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1412481\",\n", + " \"label\": \"APOE gene\"\n", + " },\n", + " {\n", + " \"identifier\": \"UniProtKB:A0A0S2Z3D5\",\n", + " \"label\": \"A0A0S2Z3D5_HUMAN Apolipoprotein E (Fragment) (trembl)\"\n", + " },\n", + " {\n", " \"identifier\": \"UniProtKB:P02649\",\n", " \"label\": \"APOE_HUMAN Apolipoprotein E (sprot)\"\n", + " },\n", + " {\n", + " \"identifier\": \"PR:P02649\",\n", + " \"label\": \"apolipoprotein E (human)\",\n", + " \"description\": \"An apolipoprotein E that is encoded in the genome of human.\"\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSP00000252486\"\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSP00000252486.3\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C4308468\",\n", + " \"label\": \"ApoE protein, human\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C4721561\",\n", + " \"label\": \"Apolipoprotein E4, human\"\n", " }\n", " ],\n", " \"type\": [\n", " \"biolink:Gene\",\n", - " \"biolink:Gene\",\n", - " \"biolink:GenomicEntity\",\n", - " \"biolink:MolecularEntity\",\n", " \"biolink:BiologicalEntity\",\n", " \"biolink:NamedThing\",\n", - " \"biolink:Entity\"\n", - " ]\n", + " \"biolink:GeneOrGeneProduct\",\n", + " \"biolink:GenomicEntity\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:OntologyClass\",\n", + " \"biolink:ThingWithTaxon\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\",\n", + " \"biolink:MacromolecularMachineMixin\",\n", + " \"biolink:Protein\",\n", + " \"biolink:Polypeptide\",\n", + " \"biolink:GeneProductMixin\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\"\n", + " ],\n", + " \"information_content\": 100.0\n", " },\n", " \"CURIE:NOTHING\": null\n", "}\n" @@ -578,7 +802,7 @@ ], "source": [ "result = requests.post('https://nodenormalization-sri.renci.org/get_normalized_nodes',\n", - " json={\"curies\":[\"HP:0007354\", \"HGNC:613\", \"CURIE:NOTHING\"]})\n", + " json={\"curies\":[\"HP:0007354\", \"HGNC:613\", \"CURIE:NOTHING\"], \"description\": True})\n", "print( json.dumps( result.json(), indent = 2))" ] }, @@ -593,14 +817,12 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Node normalization will now operate on TRAPI messages (version 1.0)\n", - "\n", - "Here we have a message in terms of HGNC and DOID, and the normalizer returns a message using NCBIGene and MONDO." + "NodeNorm can normalize entire TRAPI messages. Here we have a message in terms of HGNC and DOID, and the normalizer returns a message using NCBIGene and MONDO." ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 24, "metadata": {}, "outputs": [], "source": [ @@ -610,12 +832,12 @@ " \"nodes\": {\n", " \"n1\": {\n", " \"id\": \"HGNC:11603\",\n", - " \"category\": [\n", + " \"categories\": [\n", " \"biolink:Gene\"\n", " ]\n", " },\n", " \"n2\": {\n", - " \"category\": [\n", + " \"categories\": [\n", " \"biolink:Disease\"\n", " ]\n", " }\n", @@ -631,13 +853,13 @@ " \"nodes\": {\n", " \"HGNC:11603\": {\n", " \"name\": \"TBX4\",\n", - " \"category\": [\n", + " \"categories\": [\n", " \"biolink:Gene\"\n", " ]\n", " },\n", " \"DOID:3083\": {\n", " \"name\": \"chronic obstructive pulmonary disease\",\n", - " \"category\": [\n", + " \"categories\": [\n", " \"biolink:Disease\"\n", " ]\n", " }\n", @@ -647,7 +869,7 @@ " \"subject\": \"NCBIGene:9496\",\n", " \"object\": \"DOID:3083\",\n", " \"predicate\": \"biolink:related_to\",\n", - " \"relation\": \"RO:0003304\"\n", + " \"sources\": []\n", " }\n", " }\n", " },\n", @@ -665,13 +887,18 @@ " }\n", " ]\n", " },\n", - " \"edge_bindings\": {\n", - " \"e1\": [\n", - " {\n", - " \"id\": \"2d38345a-e9bf-4943-accb-dccba351dd04\"\n", - " }\n", - " ]\n", - " }\n", + " \"analyses\": [{\n", + " \"resource_id\": \"infores:openpredict\",\n", + " \"score\": \"0.682246949249408\",\n", + " \"scoring_method\": \"Model confidence between 0 and 1\",\n", + " \"edge_bindings\": {\n", + " \"e1\": [\n", + " {\n", + " \"id\": \"2d38345a-e9bf-4943-accb-dccba351dd04\"\n", + " }\n", + " ]\n", + " }\n", + " }]\n", " }\n", " ]\n", " }\n", @@ -680,7 +907,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 25, "metadata": {}, "outputs": [ { @@ -692,13 +919,13 @@ } ], "source": [ - "result = requests.post('https://nodenormalization-sri.renci.org/response',json=trapi_message)\n", + "result = requests.post('https://nodenormalization-sri.renci.org/1.4/query',json=trapi_message)\n", "print(result.status_code)" ] }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 26, "metadata": {}, "outputs": [ { @@ -710,83 +937,106 @@ " \"query_graph\": {\n", " \"nodes\": {\n", " \"n1\": {\n", - " \"id\": \"NCBIGene:9496\",\n", - " \"category\": [\n", + " \"categories\": [\n", " \"biolink:Gene\"\n", " ],\n", - " \"is_set\": false\n", + " \"is_set\": false,\n", + " \"constraints\": [],\n", + " \"id\": \"HGNC:11603\"\n", " },\n", " \"n2\": {\n", - " \"id\": null,\n", - " \"category\": [\n", + " \"categories\": [\n", " \"biolink:Disease\"\n", " ],\n", - " \"is_set\": false\n", + " \"is_set\": false,\n", + " \"constraints\": []\n", " }\n", " },\n", " \"edges\": {\n", " \"e1\": {\n", " \"subject\": \"n1\",\n", - " \"object\": \"n2\",\n", - " \"predicate\": null,\n", - " \"relation\": null\n", + " \"object\": \"n2\"\n", " }\n", " }\n", " },\n", " \"knowledge_graph\": {\n", " \"nodes\": {\n", " \"NCBIGene:9496\": {\n", - " \"category\": [\n", - " \"biolink:Gene\",\n", - " \"biolink:Gene\",\n", - " \"biolink:GenomicEntity\",\n", - " \"biolink:MolecularEntity\",\n", - " \"biolink:BiologicalEntity\",\n", + " \"categories\": [\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:MacromolecularMachineMixin\",\n", + " \"biolink:OntologyClass\",\n", + " \"biolink:GeneOrGeneProduct\",\n", " \"biolink:NamedThing\",\n", - " \"biolink:Entity\"\n", + " \"biolink:BiologicalEntity\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\",\n", + " \"biolink:Protein\",\n", + " \"biolink:GenomicEntity\",\n", + " \"biolink:ThingWithTaxon\",\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:Polypeptide\",\n", + " \"biolink:GeneProductMixin\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", + " \"biolink:Gene\"\n", " ],\n", " \"name\": \"TBX4\",\n", " \"attributes\": [\n", " {\n", - " \"type\": \"biolink:same_as\",\n", + " \"attribute_type_id\": \"biolink:same_as\",\n", " \"value\": [\n", " \"NCBIGene:9496\",\n", " \"ENSEMBL:ENSG00000121075\",\n", " \"HGNC:11603\",\n", - " \"UniProtKB:P57082\"\n", + " \"OMIM:601719\",\n", + " \"UMLS:C1420614\",\n", + " \"UniProtKB:P57082\",\n", + " \"PR:P57082\",\n", + " \"UMLS:C3815898\"\n", " ],\n", - " \"name\": \"same_as\",\n", - " \"url\": null,\n", - " \"source\": null\n", + " \"value_type_id\": \"EDAM:data_0006\",\n", + " \"original_attribute_name\": \"equivalent_identifiers\"\n", " }\n", " ]\n", " },\n", " \"MONDO:0005002\": {\n", - " \"category\": [\n", - " \"biolink:Disease\",\n", - " \"biolink:Disease\",\n", + " \"categories\": [\n", " \"biolink:DiseaseOrPhenotypicFeature\",\n", - " \"biolink:BiologicalEntity\",\n", " \"biolink:NamedThing\",\n", - " \"biolink:Entity\"\n", + " \"biolink:BiologicalEntity\",\n", + " \"biolink:Disease\",\n", + " \"biolink:ThingWithTaxon\"\n", " ],\n", " \"name\": \"chronic obstructive pulmonary disease\",\n", " \"attributes\": [\n", " {\n", - " \"type\": \"biolink:same_as\",\n", + " \"attribute_type_id\": \"biolink:same_as\",\n", " \"value\": [\n", " \"MONDO:0005002\",\n", " \"DOID:3083\",\n", + " \"OMIM:606963\",\n", " \"EFO:0000341\",\n", " \"UMLS:C0024117\",\n", + " \"UMLS:C1527303\",\n", + " \"UMLS:C1847014\",\n", + " \"UMLS:C2751329\",\n", + " \"MESH:C564641\",\n", " \"MESH:D029424\",\n", + " \"MEDDRA:10008828\",\n", + " \"MEDDRA:10009025\",\n", + " \"MEDDRA:10009026\",\n", + " \"MEDDRA:10009032\",\n", + " \"MEDDRA:10009033\",\n", + " \"MEDDRA:10010952\",\n", + " \"MEDDRA:10029972\",\n", + " \"MEDDRA:10064611\",\n", + " \"MEDDRA:10070975\",\n", " \"NCIT:C3199\",\n", " \"SNOMEDCT:13645005\",\n", + " \"ICD10:J44.9\",\n", " \"HP:0006510\"\n", " ],\n", - " \"name\": \"same_as\",\n", - " \"url\": null,\n", - " \"source\": null\n", + " \"value_type_id\": \"EDAM:data_0006\",\n", + " \"original_attribute_name\": \"equivalent_identifiers\"\n", " }\n", " ]\n", " }\n", @@ -796,8 +1046,7 @@ " \"subject\": \"NCBIGene:9496\",\n", " \"object\": \"MONDO:0005002\",\n", " \"predicate\": \"biolink:related_to\",\n", - " \"relation\": \"RO:0003304\",\n", - " \"attributes\": null\n", + " \"sources\": []\n", " }\n", " }\n", " },\n", @@ -806,27 +1055,48 @@ " \"node_bindings\": {\n", " \"n1\": [\n", " {\n", - " \"id\": \"NCBIGene:9496\"\n", + " \"id\": \"NCBIGene:9496\",\n", + " \"attributes\": [\n", + " {\n", + " \"attribute_type_id\": \"biolink:has_numeric_value\",\n", + " \"value\": 100.0,\n", + " \"value_type_id\": \"EDAM:data_0006\",\n", + " \"original_attribute_name\": \"information_content\"\n", + " }\n", + " ]\n", " }\n", " ],\n", " \"n2\": [\n", " {\n", - " \"id\": \"MONDO:0005002\"\n", + " \"id\": \"MONDO:0005002\",\n", + " \"attributes\": [\n", + " {\n", + " \"attribute_type_id\": \"biolink:has_numeric_value\",\n", + " \"value\": 100.0,\n", + " \"value_type_id\": \"EDAM:data_0006\",\n", + " \"original_attribute_name\": \"information_content\"\n", + " }\n", + " ]\n", " }\n", " ]\n", " },\n", - " \"edge_bindings\": {\n", - " \"e1\": [\n", - " {\n", - " \"id\": \"2d38345a-e9bf-4943-accb-dccba351dd04\"\n", - " }\n", - " ]\n", - " }\n", + " \"analyses\": [\n", + " {\n", + " \"resource_id\": \"infores:openpredict\",\n", + " \"edge_bindings\": {\n", + " \"e1\": [\n", + " {\n", + " \"id\": \"2d38345a-e9bf-4943-accb-dccba351dd04\"\n", + " }\n", + " ]\n", + " },\n", + " \"score\": 0.682246949249408,\n", + " \"scoring_method\": \"Model confidence between 0 and 1\"\n", + " }\n", + " ]\n", " }\n", " ]\n", - " },\n", - " \"logs\": null,\n", - " \"status\": null\n", + " }\n", "}\n" ] } @@ -834,13 +1104,6 @@ "source": [ "print(json.dumps(result.json(), indent=2))" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { From 4058e73176665c816d7f37b1e64bf65bf67dfbd1 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 17 Jun 2024 18:33:03 -0400 Subject: [PATCH 5/7] Added a section on Conflation, although this needs to be expanded. --- documentation/NodeNormalization.ipynb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/documentation/NodeNormalization.ipynb b/documentation/NodeNormalization.ipynb index e786030..c796d17 100644 --- a/documentation/NodeNormalization.ipynb +++ b/documentation/NodeNormalization.ipynb @@ -806,6 +806,15 @@ "print( json.dumps( result.json(), indent = 2))" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Conflation\n", + "\n", + "TODO" + ] + }, { "cell_type": "markdown", "metadata": {}, From 7617e8d1236b17d4b37933c426a45962eb6fab2a Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Tue, 9 Dec 2025 12:49:27 -0500 Subject: [PATCH 6/7] Added /status and table. --- documentation/NodeNormalization.ipynb | 846 +++++++++++++++----------- 1 file changed, 477 insertions(+), 369 deletions(-) diff --git a/documentation/NodeNormalization.ipynb b/documentation/NodeNormalization.ipynb index c796d17..10a3ce4 100644 --- a/documentation/NodeNormalization.ipynb +++ b/documentation/NodeNormalization.ipynb @@ -36,22 +36,109 @@ "source": [ "## Instances of NodeNorm\n", "\n", - "For the examples in this document, we will use the _development_ version of the Node Normalization Service, hosted at https://nodenormalization-sri.renci.org/ by the Renaissance Computing Institute (RENCI) at the University of North Carolina. This version is updated more frequently than the production instance listed below.\n", + "For the examples in this document, we will use the _development_ version of the Node Normalization Service, hosted at https://nodenormalization-sri.renci.org/ by the [Renaissance Computing Institute](https://renci.org/) (RENCI) at the University of North Carolina. This version is updated more frequently than the production instance listed below.\n", "\n", "The production instance of NodeNorm is hosted by the NCATS Translator project at https://nodenorm.transltr.io/docs, and may be older than the development version hosted below. As with other NCATS Translator tools, a [CI instance](https://nodenorm.ci.transltr.io/docs) and a [Test instance](https://nodenorm.test.transltr.io/docs) have also been deployed, but are not likely to be useful for non-Translator users." ] }, { "cell_type": "markdown", - "metadata": { - "slideshow": { - "slide_type": "slide" + "metadata": {}, + "source": [ + "## Status\n", + "\n", + "The NodeNorm instance can be queried with information about the status and size of its databases. Most importantly, this will tell you what version of Babel outputs have been loaded into a NodeNorm instance and whether " + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"status\": \"running\",\n", + " \"babel_version\": \"2025sep1\",\n", + " \"babel_version_url\": \"https://github.com/ncatstranslator/Babel/blob/master/releases/2025sep1.md\",\n", + " \"databases\": {\n", + " \"eq_id_to_id_db\": {\n", + " \"dbname\": \"id-id\",\n", + " \"count\": 688874821,\n", + " \"used_memory_rss_human\": \"58.86G\",\n", + " \"is_cluster\": false\n", + " },\n", + " \"id_to_eqids_db\": {\n", + " \"dbname\": \"id-eq-id\",\n", + " \"count\": 490286665,\n", + " \"used_memory_rss_human\": \"110.77G\",\n", + " \"is_cluster\": false\n", + " },\n", + " \"id_to_type_db\": {\n", + " \"dbname\": \"id-categories\",\n", + " \"count\": 490286665,\n", + " \"used_memory_rss_human\": \"36.53G\",\n", + " \"is_cluster\": false\n", + " },\n", + " \"curie_to_bl_type_db\": {\n", + " \"dbname\": \"semantic-count\",\n", + " \"count\": 137,\n", + " \"used_memory_rss_human\": \"27.71M\",\n", + " \"is_cluster\": false\n", + " },\n", + " \"info_content_db\": {\n", + " \"dbname\": \"info-content\",\n", + " \"count\": 3315882,\n", + " \"used_memory_rss_human\": \"232.72M\",\n", + " \"is_cluster\": false\n", + " },\n", + " \"gene_protein_db\": {\n", + " \"dbname\": \"conflation-db\",\n", + " \"count\": 33592119,\n", + " \"used_memory_rss_human\": \"4.70G\",\n", + " \"is_cluster\": false\n", + " },\n", + " \"chemical_drug_db\": {\n", + " \"dbname\": \"chemical-drug-db\",\n", + " \"count\": 106507,\n", + " \"used_memory_rss_human\": \"210.62M\",\n", + " \"is_cluster\": false\n", + " }\n", + " }\n", + "}\n" + ] } - }, + ], "source": [ - "## Metadata\n", + "import json\n", + "import requests\n", "\n", - "There are two metadata services that can be used to find out what sorts of results have been incorporated into the Node Normalization service. These return the semantic types that are included, and the prefixes included for each type." + "status = requests.get('https://nodenormalization-sri.renci.org/status')\n", + "print(json.dumps(status.json(), indent=2))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "For Babel 2025sep1, these are the seven Redis NodeNorm databases:" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "| Redis database name | Database purpose | Number of keys | Memory used as of Babel 2025sep1 |\n", + "| ------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------- | -------------------------------- |\n", + "| id-id | Maps CURIEs to their preferred CURIE | 688,874,821 | 69.84G |\n", + "| id-eq-id | Maps preferred CURIEs to a list of equivalent identifiers, labels, descriptions and other information. | 490,286,665 | 119.51G |\n", + "| id-categories | Maps preferred CURIEs to their Biolink type. | 490,286,665 | 45.90G |\n", + "| semantic-count | Records prefixes for each Biolink type. | 137 | 13.90M |\n", + "| info-content | Maps preferred CURIEs to their information content value. | 3,315,882 | 302.98M |\n", + "| conflation-db | Maps CURIEs conflated under GeneProtein conflation to the entire conflation (e.g. “UniProtKB:P00734” will be mapped to [“NCBIGene:2147”, “UniProtKB:P00734”, …] | 33,592,119 | 5.29G |\n", + "| chemical-drug-db | Maps CURIEs conflated under DrugChemical conflation to the entire conflation (e.g. “CHEBI:9919” is mapped to “[\"CHEBI:35854”, “CHEBI:9919”, “UMLS:C5679319\", …]” | 106,507 | 198.23M |" ] }, { @@ -62,103 +149,18 @@ } }, "source": [ - "#### Which types have been normalized?" + "## Normalization" ] }, { - "cell_type": "code", - "execution_count": 2, + "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "subslide" } }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"semantic_types\": {\n", - " \"types\": [\n", - " \"biolink:BiologicalProcess\",\n", - " \"biolink:BiologicalEntity\",\n", - " \"biolink:OrganismTaxon\",\n", - " \"biolink:Device\",\n", - " \"biolink:PlanetaryEntity\",\n", - " \"biolink:GeneOrGeneProduct\",\n", - " \"biolink:ChemicalMixture\",\n", - " \"biolink:ComplexMolecularMixture\",\n", - " \"biolink:StudyPopulation\",\n", - " \"biolink:Phenomenon\",\n", - " \"biolink:ClinicalAttribute\",\n", - " \"biolink:MolecularActivity\",\n", - " \"biolink:Food\",\n", - " \"biolink:Publication\",\n", - " \"biolink:ChemicalEntity\",\n", - " \"biolink:NamedThing\",\n", - " \"biolink:MolecularMixture\",\n", - " \"biolink:GeneGroupingMixin\",\n", - " \"biolink:BiologicalProcessOrActivity\",\n", - " \"biolink:Gene\",\n", - " \"biolink:Disease\",\n", - " \"biolink:OntologyClass\",\n", - " \"biolink:Cohort\",\n", - " \"biolink:GrossAnatomicalStructure\",\n", - " \"biolink:Drug\",\n", - " \"biolink:SubjectOfInvestigation\",\n", - " \"biolink:PhenotypicFeature\",\n", - " \"biolink:MacromolecularComplex\",\n", - " \"biolink:Event\",\n", - " \"biolink:ActivityAndBehavior\",\n", - " \"biolink:PopulationOfIndividualOrganisms\",\n", - " \"biolink:NucleicAcidEntity\",\n", - " \"biolink:OrganismalEntity\",\n", - " \"biolink:Protein\",\n", - " \"biolink:Human\",\n", - " \"biolink:Agent\",\n", - " \"biolink:GeneFamily\",\n", - " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", - " \"biolink:Attribute\",\n", - " \"biolink:SmallMolecule\",\n", - " \"biolink:CellularComponent\",\n", - " \"biolink:ChemicalOrDrugOrTreatment\",\n", - " \"biolink:MolecularEntity\",\n", - " \"biolink:InformationContentEntity\",\n", - " \"biolink:PhysicalEssenceOrOccurrent\",\n", - " \"biolink:Cell\",\n", - " \"biolink:GenomicEntity\",\n", - " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", - " \"biolink:GeneProductMixin\",\n", - " \"biolink:Polypeptide\",\n", - " \"biolink:PhysicalEssence\",\n", - " \"biolink:PhysiologicalProcess\",\n", - " \"biolink:Occurrent\",\n", - " \"biolink:Procedure\",\n", - " \"biolink:PhysicalEntity\",\n", - " \"biolink:Entity\",\n", - " \"biolink:OrganismAttribute\",\n", - " \"biolink:Behavior\",\n", - " \"biolink:Activity\",\n", - " \"biolink:AdministrativeEntity\",\n", - " \"biolink:GeographicLocation\",\n", - " \"biolink:AnatomicalEntity\",\n", - " \"biolink:MacromolecularMachineMixin\",\n", - " \"biolink:ThingWithTaxon\",\n", - " \"biolink:DiseaseOrPhenotypicFeature\",\n", - " \"biolink:Pathway\"\n", - " ]\n", - " }\n", - "}\n" - ] - } - ], "source": [ - "import json \n", - "import requests\n", - "\n", - "result = requests.get('https://nodenormalization-sri.renci.org/get_semantic_types')\n", - "print( json.dumps( result.json(), indent = 2))" + "Given one or more Compact URIs (CURIES), `get_normalized_node` will return a list of equivalent identifiers for the entity, along with the Translator-preferred identifier, and the semantic type(s) for the entity. This service is merely returning pre-computed values, and does no equivalence inference on its own. If a CURIE is unknown to it, then null is returned." ] }, { @@ -169,15 +171,14 @@ } }, "source": [ - "#### Which prefixes are supported?\n", - "\n", - "Even if a semantic type has some identifier equivalence, not every vocabulary has been included. To see which vocabularies are likely to give useful results for a specific Biolink class, call:" + "In this example, `get_normalized_node` is called with a MeSH identifier. MeSH contains many different semantic types, but the service correctly identifies the term." ] }, { "cell_type": "code", "execution_count": 3, "metadata": { + "scrolled": true, "slideshow": { "slide_type": "subslide" } @@ -188,31 +189,77 @@ "output_type": "stream", "text": [ "{\n", - " \"biolink:ChemicalEntity\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"124460882\",\n", - " \"INCHIKEY\": \"110336273\",\n", - " \"CHEMBL.COMPOUND\": \"2399641\",\n", - " \"CHEBI\": \"196937\",\n", - " \"CAS\": \"3556698\",\n", - " \"HMDB\": \"217920\",\n", - " \"UNII\": \"126327\",\n", - " \"MESH\": \"258102\",\n", - " \"KEGG.COMPOUND\": \"16020\",\n", - " \"UMLS\": \"549120\",\n", - " \"DRUGBANK\": \"15179\",\n", - " \"DrugCentral\": \"4995\",\n", - " \"GTOPDB\": \"12347\",\n", - " \"RXCUI\": \"123395\"\n", - " }\n", + " \"MESH:D014867\": {\n", + " \"id\": {\n", + " \"identifier\": \"CHEBI:15377\",\n", + " \"label\": \"WATER\"\n", + " },\n", + " \"equivalent_identifiers\": [\n", + " {\n", + " \"identifier\": \"CHEBI:15377\",\n", + " \"label\": \"water\"\n", + " },\n", + " {\n", + " \"identifier\": \"PUBCHEM.COMPOUND:962\",\n", + " \"label\": \"Water\"\n", + " },\n", + " {\n", + " \"identifier\": \"CHEMBL.COMPOUND:CHEMBL1098659\",\n", + " \"label\": \"WATER\"\n", + " },\n", + " {\n", + " \"identifier\": \"UNII:059QF0KO0R\",\n", + " \"label\": \"WATER\"\n", + " },\n", + " {\n", + " \"identifier\": \"DRUGBANK:DB09145\"\n", + " },\n", + " {\n", + " \"identifier\": \"MESH:D014867\",\n", + " \"label\": \"Water\"\n", + " },\n", + " {\n", + " \"identifier\": \"CAS:7732-18-5\"\n", + " },\n", + " {\n", + " \"identifier\": \"HMDB:HMDB0002111\",\n", + " \"label\": \"Water\"\n", + " },\n", + " {\n", + " \"identifier\": \"KEGG.COMPOUND:C00001\",\n", + " \"label\": \"H2O\"\n", + " },\n", + " {\n", + " \"identifier\": \"INCHIKEY:XLYOFNOQVPJJNP-UHFFFAOYSA-N\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0043047\",\n", + " \"label\": \"water\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:11295\"\n", + " }\n", + " ],\n", + " \"type\": [\n", + " \"biolink:SmallMolecule\",\n", + " \"biolink:MolecularEntity\",\n", + " \"biolink:ChemicalEntity\",\n", + " \"biolink:NamedThing\",\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:ChemicalOrDrugOrTreatment\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\"\n", + " ],\n", + " \"information_content\": 47.5\n", " }\n", "}\n" ] } ], "source": [ - "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes/',\n", - " params={'semantic_type':\"biolink:ChemicalEntity\"})\n", + "result = requests.get('https://nodenormalization-sri.renci.org/get_normalized_nodes',\n", + " params={'curie':\"MESH:D014867\"})\n", "print( json.dumps( result.json(), indent = 2))" ] }, @@ -220,11 +267,13 @@ "cell_type": "markdown", "metadata": { "slideshow": { - "slide_type": "skip" + "slide_type": "slide" } }, "source": [ - "More than one type can be queried:" + "#### Batching\n", + "\n", + "To improve performance, multiple CURIEs may be batched into a single function call as a POST:" ] }, { @@ -233,255 +282,7 @@ "metadata": { "scrolled": true, "slideshow": { - "slide_type": "skip" - } - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"biolink:ChemicalEntity\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"124460882\",\n", - " \"INCHIKEY\": \"110336273\",\n", - " \"CHEMBL.COMPOUND\": \"2399641\",\n", - " \"CHEBI\": \"196937\",\n", - " \"CAS\": \"3556698\",\n", - " \"HMDB\": \"217920\",\n", - " \"UNII\": \"126327\",\n", - " \"MESH\": \"258102\",\n", - " \"KEGG.COMPOUND\": \"16020\",\n", - " \"UMLS\": \"549120\",\n", - " \"DRUGBANK\": \"15179\",\n", - " \"DrugCentral\": \"4995\",\n", - " \"GTOPDB\": \"12347\",\n", - " \"RXCUI\": \"123395\"\n", - " }\n", - " },\n", - " \"biolink:Disease\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"336767\",\n", - " \"SNOMEDCT\": \"94514\",\n", - " \"MEDDRA\": \"46033\",\n", - " \"MONDO\": \"24012\",\n", - " \"DOID\": \"11498\",\n", - " \"NCIT\": \"25540\",\n", - " \"HP\": \"2182\",\n", - " \"EFO\": \"3711\",\n", - " \"orphanet\": \"10780\",\n", - " \"MESH\": \"11238\",\n", - " \"OMIM\": \"10314\",\n", - " \"ICD10\": \"2429\",\n", - " \"ICD9\": \"2218\",\n", - " \"OMIM.PS\": \"556\",\n", - " \"KEGG.DISEASE\": \"40\",\n", - " \"MP\": \"1\"\n", - " }\n", - " }\n", - "}\n" - ] - } - ], - "source": [ - "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes/',\n", - " params={'semantic_type':[\"biolink:ChemicalEntity\",\"biolink:Disease\"]})\n", - "print( json.dumps( result.json(), indent = 2))" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Or you can just ask for all the prefix counts for every type:" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"biolink:Pathway\": {\n", - " \"curie_prefix\": {\n", - " \"REACT\": \"21784\",\n", - " \"SMPDB\": \"30248\",\n", - " \"GO\": \"642\",\n", - " \"PANTHER.PATHWAY\": \"175\"\n", - " }\n", - " },\n", - " \"biolink:OrganismTaxon\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"749649\",\n", - " \"NCBITaxon\": \"2546095\",\n", - " \"MESH\": \"70628\"\n", - " }\n", - " },\n", - " \"biolink:GeneFamily\": {\n", - " \"curie_prefix\": {\n", - " \"PANTHER.FAMILY\": \"26138\",\n", - " \"HGNC.FAMILY\": \"1807\"\n", - " }\n", - " }\n", - "}\n" - ] - } - ], - "source": [ - "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes')\n", - "responses = result.json()\n", - "\n", - "# Display only the first three responses. \n", - "print( json.dumps( dict(list(responses.items())[:3]), indent = 2))" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "slideshow": { - "slide_type": "slide" - } - }, - "source": [ - "## Normalization" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "slideshow": { - "slide_type": "subslide" - } - }, - "source": [ - "Given one or more Compact URIs (CURIES), `get_normalized_node` will return a list of equivalent identifiers for the entity, along with the Translator-preferred identifier, and the semantic type(s) for the entity. This service is merely returning pre-computed values, and does no equivalence inference on its own. If a CURIE is unknown to it, then null is returned." - ] - }, - { - "cell_type": "markdown", - "metadata": { - "slideshow": { - "slide_type": "slide" - } - }, - "source": [ - "In this example, `get_normalized_node` is called with a MeSH identifier. MeSH contains many different semantic types, but the service correctly identifies the term." - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": { - "scrolled": true, - "slideshow": { - "slide_type": "subslide" - } - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"MESH:D014867\": {\n", - " \"id\": {\n", - " \"identifier\": \"CHEBI:15377\",\n", - " \"label\": \"WATER\"\n", - " },\n", - " \"equivalent_identifiers\": [\n", - " {\n", - " \"identifier\": \"CHEBI:15377\",\n", - " \"label\": \"water\"\n", - " },\n", - " {\n", - " \"identifier\": \"PUBCHEM.COMPOUND:962\",\n", - " \"label\": \"Water\"\n", - " },\n", - " {\n", - " \"identifier\": \"CHEMBL.COMPOUND:CHEMBL1098659\",\n", - " \"label\": \"WATER\"\n", - " },\n", - " {\n", - " \"identifier\": \"UNII:059QF0KO0R\",\n", - " \"label\": \"WATER\"\n", - " },\n", - " {\n", - " \"identifier\": \"DRUGBANK:DB09145\"\n", - " },\n", - " {\n", - " \"identifier\": \"MESH:D014867\",\n", - " \"label\": \"Water\"\n", - " },\n", - " {\n", - " \"identifier\": \"CAS:7732-18-5\"\n", - " },\n", - " {\n", - " \"identifier\": \"HMDB:HMDB0002111\",\n", - " \"label\": \"Water\"\n", - " },\n", - " {\n", - " \"identifier\": \"KEGG.COMPOUND:C00001\",\n", - " \"label\": \"H2O\"\n", - " },\n", - " {\n", - " \"identifier\": \"INCHIKEY:XLYOFNOQVPJJNP-UHFFFAOYSA-N\"\n", - " },\n", - " {\n", - " \"identifier\": \"UMLS:C0043047\",\n", - " \"label\": \"water\"\n", - " },\n", - " {\n", - " \"identifier\": \"RXCUI:11295\"\n", - " }\n", - " ],\n", - " \"type\": [\n", - " \"biolink:SmallMolecule\",\n", - " \"biolink:MolecularEntity\",\n", - " \"biolink:ChemicalEntity\",\n", - " \"biolink:NamedThing\",\n", - " \"biolink:PhysicalEssence\",\n", - " \"biolink:ChemicalOrDrugOrTreatment\",\n", - " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", - " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", - " \"biolink:PhysicalEssenceOrOccurrent\"\n", - " ],\n", - " \"information_content\": 47.5\n", - " }\n", - "}\n" - ] - } - ], - "source": [ - "result = requests.get('https://nodenormalization-sri.renci.org/get_normalized_nodes',\n", - " params={'curie':\"MESH:D014867\"})\n", - "print( json.dumps( result.json(), indent = 2))" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "slideshow": { - "slide_type": "slide" - } - }, - "source": [ - "#### Batching\n", - "\n", - "To improve performance, multiple CURIEs may be batched into a single function call as a POST:" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": { - "scrolled": true, - "slideshow": { - "slide_type": "subslide" + "slide_type": "subslide" } }, "outputs": [ @@ -1113,6 +914,313 @@ "source": [ "print(json.dumps(result.json(), indent=2))" ] + }, + { + "cell_type": "markdown", + "metadata": { + "slideshow": { + "slide_type": "slide" + } + }, + "source": [ + "## Metadata\n", + "\n", + "There are two metadata services that can be used to find out what sorts of results have been incorporated into the Node Normalization service. These return the semantic types that are included, and the prefixes included for each type." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "slideshow": { + "slide_type": "slide" + } + }, + "source": [ + "#### Which types have been normalized?" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "slideshow": { + "slide_type": "subslide" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"semantic_types\": {\n", + " \"types\": [\n", + " \"biolink:BiologicalProcess\",\n", + " \"biolink:BiologicalEntity\",\n", + " \"biolink:OrganismTaxon\",\n", + " \"biolink:Device\",\n", + " \"biolink:PlanetaryEntity\",\n", + " \"biolink:GeneOrGeneProduct\",\n", + " \"biolink:ChemicalMixture\",\n", + " \"biolink:ComplexMolecularMixture\",\n", + " \"biolink:StudyPopulation\",\n", + " \"biolink:Phenomenon\",\n", + " \"biolink:ClinicalAttribute\",\n", + " \"biolink:MolecularActivity\",\n", + " \"biolink:Food\",\n", + " \"biolink:Publication\",\n", + " \"biolink:ChemicalEntity\",\n", + " \"biolink:NamedThing\",\n", + " \"biolink:MolecularMixture\",\n", + " \"biolink:GeneGroupingMixin\",\n", + " \"biolink:BiologicalProcessOrActivity\",\n", + " \"biolink:Gene\",\n", + " \"biolink:Disease\",\n", + " \"biolink:OntologyClass\",\n", + " \"biolink:Cohort\",\n", + " \"biolink:GrossAnatomicalStructure\",\n", + " \"biolink:Drug\",\n", + " \"biolink:SubjectOfInvestigation\",\n", + " \"biolink:PhenotypicFeature\",\n", + " \"biolink:MacromolecularComplex\",\n", + " \"biolink:Event\",\n", + " \"biolink:ActivityAndBehavior\",\n", + " \"biolink:PopulationOfIndividualOrganisms\",\n", + " \"biolink:NucleicAcidEntity\",\n", + " \"biolink:OrganismalEntity\",\n", + " \"biolink:Protein\",\n", + " \"biolink:Human\",\n", + " \"biolink:Agent\",\n", + " \"biolink:GeneFamily\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:Attribute\",\n", + " \"biolink:SmallMolecule\",\n", + " \"biolink:CellularComponent\",\n", + " \"biolink:ChemicalOrDrugOrTreatment\",\n", + " \"biolink:MolecularEntity\",\n", + " \"biolink:InformationContentEntity\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\",\n", + " \"biolink:Cell\",\n", + " \"biolink:GenomicEntity\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", + " \"biolink:GeneProductMixin\",\n", + " \"biolink:Polypeptide\",\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:PhysiologicalProcess\",\n", + " \"biolink:Occurrent\",\n", + " \"biolink:Procedure\",\n", + " \"biolink:PhysicalEntity\",\n", + " \"biolink:Entity\",\n", + " \"biolink:OrganismAttribute\",\n", + " \"biolink:Behavior\",\n", + " \"biolink:Activity\",\n", + " \"biolink:AdministrativeEntity\",\n", + " \"biolink:GeographicLocation\",\n", + " \"biolink:AnatomicalEntity\",\n", + " \"biolink:MacromolecularMachineMixin\",\n", + " \"biolink:ThingWithTaxon\",\n", + " \"biolink:DiseaseOrPhenotypicFeature\",\n", + " \"biolink:Pathway\"\n", + " ]\n", + " }\n", + "}\n" + ] + } + ], + "source": [ + "import json \n", + "import requests\n", + "\n", + "result = requests.get('https://nodenormalization-sri.renci.org/get_semantic_types')\n", + "print( json.dumps( result.json(), indent = 2))" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "slideshow": { + "slide_type": "slide" + } + }, + "source": [ + "#### Which prefixes are supported?\n", + "\n", + "Even if a semantic type has some identifier equivalence, not every vocabulary has been included. To see which vocabularies are likely to give useful results for a specific Biolink class, call:" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "slideshow": { + "slide_type": "skip" + } + }, + "source": [ + "More than one type can be queried:" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "collapsed": true, + "jupyter": { + "outputs_hidden": true + }, + "scrolled": true, + "slideshow": { + "slide_type": "skip" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"biolink:ChemicalEntity\": {\n", + " \"curie_prefix\": {\n", + " \"PUBCHEM.COMPOUND\": \"124460882\",\n", + " \"INCHIKEY\": \"110336273\",\n", + " \"CHEMBL.COMPOUND\": \"2399641\",\n", + " \"CHEBI\": \"196937\",\n", + " \"CAS\": \"3556698\",\n", + " \"HMDB\": \"217920\",\n", + " \"UNII\": \"126327\",\n", + " \"MESH\": \"258102\",\n", + " \"KEGG.COMPOUND\": \"16020\",\n", + " \"UMLS\": \"549120\",\n", + " \"DRUGBANK\": \"15179\",\n", + " \"DrugCentral\": \"4995\",\n", + " \"GTOPDB\": \"12347\",\n", + " \"RXCUI\": \"123395\"\n", + " }\n", + " },\n", + " \"biolink:Disease\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"336767\",\n", + " \"SNOMEDCT\": \"94514\",\n", + " \"MEDDRA\": \"46033\",\n", + " \"MONDO\": \"24012\",\n", + " \"DOID\": \"11498\",\n", + " \"NCIT\": \"25540\",\n", + " \"HP\": \"2182\",\n", + " \"EFO\": \"3711\",\n", + " \"orphanet\": \"10780\",\n", + " \"MESH\": \"11238\",\n", + " \"OMIM\": \"10314\",\n", + " \"ICD10\": \"2429\",\n", + " \"ICD9\": \"2218\",\n", + " \"OMIM.PS\": \"556\",\n", + " \"KEGG.DISEASE\": \"40\",\n", + " \"MP\": \"1\"\n", + " }\n", + " }\n", + "}\n" + ] + } + ], + "source": [ + "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes/',\n", + " params={'semantic_type':[\"biolink:ChemicalEntity\",\"biolink:Disease\"]})\n", + "print( json.dumps( result.json(), indent = 2))" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "jupyter": { + "source_hidden": true + } + }, + "source": [ + "Or you can just ask for all the prefix counts for every type:" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"biolink:Pathway\": {\n", + " \"curie_prefix\": {\n", + " \"REACT\": \"21784\",\n", + " \"SMPDB\": \"30248\",\n", + " \"GO\": \"642\",\n", + " \"PANTHER.PATHWAY\": \"175\"\n", + " }\n", + " },\n", + " \"biolink:OrganismTaxon\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"749649\",\n", + " \"NCBITaxon\": \"2546095\",\n", + " \"MESH\": \"70628\"\n", + " }\n", + " },\n", + " \"biolink:GeneFamily\": {\n", + " \"curie_prefix\": {\n", + " \"PANTHER.FAMILY\": \"26138\",\n", + " \"HGNC.FAMILY\": \"1807\"\n", + " }\n", + " }\n", + "}\n" + ] + } + ], + "source": [ + "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes')\n", + "responses = result.json()\n", + "\n", + "# Display only the first three responses. \n", + "print( json.dumps( dict(list(responses.items())[:3]), indent = 2))" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "slideshow": { + "slide_type": "subslide" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"biolink:ChemicalEntity\": {\n", + " \"curie_prefix\": {\n", + " \"PUBCHEM.COMPOUND\": \"124460882\",\n", + " \"INCHIKEY\": \"110336273\",\n", + " \"CHEMBL.COMPOUND\": \"2399641\",\n", + " \"CHEBI\": \"196937\",\n", + " \"CAS\": \"3556698\",\n", + " \"HMDB\": \"217920\",\n", + " \"UNII\": \"126327\",\n", + " \"MESH\": \"258102\",\n", + " \"KEGG.COMPOUND\": \"16020\",\n", + " \"UMLS\": \"549120\",\n", + " \"DRUGBANK\": \"15179\",\n", + " \"DrugCentral\": \"4995\",\n", + " \"GTOPDB\": \"12347\",\n", + " \"RXCUI\": \"123395\"\n", + " }\n", + " }\n", + "}\n" + ] + } + ], + "source": [ + "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes/',\n", + " params={'semantic_type':\"biolink:ChemicalEntity\"})\n", + "print( json.dumps( result.json(), indent = 2))" + ] } ], "metadata": { @@ -1131,7 +1239,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.4" + "version": "3.14.0" } }, "nbformat": 4, From 582f30d48ba63009e6408892b1b32745499ab1ed Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Tue, 9 Dec 2025 17:17:59 -0500 Subject: [PATCH 7/7] Updated NodeNorm Jupyter Notebook. --- documentation/NodeNormalization.ipynb | 3456 ++++++++++++++++++++++--- 1 file changed, 3060 insertions(+), 396 deletions(-) diff --git a/documentation/NodeNormalization.ipynb b/documentation/NodeNormalization.ipynb index 10a3ce4..25a5971 100644 --- a/documentation/NodeNormalization.ipynb +++ b/documentation/NodeNormalization.ipynb @@ -32,9 +32,11 @@ }, { "cell_type": "markdown", - "metadata": {}, + "metadata": { + "jp-MarkdownHeadingCollapsed": true + }, "source": [ - "## Instances of NodeNorm\n", + "### Instances of NodeNorm\n", "\n", "For the examples in this document, we will use the _development_ version of the Node Normalization Service, hosted at https://nodenormalization-sri.renci.org/ by the [Renaissance Computing Institute](https://renci.org/) (RENCI) at the University of North Carolina. This version is updated more frequently than the production instance listed below.\n", "\n", @@ -47,12 +49,12 @@ "source": [ "## Status\n", "\n", - "The NodeNorm instance can be queried with information about the status and size of its databases. Most importantly, this will tell you what version of Babel outputs have been loaded into a NodeNorm instance and whether " + "The NodeNorm instance can be queried with information about the status and size of its databases. Most importantly, this will tell you what version of Babel outputs have been loaded into a NodeNorm instance and how much memory all of its seven databases are using." ] }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 13, "metadata": {}, "outputs": [ { @@ -91,7 +93,7 @@ " \"info_content_db\": {\n", " \"dbname\": \"info-content\",\n", " \"count\": 3315882,\n", - " \"used_memory_rss_human\": \"232.72M\",\n", + " \"used_memory_rss_human\": \"232.67M\",\n", " \"is_cluster\": false\n", " },\n", " \"gene_protein_db\": {\n", @@ -103,7 +105,7 @@ " \"chemical_drug_db\": {\n", " \"dbname\": \"chemical-drug-db\",\n", " \"count\": 106507,\n", - " \"used_memory_rss_human\": \"210.62M\",\n", + " \"used_memory_rss_human\": \"210.74M\",\n", " \"is_cluster\": false\n", " }\n", " }\n", @@ -130,15 +132,15 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "| Redis database name | Database purpose | Number of keys | Memory used as of Babel 2025sep1 |\n", + "| Redis database name | Database purpose | Number of keys | Memory used |\n", "| ------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------- | -------------------------------- |\n", - "| id-id | Maps CURIEs to their preferred CURIE | 688,874,821 | 69.84G |\n", - "| id-eq-id | Maps preferred CURIEs to a list of equivalent identifiers, labels, descriptions and other information. | 490,286,665 | 119.51G |\n", - "| id-categories | Maps preferred CURIEs to their Biolink type. | 490,286,665 | 45.90G |\n", - "| semantic-count | Records prefixes for each Biolink type. | 137 | 13.90M |\n", - "| info-content | Maps preferred CURIEs to their information content value. | 3,315,882 | 302.98M |\n", - "| conflation-db | Maps CURIEs conflated under GeneProtein conflation to the entire conflation (e.g. “UniProtKB:P00734” will be mapped to [“NCBIGene:2147”, “UniProtKB:P00734”, …] | 33,592,119 | 5.29G |\n", - "| chemical-drug-db | Maps CURIEs conflated under DrugChemical conflation to the entire conflation (e.g. “CHEBI:9919” is mapped to “[\"CHEBI:35854”, “CHEBI:9919”, “UMLS:C5679319\", …]” | 106,507 | 198.23M |" + "| id-id | Maps CURIEs to their preferred CURIE | 688,874,821 | 58.86G |\n", + "| id-eq-id | Maps preferred CURIEs to a list of equivalent identifiers, labels, descriptions and other information. | 490,286,665 | 110.77G |\n", + "| id-categories | Maps preferred CURIEs to their Biolink type. | 490,286,665 | 36.53G |\n", + "| semantic-count | Records prefixes for each Biolink type. | 137 | 27.71M |\n", + "| info-content | Maps preferred CURIEs to their information content value. | 3,315,882 | 232.72M |\n", + "| conflation-db | Maps CURIEs conflated under GeneProtein conflation to the entire conflation (e.g. “UniProtKB:P00734” will be mapped to [“NCBIGene:2147”, “UniProtKB:P00734”, …] | 33,592,119 | 4.70G |\n", + "| chemical-drug-db | Maps CURIEs conflated under DrugChemical conflation to the entire conflation (e.g. “CHEBI:9919” is mapped to “[\"CHEBI:35854”, “CHEBI:9919”, “UMLS:C5679319\", …]” | 106,507 | 210.62M |" ] }, { @@ -171,12 +173,19 @@ } }, "source": [ - "In this example, `get_normalized_node` is called with a MeSH identifier. MeSH contains many different semantic types, but the service correctly identifies the term." + "In this example, `get_normalized_node` is called with a MeSH identifier for water. This is normalized to [CHEBI:15377](https://www.ebi.ac.uk/chebi/CHEBI:15377), the ChEBI identifier for water. Other equivalent identifiers are returned as well, including UNII, PubChem Compound, ChEMBL Compound and DrugBank identifiers. Note that several MeSH identifiers are combined, including MESH:D060766 \"Drinking Water\". This class is typed as a [biolink:SmallMolecule](https://biolink.github.io/biolink-model/SmallMolecule/), and has an [information content](https://github.com/NCATSTranslator/Babel/blob/master/docs/README.md#what-are-information-content-values) of 47.5." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**Note**: by default, GeneProtein conflation is turned on but DrugChemical conflation is turned off. You can read more about conflation later on in this document." ] }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 14, "metadata": { "scrolled": true, "slideshow": { @@ -192,7 +201,7 @@ " \"MESH:D014867\": {\n", " \"id\": {\n", " \"identifier\": \"CHEBI:15377\",\n", - " \"label\": \"WATER\"\n", + " \"label\": \"Water\"\n", " },\n", " \"equivalent_identifiers\": [\n", " {\n", @@ -200,25 +209,81 @@ " \"label\": \"water\"\n", " },\n", " {\n", - " \"identifier\": \"PUBCHEM.COMPOUND:962\",\n", - " \"label\": \"Water\"\n", + " \"identifier\": \"CHEBI:44701\"\n", " },\n", " {\n", - " \"identifier\": \"CHEMBL.COMPOUND:CHEMBL1098659\",\n", - " \"label\": \"WATER\"\n", + " \"identifier\": \"CHEBI:27313\"\n", + " },\n", + " {\n", + " \"identifier\": \"CHEBI:10743\"\n", + " },\n", + " {\n", + " \"identifier\": \"CHEBI:44819\"\n", + " },\n", + " {\n", + " \"identifier\": \"CHEBI:44292\"\n", + " },\n", + " {\n", + " \"identifier\": \"CHEBI:43228\"\n", + " },\n", + " {\n", + " \"identifier\": \"CHEBI:42043\"\n", + " },\n", + " {\n", + " \"identifier\": \"CHEBI:42857\"\n", + " },\n", + " {\n", + " \"identifier\": \"CHEBI:13352\"\n", + " },\n", + " {\n", + " \"identifier\": \"CHEBI:5585\"\n", " },\n", " {\n", " \"identifier\": \"UNII:059QF0KO0R\",\n", " \"label\": \"WATER\"\n", " },\n", " {\n", - " \"identifier\": \"DRUGBANK:DB09145\"\n", + " \"identifier\": \"PUBCHEM.COMPOUND:962\",\n", + " \"label\": \"Water\"\n", + " },\n", + " {\n", + " \"identifier\": \"CHEMBL.COMPOUND:CHEMBL1098659\",\n", + " \"label\": \"WATER\"\n", + " },\n", + " {\n", + " \"identifier\": \"DRUGBANK:DB09145\",\n", + " \"label\": \"Water\"\n", " },\n", " {\n", " \"identifier\": \"MESH:D014867\",\n", " \"label\": \"Water\"\n", " },\n", " {\n", + " \"identifier\": \"MESH:D060766\",\n", + " \"label\": \"Drinking Water\"\n", + " },\n", + " {\n", + " \"identifier\": \"CAS:146915-49-3\"\n", + " },\n", + " {\n", + " \"identifier\": \"CAS:146915-50-6\"\n", + " },\n", + " {\n", + " \"identifier\": \"CAS:158061-35-9\"\n", + " },\n", + " {\n", + " \"identifier\": \"CAS:191612-61-0\"\n", + " },\n", + " {\n", + " \"identifier\": \"CAS:191612-63-2\"\n", + " },\n", + " {\n", + " \"identifier\": \"CAS:231-791-2\"\n", + " },\n", + " {\n", + " \"identifier\": \"CAS:686-299-4\"\n", + " },\n", + " {\n", " \"identifier\": \"CAS:7732-18-5\"\n", " },\n", " {\n", @@ -244,11 +309,11 @@ " \"biolink:SmallMolecule\",\n", " \"biolink:MolecularEntity\",\n", " \"biolink:ChemicalEntity\",\n", - " \"biolink:NamedThing\",\n", " \"biolink:PhysicalEssence\",\n", " \"biolink:ChemicalOrDrugOrTreatment\",\n", " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", + " \"biolink:NamedThing\",\n", " \"biolink:PhysicalEssenceOrOccurrent\"\n", " ],\n", " \"information_content\": 47.5\n", @@ -273,12 +338,12 @@ "source": [ "#### Batching\n", "\n", - "To improve performance, multiple CURIEs may be batched into a single function call as a POST:" + "To improve performance, multiple CURIEs may be batched into a single function call as a POST request:" ] }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 15, "metadata": { "scrolled": true, "slideshow": { @@ -306,9 +371,6 @@ " \"label\": \"amyotrophic lateral sclerosis\"\n", " },\n", " {\n", - " \"identifier\": \"OMIM:PS105400\"\n", - " },\n", - " {\n", " \"identifier\": \"orphanet:803\"\n", " },\n", " {\n", @@ -326,6 +388,9 @@ " \"identifier\": \"MEDDRA:10052889\"\n", " },\n", " {\n", + " \"identifier\": \"MEDDRA:10090869\"\n", + " },\n", + " {\n", " \"identifier\": \"NCIT:C34373\",\n", " \"label\": \"Amyotrophic Lateral Sclerosis\"\n", " },\n", @@ -333,6 +398,12 @@ " \"identifier\": \"SNOMEDCT:86044005\"\n", " },\n", " {\n", + " \"identifier\": \"medgen:274\"\n", + " },\n", + " {\n", + " \"identifier\": \"icd11.foundation:1982355687\"\n", + " },\n", + " {\n", " \"identifier\": \"ICD10:G12.21\"\n", " },\n", " {\n", @@ -350,8 +421,8 @@ " \"biolink:Disease\",\n", " \"biolink:DiseaseOrPhenotypicFeature\",\n", " \"biolink:BiologicalEntity\",\n", - " \"biolink:NamedThing\",\n", - " \"biolink:ThingWithTaxon\"\n", + " \"biolink:ThingWithTaxon\",\n", + " \"biolink:NamedThing\"\n", " ],\n", " \"information_content\": 74.9\n", " },\n", @@ -363,7 +434,10 @@ " \"equivalent_identifiers\": [\n", " {\n", " \"identifier\": \"NCBIGene:348\",\n", - " \"label\": \"APOE\"\n", + " \"label\": \"APOE\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:9606\"\n", + " ]\n", " },\n", " {\n", " \"identifier\": \"ENSEMBL:ENSG00000130203\",\n", @@ -382,11 +456,17 @@ " },\n", " {\n", " \"identifier\": \"UniProtKB:A0A0S2Z3D5\",\n", - " \"label\": \"A0A0S2Z3D5_HUMAN Apolipoprotein E (Fragment) (trembl)\"\n", + " \"label\": \"A0A0S2Z3D5_HUMAN Apolipoprotein E (Fragment) (trembl)\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:9606\"\n", + " ]\n", " },\n", " {\n", " \"identifier\": \"UniProtKB:P02649\",\n", - " \"label\": \"APOE_HUMAN Apolipoprotein E (sprot)\"\n", + " \"label\": \"APOE_HUMAN Apolipoprotein E (sprot)\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:9606\"\n", + " ]\n", " },\n", " {\n", " \"identifier\": \"PR:P02649\",\n", @@ -405,26 +485,33 @@ " {\n", " \"identifier\": \"UMLS:C4721561\",\n", " \"label\": \"Apolipoprotein E4, human\"\n", + " },\n", + " {\n", + " \"identifier\": \"MESH:C000612345\",\n", + " \"label\": \"ApoE protein, human\"\n", " }\n", " ],\n", + " \"taxa\": [\n", + " \"NCBITaxon:9606\"\n", + " ],\n", " \"type\": [\n", " \"biolink:Gene\",\n", - " \"biolink:BiologicalEntity\",\n", - " \"biolink:NamedThing\",\n", " \"biolink:GeneOrGeneProduct\",\n", " \"biolink:GenomicEntity\",\n", " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", " \"biolink:PhysicalEssence\",\n", " \"biolink:OntologyClass\",\n", + " \"biolink:BiologicalEntity\",\n", " \"biolink:ThingWithTaxon\",\n", + " \"biolink:NamedThing\",\n", " \"biolink:PhysicalEssenceOrOccurrent\",\n", " \"biolink:MacromolecularMachineMixin\",\n", " \"biolink:Protein\",\n", - " \"biolink:Polypeptide\",\n", " \"biolink:GeneProductMixin\",\n", + " \"biolink:Polypeptide\",\n", " \"biolink:ChemicalEntityOrProteinOrPolypeptide\"\n", " ],\n", - " \"information_content\": 100.0\n", + " \"information_content\": 81.3\n", " },\n", " \"CURIE:NOTHING\": null\n", "}\n" @@ -448,7 +535,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 16, "metadata": {}, "outputs": [ { @@ -459,8 +546,7 @@ " \"HP:0007354\": {\n", " \"id\": {\n", " \"identifier\": \"MONDO:0004976\",\n", - " \"label\": \"amyotrophic lateral sclerosis\",\n", - " \"description\": \"Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive muscular paralysis reflecting degeneration of motor neurons in the primary motor cortex, corticospinal tracts, brainstem and spinal cord.\"\n", + " \"label\": \"amyotrophic lateral sclerosis\"\n", " },\n", " \"equivalent_identifiers\": [\n", " {\n", @@ -473,9 +559,6 @@ " \"label\": \"amyotrophic lateral sclerosis\"\n", " },\n", " {\n", - " \"identifier\": \"OMIM:PS105400\"\n", - " },\n", - " {\n", " \"identifier\": \"orphanet:803\"\n", " },\n", " {\n", @@ -493,6 +576,9 @@ " \"identifier\": \"MEDDRA:10052889\"\n", " },\n", " {\n", + " \"identifier\": \"MEDDRA:10090869\"\n", + " },\n", + " {\n", " \"identifier\": \"NCIT:C34373\",\n", " \"label\": \"Amyotrophic Lateral Sclerosis\",\n", " \"description\": \"A neurodegenerative disorder characterized by progressive degeneration of the motor neurons of the central nervous system. It results in weakness and atrophy of the muscles which leads to an inability to initiate and control voluntary movements.\"\n", @@ -501,6 +587,12 @@ " \"identifier\": \"SNOMEDCT:86044005\"\n", " },\n", " {\n", + " \"identifier\": \"medgen:274\"\n", + " },\n", + " {\n", + " \"identifier\": \"icd11.foundation:1982355687\"\n", + " },\n", + " {\n", " \"identifier\": \"ICD10:G12.21\"\n", " },\n", " {\n", @@ -514,25 +606,29 @@ " \"label\": \"Amyotrophic lateral sclerosis\"\n", " }\n", " ],\n", + " \"description\": \"Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive muscular paralysis reflecting degeneration of motor neurons in the primary motor cortex, corticospinal tracts, brainstem and spinal cord.\",\n", " \"type\": [\n", " \"biolink:Disease\",\n", " \"biolink:DiseaseOrPhenotypicFeature\",\n", " \"biolink:BiologicalEntity\",\n", - " \"biolink:NamedThing\",\n", - " \"biolink:ThingWithTaxon\"\n", + " \"biolink:ThingWithTaxon\",\n", + " \"biolink:NamedThing\"\n", " ],\n", " \"information_content\": 74.9\n", " },\n", " \"HGNC:613\": {\n", " \"id\": {\n", " \"identifier\": \"NCBIGene:348\",\n", - " \"label\": \"APOE\",\n", - " \"description\": \"An apolipoprotein E that is encoded in the genome of human.\"\n", + " \"label\": \"APOE\"\n", " },\n", " \"equivalent_identifiers\": [\n", " {\n", " \"identifier\": \"NCBIGene:348\",\n", - " \"label\": \"APOE\"\n", + " \"label\": \"APOE\",\n", + " \"description\": \"apolipoprotein E\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:9606\"\n", + " ]\n", " },\n", " {\n", " \"identifier\": \"ENSEMBL:ENSG00000130203\",\n", @@ -551,11 +647,17 @@ " },\n", " {\n", " \"identifier\": \"UniProtKB:A0A0S2Z3D5\",\n", - " \"label\": \"A0A0S2Z3D5_HUMAN Apolipoprotein E (Fragment) (trembl)\"\n", + " \"label\": \"A0A0S2Z3D5_HUMAN Apolipoprotein E (Fragment) (trembl)\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:9606\"\n", + " ]\n", " },\n", " {\n", " \"identifier\": \"UniProtKB:P02649\",\n", - " \"label\": \"APOE_HUMAN Apolipoprotein E (sprot)\"\n", + " \"label\": \"APOE_HUMAN Apolipoprotein E (sprot)\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:9606\"\n", + " ]\n", " },\n", " {\n", " \"identifier\": \"PR:P02649\",\n", @@ -575,26 +677,34 @@ " {\n", " \"identifier\": \"UMLS:C4721561\",\n", " \"label\": \"Apolipoprotein E4, human\"\n", + " },\n", + " {\n", + " \"identifier\": \"MESH:C000612345\",\n", + " \"label\": \"ApoE protein, human\"\n", " }\n", " ],\n", + " \"description\": \"apolipoprotein E\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:9606\"\n", + " ],\n", " \"type\": [\n", " \"biolink:Gene\",\n", - " \"biolink:BiologicalEntity\",\n", - " \"biolink:NamedThing\",\n", " \"biolink:GeneOrGeneProduct\",\n", " \"biolink:GenomicEntity\",\n", " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", " \"biolink:PhysicalEssence\",\n", " \"biolink:OntologyClass\",\n", + " \"biolink:BiologicalEntity\",\n", " \"biolink:ThingWithTaxon\",\n", + " \"biolink:NamedThing\",\n", " \"biolink:PhysicalEssenceOrOccurrent\",\n", " \"biolink:MacromolecularMachineMixin\",\n", " \"biolink:Protein\",\n", - " \"biolink:Polypeptide\",\n", " \"biolink:GeneProductMixin\",\n", + " \"biolink:Polypeptide\",\n", " \"biolink:ChemicalEntityOrProteinOrPolypeptide\"\n", " ],\n", - " \"information_content\": 100.0\n", + " \"information_content\": 81.3\n", " },\n", " \"CURIE:NOTHING\": null\n", "}\n" @@ -611,40 +721,2899 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Conflation\n", + "#### Taxa\n", "\n", - "TODO" + "You can use the `include_taxa` flag to return taxa for concepts that are specific to a concept, such as genes and proteins. Taxa are returned as a list of NCBI Taxon identifiers (such as `NCBITaxon:9606` [\"_Homo sapiens_\"](https://www.ncbi.nlm.nih.gov/datasets/taxonomy/9606/)) for each identifier, with a combined list for the overall identifier." ] }, { - "cell_type": "markdown", + "cell_type": "code", + "execution_count": 17, "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"HGNC:613\": {\n", + " \"id\": {\n", + " \"identifier\": \"NCBIGene:348\",\n", + " \"label\": \"APOE\"\n", + " },\n", + " \"equivalent_identifiers\": [\n", + " {\n", + " \"identifier\": \"NCBIGene:348\",\n", + " \"label\": \"APOE\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:9606\"\n", + " ]\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSG00000130203\",\n", + " \"label\": \"APOE (Hsap)\"\n", + " },\n", + " {\n", + " \"identifier\": \"HGNC:613\",\n", + " \"label\": \"APOE\"\n", + " },\n", + " {\n", + " \"identifier\": \"OMIM:107741\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1412481\",\n", + " \"label\": \"APOE gene\"\n", + " },\n", + " {\n", + " \"identifier\": \"UniProtKB:A0A0S2Z3D5\",\n", + " \"label\": \"A0A0S2Z3D5_HUMAN Apolipoprotein E (Fragment) (trembl)\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:9606\"\n", + " ]\n", + " },\n", + " {\n", + " \"identifier\": \"UniProtKB:P02649\",\n", + " \"label\": \"APOE_HUMAN Apolipoprotein E (sprot)\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:9606\"\n", + " ]\n", + " },\n", + " {\n", + " \"identifier\": \"PR:P02649\",\n", + " \"label\": \"apolipoprotein E (human)\"\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSP00000252486\"\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSP00000252486.3\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C4308468\",\n", + " \"label\": \"ApoE protein, human\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C4721561\",\n", + " \"label\": \"Apolipoprotein E4, human\"\n", + " },\n", + " {\n", + " \"identifier\": \"MESH:C000612345\",\n", + " \"label\": \"ApoE protein, human\"\n", + " }\n", + " ],\n", + " \"taxa\": [\n", + " \"NCBITaxon:9606\"\n", + " ],\n", + " \"type\": [\n", + " \"biolink:Gene\",\n", + " \"biolink:GeneOrGeneProduct\",\n", + " \"biolink:GenomicEntity\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:OntologyClass\",\n", + " \"biolink:BiologicalEntity\",\n", + " \"biolink:ThingWithTaxon\",\n", + " \"biolink:NamedThing\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\",\n", + " \"biolink:MacromolecularMachineMixin\",\n", + " \"biolink:Protein\",\n", + " \"biolink:GeneProductMixin\",\n", + " \"biolink:Polypeptide\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\"\n", + " ],\n", + " \"information_content\": 81.3\n", + " },\n", + " \"UniProtKB:P05503\": {\n", + " \"id\": {\n", + " \"identifier\": \"NCBIGene:26195\",\n", + " \"label\": \"mt-Co1\"\n", + " },\n", + " \"equivalent_identifiers\": [\n", + " {\n", + " \"identifier\": \"NCBIGene:26195\",\n", + " \"label\": \"mt-Co1\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:10116\"\n", + " ]\n", + " },\n", + " {\n", + " \"identifier\": \"RGD:621871\",\n", + " \"label\": \"Mt-co1\"\n", + " },\n", + " {\n", + " \"identifier\": \"UniProtKB:P05503\",\n", + " \"label\": \"COX1_RAT Cytochrome c oxidase subunit 1 (sprot)\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:10116\"\n", + " ]\n", + " },\n", + " {\n", + " \"identifier\": \"PR:P05503\",\n", + " \"label\": \"cytochrome c oxidase subunit 1 (rat)\"\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSRNOP00000039048\"\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSRNOP00000039048.3\"\n", + " },\n", + " {\n", + " \"identifier\": \"UniProtKB:Q8HIC9\",\n", + " \"label\": \"Q8HIC9_RAT Cytochrome c oxidase subunit 1 (trembl)\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:10116\"\n", + " ]\n", + " }\n", + " ],\n", + " \"taxa\": [\n", + " \"NCBITaxon:10116\"\n", + " ],\n", + " \"type\": [\n", + " \"biolink:Gene\",\n", + " \"biolink:GeneOrGeneProduct\",\n", + " \"biolink:GenomicEntity\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:OntologyClass\",\n", + " \"biolink:BiologicalEntity\",\n", + " \"biolink:ThingWithTaxon\",\n", + " \"biolink:NamedThing\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\",\n", + " \"biolink:MacromolecularMachineMixin\",\n", + " \"biolink:Protein\",\n", + " \"biolink:GeneProductMixin\",\n", + " \"biolink:Polypeptide\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\"\n", + " ],\n", + " \"information_content\": 100.0\n", + " }\n", + "}\n" + ] + } + ], "source": [ - "## TRAPI" + "result = requests.post('https://nodenormalization-sri.renci.org/get_normalized_nodes',\n", + " json={\"curies\":[\"HGNC:613\", \"UniProtKB:P05503\"], \"include_taxa\": True})\n", + "print( json.dumps( result.json(), indent = 2))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "NodeNorm can normalize entire TRAPI messages. Here we have a message in terms of HGNC and DOID, and the normalizer returns a message using NCBIGene and MONDO." + "## Conflation\n", + "\n", + "NodeNorm allows identifiers to be optionally combined into broader concepts at query time. There are two conflations currently available:\n", + "* GeneProtein conflation combines protein-encoding genes with their gene products, which can combine\n", + "* DrugChemical conflation combines drug formulations with their active ingredients, allowing you to normalize a specific formulation of a drug (such as [UMLS:C0704942 \"acetaminophen 16 MG/ML Oral Solution\"](https://uts.nlm.nih.gov/uts/umls/concept/C0704942)) to the active ingredient (in this case, [CHEBI:46195 \"Acetaminophen\"](https://www.ebi.ac.uk/chebi/CHEBI:46195)).\n", + "\n", + "More details about conflation is available [in the Babel repository](https://github.com/NCATSTranslator/Babel/blob/master/docs/Conflation.md)." ] }, { - "cell_type": "code", - "execution_count": 24, + "cell_type": "markdown", "metadata": {}, - "outputs": [], "source": [ - "trapi_message = {\n", - " \"message\": {\n", - " \"query_graph\": {\n", - " \"nodes\": {\n", - " \"n1\": {\n", - " \"id\": \"HGNC:11603\",\n", - " \"categories\": [\n", - " \"biolink:Gene\"\n", - " ]\n", + "### Conflation examples\n", + "\n", + "First, let's try to normalize a protein ([UniProtKB:P05503 \"Cytochrome c oxidase subunit 1\" in rats](https://www.uniprot.org/uniprotkb/P05503/entry)) and a drug formulation ([UMLS:C0704942 \"acetaminophen 16 MG/ML Oral Solution\"](https://uts.nlm.nih.gov/uts/umls/concept/C0704942)) with both NGeneProtein conflation (`conflate`) and DrugChemical conflation (`drug_chemical_conflate`) turned off." + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"UniProtKB:P05503\": {\n", + " \"id\": {\n", + " \"identifier\": \"UniProtKB:P05503\",\n", + " \"label\": \"COX1_RAT Cytochrome c oxidase subunit 1 (sprot)\"\n", + " },\n", + " \"equivalent_identifiers\": [\n", + " {\n", + " \"identifier\": \"UniProtKB:P05503\",\n", + " \"label\": \"COX1_RAT Cytochrome c oxidase subunit 1 (sprot)\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:10116\"\n", + " ]\n", + " },\n", + " {\n", + " \"identifier\": \"PR:P05503\",\n", + " \"label\": \"cytochrome c oxidase subunit 1 (rat)\"\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSRNOP00000039048\"\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSRNOP00000039048.3\"\n", + " }\n", + " ],\n", + " \"taxa\": [\n", + " \"NCBITaxon:10116\"\n", + " ],\n", + " \"type\": [\n", + " \"biolink:Protein\",\n", + " \"biolink:GeneProductMixin\",\n", + " \"biolink:Polypeptide\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", + " \"biolink:BiologicalEntity\",\n", + " \"biolink:ThingWithTaxon\",\n", + " \"biolink:NamedThing\",\n", + " \"biolink:GeneOrGeneProduct\",\n", + " \"biolink:MacromolecularMachineMixin\"\n", + " ],\n", + " \"information_content\": 100.0\n", + " },\n", + " \"UMLS:C0704942\": {\n", + " \"id\": {\n", + " \"identifier\": \"RXCUI:204900\",\n", + " \"label\": \"acetaminophen 16 MG/ML Oral Solution\"\n", + " },\n", + " \"equivalent_identifiers\": [\n", + " {\n", + " \"identifier\": \"RXCUI:204900\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0704942\",\n", + " \"label\": \"acetaminophen 16 MG/ML Oral Solution\"\n", + " }\n", + " ],\n", + " \"type\": [\n", + " \"biolink:Drug\",\n", + " \"biolink:ChemicalOrDrugOrTreatment\",\n", + " \"biolink:OntologyClass\",\n", + " \"biolink:MolecularMixture\",\n", + " \"biolink:ChemicalMixture\",\n", + " \"biolink:ChemicalEntity\",\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", + " \"biolink:NamedThing\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\"\n", + " ]\n", + " }\n", + "}\n" + ] + } + ], + "source": [ + "result = requests.post('https://nodenormalization-sri.renci.org/get_normalized_nodes',\n", + " json={\"curies\":[\"UniProtKB:P05503\", \"UMLS:C0704942\"],\n", + " \"conflate\": False,\n", + " \"drug_chemical_conflate\": False})\n", + "print( json.dumps( result.json(), indent = 2))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Now let's retry that query with both GeneProtein conflation (`conflate`) and DrugChemical conflation (`drug_chemical_conflate`) turned on. You will see the larger conflated cliques returned for both identifiers." + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"UniProtKB:P05503\": {\n", + " \"id\": {\n", + " \"identifier\": \"NCBIGene:26195\",\n", + " \"label\": \"mt-Co1\"\n", + " },\n", + " \"equivalent_identifiers\": [\n", + " {\n", + " \"identifier\": \"NCBIGene:26195\",\n", + " \"label\": \"mt-Co1\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:10116\"\n", + " ]\n", + " },\n", + " {\n", + " \"identifier\": \"RGD:621871\",\n", + " \"label\": \"Mt-co1\"\n", + " },\n", + " {\n", + " \"identifier\": \"UniProtKB:P05503\",\n", + " \"label\": \"COX1_RAT Cytochrome c oxidase subunit 1 (sprot)\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:10116\"\n", + " ]\n", + " },\n", + " {\n", + " \"identifier\": \"PR:P05503\",\n", + " \"label\": \"cytochrome c oxidase subunit 1 (rat)\"\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSRNOP00000039048\"\n", + " },\n", + " {\n", + " \"identifier\": \"ENSEMBL:ENSRNOP00000039048.3\"\n", + " },\n", + " {\n", + " \"identifier\": \"UniProtKB:Q8HIC9\",\n", + " \"label\": \"Q8HIC9_RAT Cytochrome c oxidase subunit 1 (trembl)\",\n", + " \"taxa\": [\n", + " \"NCBITaxon:10116\"\n", + " ]\n", + " }\n", + " ],\n", + " \"taxa\": [\n", + " \"NCBITaxon:10116\"\n", + " ],\n", + " \"type\": [\n", + " \"biolink:Gene\",\n", + " \"biolink:GeneOrGeneProduct\",\n", + " \"biolink:GenomicEntity\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:OntologyClass\",\n", + " \"biolink:BiologicalEntity\",\n", + " \"biolink:ThingWithTaxon\",\n", + " \"biolink:NamedThing\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\",\n", + " \"biolink:MacromolecularMachineMixin\",\n", + " \"biolink:Protein\",\n", + " \"biolink:GeneProductMixin\",\n", + " \"biolink:Polypeptide\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\"\n", + " ],\n", + " \"information_content\": 100.0\n", + " },\n", + " \"UMLS:C0704942\": {\n", + " \"id\": {\n", + " \"identifier\": \"CHEBI:46195\",\n", + " \"label\": \"Acetaminophen\"\n", + " },\n", + " \"equivalent_identifiers\": [\n", + " {\n", + " \"identifier\": \"CHEBI:46195\",\n", + " \"label\": \"paracetamol\"\n", + " },\n", + " {\n", + " \"identifier\": \"CHEBI:46191\"\n", + " },\n", + " {\n", + " \"identifier\": \"CHEBI:2386\"\n", + " },\n", + " {\n", + " \"identifier\": \"UNII:362O9ITL9D\",\n", + " \"label\": \"ACETAMINOPHEN\"\n", + " },\n", + " {\n", + " \"identifier\": \"PUBCHEM.COMPOUND:1983\",\n", + " \"label\": \"Acetaminophen\"\n", + " },\n", + " {\n", + " \"identifier\": \"CHEMBL.COMPOUND:CHEMBL112\",\n", + " \"label\": \"ACETAMINOPHEN\"\n", + " },\n", + " {\n", + " \"identifier\": \"DRUGBANK:DB00316\",\n", + " \"label\": \"Acetaminophen\"\n", + " },\n", + " {\n", + " \"identifier\": \"MESH:D000082\",\n", + " 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\"identifier\": \"RXCUI:209501\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0711274\",\n", + " \"label\": \"acetaminophen 80 MG Chewable Tablet [Tempra Quicklets]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:209531\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0711308\",\n", + " \"label\": \"acetaminophen 80 MG Rectal Suppository [Feverall]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:209870\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0711682\",\n", + " \"label\": \"acetaminophen 160 MG Chewable Tablet [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:209873\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0711685\",\n", + " \"label\": \"acetaminophen 160 MG Chewable Tablet [Tempra Quicklets]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:209890\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0711707\",\n", + " \"label\": \"acetaminophen 500 MG Oral Capsule [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:215257\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0718505\",\n", + " \"label\": \"Anacin AF\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:217115\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0720427\",\n", + " \"label\": \"Feverall\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:218205\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0721555\",\n", + " \"label\": \"Mapap\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:219598\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0723000\",\n", + " \"label\": \"Redutemp\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:220207\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0723636\",\n", + " \"label\": \"Tempra Quicklets\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:220562\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0724005\",\n", + " \"label\": \"Tycolene\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:225064\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0729009\",\n", + " \"label\": \"Acephen\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:226882\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0732606\",\n", + " \"label\": \"acetaminophen 60 MG Rectal Suppository\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:238159\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0774375\",\n", + " \"label\": \"acetaminophen 100 MG/ML Oral Solution\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:243675\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0783434\",\n", + " \"label\": \"acetaminophen 100 MG/ML Oral Suspension\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:248316\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0789706\",\n", + " \"label\": \"acetaminophen 50 MG/ML Oral Solution\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:249875\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0791728\",\n", + " \"label\": \"acetaminophen 250 MG Rectal Suppository\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:250649\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0792575\",\n", + " \"label\": \"acetaminophen 50 MG/ML Oral Suspension\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:250650\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0792576\",\n", + " \"label\": \"acetaminophen 24 MG/ML Oral Suspension\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:250651\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0792577\",\n", + " \"label\": \"acetaminophen 500 MG Rectal Suppository\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:251374\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0793407\",\n", + " \"label\": \"acetaminophen 80 MG Disintegrating Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:251698\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0793792\",\n", + " \"label\": \"acetaminophen 300 MG Rectal Suppository\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:282464\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0936176\",\n", + " \"label\": \"acetaminophen 160 MG Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:307666\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0973747\",\n", + " \"label\": \"acetaminophen 125 MG Rectal Suppository\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:307667\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0973748\",\n", + " \"label\": \"acetaminophen 160 MG Oral Capsule\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:307668\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0973749\",\n", + " \"label\": \"acetaminophen 32 MG/ML Oral Suspension\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:307675\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0973757\",\n", + " \"label\": \"acetaminophen 32 MG/ML Oral Solution\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:307684\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0973766\",\n", + " \"label\": \"acetaminophen 33.3 MG/ML Oral Solution\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:307695\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0973777\",\n", + " \"label\": \"acetaminophen 80 MG Oral Capsule\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:307696\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0973778\",\n", + " \"label\": \"acetaminophen 80 MG Chewable Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:313782\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0981193\",\n", + " \"label\": \"acetaminophen 325 MG Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:313820\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0981235\",\n", + " \"label\": \"acetaminophen 160 MG Chewable Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:315249\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0982928\",\n", + " \"label\": \"acetaminophen 100 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\"label\": \"acetaminophen 24 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:315257\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0982944\",\n", + " \"label\": \"acetaminophen 240 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:315258\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0982945\",\n", + " \"label\": \"acetaminophen 25 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:315259\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0982946\",\n", + " \"label\": \"acetaminophen 250 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:315261\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0982950\",\n", + " \"label\": \"acetaminophen 300 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:315262\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0982951\",\n", + " \"label\": \"acetaminophen 32 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:315263\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0982952\",\n", + " \"label\": \"acetaminophen 325 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:315264\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0982956\",\n", + " \"label\": \"acetaminophen 400 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:315266\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0982958\",\n", + " \"label\": \"acetaminophen 500 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:315268\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0982960\",\n", + " \"label\": \"acetaminophen 650 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:315269\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0982961\",\n", + " \"label\": \"acetaminophen 750 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:315270\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0982962\",\n", + " \"label\": \"acetaminophen 80 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:317285\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0991892\",\n", + " \"label\": \"acetaminophen 50 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:317286\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C0991893\",\n", + " \"label\": \"acetaminophen 65 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:328877\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1123879\",\n", + " \"label\": \"acetaminophen 33.3 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:329161\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1124260\",\n", + " \"label\": \"acetaminophen 16 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:330588\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1126278\",\n", + " \"label\": \"acetaminophen 660 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:330879\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1126675\",\n", + " \"label\": \"acetaminophen 60 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:330880\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1126678\",\n", + " \"label\": \"acetaminophen 20 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:330892\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1126690\",\n", + " \"label\": \"acetaminophen 450 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:330905\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1126703\",\n", + " \"label\": \"acetaminophen 120 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:332335\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1128541\",\n", + " \"label\": \"acetaminophen 260 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:332345\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1128551\",\n", + " \"label\": \"acetaminophen 43.3 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:332581\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1128848\",\n", + " \"label\": \"acetaminophen 21.7 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:332608\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1128885\",\n", + " \"label\": \"acetaminophen 1000 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:332815\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1129124\",\n", + " \"label\": \"acetaminophen 60 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:336021\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1133124\",\n", + " \"label\": \"acetaminophen 32.5 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:336027\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1133131\",\n", + " \"label\": \"acetaminophen 356.4 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:336341\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1133572\",\n", + " \"label\": \"acetaminophen 712.8 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:336428\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1133682\",\n", + " \"label\": \"acetaminophen 194 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:336882\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1134224\",\n", + " \"label\": \"acetaminophen 115 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:348978\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1164467\",\n", + " \"label\": \"acetaminophen 300 MG Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:349113\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1164631\",\n", + " \"label\": \"acetaminophen 500 MG Delayed Release Oral Capsule\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:349882\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1165529\",\n", + " \"label\": \"acetaminophen 556 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:360415\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1178620\",\n", + " \"label\": \"acetaminophen 110 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:364161\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1238109\",\n", + " \"label\": \"acetaminophen Oral Solution [Redutemp]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:364168\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1238116\",\n", + " \"label\": \"acetaminophen Oral Solution [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:366322\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1240290\",\n", + " \"label\": \"acetaminophen Oral Capsule [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:367547\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1241519\",\n", + " \"label\": \"acetaminophen Rectal Suppository [Feverall]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:367572\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1241544\",\n", + " \"label\": \"acetaminophen Rectal Suppository [Acephen]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:369070\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1243075\",\n", + " \"label\": \"acetaminophen Oral Tablet [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:369079\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1243084\",\n", + " \"label\": \"acetaminophen Oral Tablet [Panadol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:369085\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1243090\",\n", + " \"label\": \"acetaminophen Oral Tablet [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:369094\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1243099\",\n", + " \"label\": \"acetaminophen Oral Tablet [Anacin AF]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:369097\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1243102\",\n", + " \"label\": \"acetaminophen Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:369102\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1243107\",\n", + " \"label\": \"acetaminophen Oral Tablet [Tycolene]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:369639\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1243651\",\n", + " \"label\": \"acetaminophen Chewable Tablet [Tempra Quicklets]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:369642\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1243654\",\n", + " \"label\": \"acetaminophen Chewable Tablet [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:370506\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1244527\",\n", + " \"label\": \"acetaminophen Oral Solution\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:370508\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1244529\",\n", + " \"label\": \"acetaminophen Rectal Suppository\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:370509\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1244530\",\n", + " \"label\": \"acetaminophen Oral Suspension\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:370510\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1244531\",\n", + " \"label\": \"acetaminophen Chewable Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:370511\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1244532\",\n", + " \"label\": \"acetaminophen Oral Capsule\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:370512\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1244533\",\n", + " \"label\": \"acetaminophen Extended Release Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:370744\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1244770\",\n", + " \"label\": \"acetaminophen Disintegrating Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:378268\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1252526\",\n", + " \"label\": \"acetaminophen Delayed Release Oral Capsule\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:385629\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1263012\",\n", + " \"label\": \"acetaminophen 5 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:386243\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1263642\",\n", + " \"label\": \"acetaminophen Oral Solution [Panadol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:388081\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1271604\",\n", + " \"label\": \"acetaminophen 250 MG Disintegrating Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:392293\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1300002\",\n", + " \"label\": \"acetaminophen 48.2 MG/ML Oral Solution\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:393515\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1306671\",\n", + " \"label\": \"acetaminophen 48.2 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:421071\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1350338\",\n", + " \"label\": \"acetaminophen 100 MG Rectal Suppository\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:422626\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1351894\",\n", + " \"label\": \"acetaminophen 25 MG/ML Oral Suspension\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:425723\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1354991\",\n", + " \"label\": \"acetaminophen 120 MG/ML Oral Solution\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:430837\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1360105\",\n", + " \"label\": \"acetaminophen 1000 MG Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:437158\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1366476\",\n", + " \"label\": \"acetaminophen 100 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:437160\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1366478\",\n", + " \"label\": \"acetaminophen 20 MG/ML Oral Suspension\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:477282\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1533309\",\n", + " \"label\": \"acetaminophen 160 MG Disintegrating Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:483015\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1576926\",\n", + " \"label\": \"acetaminophen 10 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:483017\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1531801\",\n", + " \"label\": \"100 ML acetaminophen 10 MG/ML Injection\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:484495\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1576986\",\n", + " \"label\": \"acetaminophen 163 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:565623\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1598055\",\n", + " \"label\": \"acetaminophen 500 MG [Panadol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:569963\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604171\",\n", + " \"label\": \"acetaminophen 120 MG [Acephen]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:569964\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604172\",\n", + " \"label\": \"acetaminophen 120 MG [Feverall]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:569971\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604179\",\n", + " \"label\": \"acetaminophen 325 MG [Acephen]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:569972\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604180\",\n", + " \"label\": \"acetaminophen 325 MG [Feverall]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:569974\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604182\",\n", + " \"label\": \"acetaminophen 650 MG [Acephen]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:569975\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604183\",\n", + " \"label\": \"acetaminophen 650 MG [Feverall]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:569986\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604194\",\n", + " \"label\": \"acetaminophen 325 MG [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:569995\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604203\",\n", + " \"label\": \"acetaminophen 325 MG [Tycolene]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:569998\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604206\",\n", + " \"label\": \"acetaminophen 325 MG [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:570008\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604216\",\n", + " \"label\": \"acetaminophen 32 MG/ML [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:570028\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604236\",\n", + " \"label\": \"acetaminophen 33.3 MG/ML [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:570036\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604244\",\n", + " \"label\": \"acetaminophen 33.3 MG/ML [Redutemp]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:570044\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604252\",\n", + " \"label\": \"acetaminophen 500 MG [Anacin AF]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:570054\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604262\",\n", + " \"label\": \"acetaminophen 500 MG [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:570070\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604278\",\n", + " \"label\": \"acetaminophen 500 MG [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:570104\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604312\",\n", + " \"label\": \"acetaminophen 80 MG [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:570110\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604318\",\n", + " \"label\": \"acetaminophen 80 MG [Tempra Quicklets]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:570127\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604335\",\n", + " \"label\": \"acetaminophen 80 MG [Feverall]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:570445\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604652\",\n", + " \"label\": \"acetaminophen 160 MG [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:570448\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1604655\",\n", + " \"label\": \"acetaminophen 160 MG [Tempra Quicklets]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:603136\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1630429\",\n", + " \"label\": \"acetaminophen 325 MG Disintegrating Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:608680\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1640784\",\n", + " \"label\": \"acetaminophen 160 MG [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:615914\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1704092\",\n", + " \"label\": \"acetaminophen 650 MG [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:615915\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1703200\",\n", + " \"label\": \"acetaminophen Extended Release Oral Tablet [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:646457\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1739190\",\n", + " \"label\": \"acetaminophen 650 MG [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:646458\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1737305\",\n", + " \"label\": \"acetaminophen Extended Release Oral Tablet [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:665056\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1813001\",\n", + " \"label\": \"acetaminophen 500 MG Chewable Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:692667\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1876006\",\n", + " \"label\": \"acetaminophen Chewable Tablet [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:707319\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1948995\",\n", + " \"label\": \"Comtrex Sore Throat Relief\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:707320\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1948996\",\n", + " \"label\": \"acetaminophen 33.3 MG/ML [Comtrex Sore Throat Relief]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:707321\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1948997\",\n", + " \"label\": \"acetaminophen Oral Solution [Comtrex Sore Throat Relief]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:707322\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1948998\",\n", + " \"label\": \"acetaminophen 33.3 MG/ML Oral Solution [Comtrex Sore Throat Relief]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:798923\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2346279\",\n", + " \"label\": \"Tactinal\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:798924\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2344513\",\n", + " \"label\": \"acetaminophen 325 MG [Tactinal]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:798925\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2344514\",\n", + " \"label\": \"acetaminophen Oral Tablet [Tactinal]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:798926\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2344515\",\n", + " \"label\": \"acetaminophen 325 MG Oral Tablet [Tactinal]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:828553\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2370687\",\n", + " \"label\": \"acetaminophen 32 MG/ML [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:828554\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2370688\",\n", + " \"label\": \"acetaminophen Oral Suspension [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:828555\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1169145\",\n", + " \"label\": \"acetaminophen 32 MG/ML Oral Suspension [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:828557\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1169160\",\n", + " \"label\": \"acetaminophen 160 MG Chewable Tablet [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1013857\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2939691\",\n", + " \"label\": \"Little Fevers\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1038776\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2946042\",\n", + " \"label\": \"Bactimicina\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1038777\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2946043\",\n", + " \"label\": \"acetaminophen 32 MG/ML [Bactimicina]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1038778\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2946044\",\n", + " \"label\": \"acetaminophen Oral Solution [Bactimicina]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1038779\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2946045\",\n", + " \"label\": \"acetaminophen 32 MG/ML Oral Solution [Bactimicina]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1041527\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2954624\",\n", + " \"label\": \"Ofirmev\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1041528\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2947387\",\n", + " \"label\": \"acetaminophen 10 MG/ML [Ofirmev]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1041530\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2947389\",\n", + " \"label\": \"100 ML acetaminophen 10 MG/ML Injection [Ofirmev]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1048904\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2954813\",\n", + " \"label\": \"acetaminophen 32 MG/ML [Little Fevers]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1095635\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3152609\",\n", + " \"label\": \"acetaminophen 32 MG/ML [Panadol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1095636\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1635235\",\n", + " \"label\": \"acetaminophen 32 MG/ML Oral Solution [Panadol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1101342\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3154290\",\n", + " \"label\": \"Nortemp\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1101343\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3154291\",\n", + " \"label\": \"acetaminophen 100 MG/ML [Nortemp]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1101344\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3154292\",\n", + " \"label\": \"acetaminophen Oral Solution [Nortemp]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1101345\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3154293\",\n", + " \"label\": \"acetaminophen 100 MG/ML Oral Solution [Nortemp]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1144912\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3190600\",\n", + " \"label\": \"acetaminophen 16.7 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1148399\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3186998\",\n", + " \"label\": \"8 HR acetaminophen 650 MG Extended Release Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1152840\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3207337\",\n", + " \"label\": \"acetaminophen Injectable Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1152841\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3207338\",\n", + " \"label\": \"acetaminophen Oral Liquid Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1152842\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3207339\",\n", + " \"label\": \"acetaminophen Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1152843\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3207340\",\n", + " \"label\": \"acetaminophen Pill\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1152844\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3207341\",\n", + " \"label\": \"acetaminophen Rectal Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1167290\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3221484\",\n", + " \"label\": \"Bactimicina Oral Liquid Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1167291\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3221485\",\n", + " \"label\": \"Bactimicina Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1168109\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3222280\",\n", + " \"label\": \"Comtrex Sore Throat Relief Oral Liquid Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1168110\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3222281\",\n", + " \"label\": \"Comtrex Sore Throat Relief Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1168295\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3222464\",\n", + " \"label\": \"Feverall Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1168297\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3222466\",\n", + " \"label\": \"Feverall Rectal Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1168402\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3222570\",\n", + " \"label\": \"Acephen Rectal Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1174224\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3228243\",\n", + " \"label\": \"Anacin AF Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1174225\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3228244\",\n", + " \"label\": \"Anacin AF Pill\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1177832\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3231748\",\n", + " \"label\": \"Tactinal Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1177833\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3231749\",\n", + " \"label\": \"Tactinal Pill\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1179123\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3233007\",\n", + " \"label\": \"Little Fevers Oral Liquid Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1179124\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3233008\",\n", + " \"label\": \"Little Fevers Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1179570\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3233438\",\n", + " \"label\": \"Redutemp Oral Liquid Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1179571\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3233439\",\n", + " \"label\": \"Redutemp Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1179922\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3233787\",\n", + " \"label\": \"Panadol Oral Liquid Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1179923\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3233788\",\n", + " \"label\": \"Panadol Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1179926\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3233791\",\n", + " \"label\": \"Panadol Pill\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1180390\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3234244\",\n", + " \"label\": \"Mapap Oral Liquid Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1180391\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3234245\",\n", + " \"label\": \"Mapap Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1180394\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3234248\",\n", + " \"label\": \"Mapap Pill\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1181153\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3235000\",\n", + " \"label\": \"Ofirmev Injectable Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1181430\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3235269\",\n", + " \"label\": \"Tempra Quicklets Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1181431\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3235270\",\n", + " \"label\": \"Tempra Quicklets Pill\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1185724\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3239496\",\n", + " \"label\": \"Nortemp Oral Liquid Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1185725\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3239497\",\n", + " \"label\": \"Nortemp Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1186911\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3240658\",\n", + " \"label\": \"Tycolene Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1186912\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3240659\",\n", + " \"label\": \"Tycolene Pill\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1187310\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3241052\",\n", + " \"label\": \"Tylenol Oral Liquid Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1187311\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3241053\",\n", + " \"label\": \"Tylenol Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1187315\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3241057\",\n", + " \"label\": \"Tylenol Pill\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1235457\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3254809\",\n", + " \"label\": \"Ringl\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1235458\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3254810\",\n", + " \"label\": \"acetaminophen 325 MG [Ringl]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1235459\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3254811\",\n", + " \"label\": \"acetaminophen Oral Tablet [Ringl]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1235460\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3254812\",\n", + " \"label\": \"Ringl Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1235461\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3254813\",\n", + " \"label\": \"Ringl Pill\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1235462\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3254814\",\n", + " \"label\": \"acetaminophen 325 MG Oral Tablet [Ringl]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1242746\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3257692\",\n", + " \"label\": \"acetaminophen 162.5 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1243439\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3264815\",\n", + " \"label\": \"8 HR acetaminophen 650 MG Extended Release Oral Tablet [Mapap]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1243440\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3264816\",\n", + " \"label\": \"8 HR acetaminophen 650 MG Extended Release Oral Tablet [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1293937\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3152621\",\n", + " \"label\": \"Pharbetol\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1293938\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3465171\",\n", + " \"label\": \"acetaminophen 500 MG [Pharbetol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1293939\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3465172\",\n", + " \"label\": \"acetaminophen Oral Tablet [Pharbetol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1293940\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3465173\",\n", + " \"label\": \"Pharbetol Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1293941\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3465174\",\n", + " \"label\": \"Pharbetol Pill\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1293942\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3465175\",\n", + " \"label\": \"acetaminophen 500 MG Oral Tablet [Pharbetol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1294852\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3465517\",\n", + " \"label\": \"acetaminophen Granule Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1294958\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3465623\",\n", + " \"label\": \"acetaminophen Disintegrating Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1295535\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3466198\",\n", + " \"label\": \"acetaminophen Chewable Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1296526\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3467140\",\n", + " \"label\": \"Tylenol Chewable Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1296787\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3467387\",\n", + " \"label\": \"Tempra Quicklets Chewable Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1296986\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3467576\",\n", + " \"label\": \"Mapap Chewable Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1298829\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3473316\",\n", + " \"label\": \"acetaminophen 325 MG [Pharbetol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1298830\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3473317\",\n", + " \"label\": \"acetaminophen 325 MG Oral Tablet [Pharbetol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1301881\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2939693\",\n", + " \"label\": \"acetaminophen Oral Suspension [Little Fevers]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1301882\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C2954814\",\n", + " \"label\": \"acetaminophen 32 MG/ML Oral Suspension [Little Fevers]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1358830\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3505562\",\n", + " \"label\": \"Cetafen\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1358831\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3505563\",\n", + " \"label\": \"acetaminophen 500 MG [Cetafen]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1358832\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3505564\",\n", + " \"label\": \"acetaminophen Oral Tablet [Cetafen]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1358833\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3505565\",\n", + " \"label\": \"Cetafen Oral Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1358834\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3505566\",\n", + " \"label\": \"Cetafen Pill\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1358835\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3495480\",\n", + " \"label\": \"acetaminophen 500 MG Oral Tablet [Cetafen]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1358836\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3505567\",\n", + " \"label\": \"acetaminophen 325 MG [Cetafen]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1358837\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3495479\",\n", + " \"label\": \"acetaminophen 325 MG Oral Tablet [Cetafen]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1536879\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3820256\",\n", + " \"label\": \"acetaminophen Effervescent Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1536880\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C1269852\",\n", + " \"label\": \"acetaminophen 500 MG Effervescent Oral Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1596107\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C3865170\",\n", + " \"label\": \"acetaminophen 320.5 MG\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1661683\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C4047105\",\n", + " \"label\": \"acetaminophen 16.7 MG/ML Oral Solution\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1738138\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C4081280\",\n", + " \"label\": \"acetaminophen Oral Capsule [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1738139\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C4073803\",\n", + " \"label\": \"acetaminophen 325 MG Oral Capsule [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1803956\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C4255161\",\n", + " \"label\": \"acetaminophen single use injection\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1803958\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C4276239\",\n", + " \"label\": \"acetaminophen Injection [Ofirmev]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2178753\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5188118\",\n", + " \"label\": \"acetaminophen Oral Powder Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2178754\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5188119\",\n", + " \"label\": \"acetaminophen Oral Powder\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2178755\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5188120\",\n", + " \"label\": \"acetaminophen 160 MG Oral Powder\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2178756\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5188121\",\n", + " \"label\": \"acetaminophen Oral Powder [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2178757\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5188122\",\n", + " \"label\": \"Tylenol Oral Powder Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2178758\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5188123\",\n", + " \"label\": \"acetaminophen 160 MG Oral Powder [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2264779\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5221483\",\n", + " \"label\": \"acetaminophen 325 MG Chewable Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2374360\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5384342\",\n", + " \"label\": \"acetaminophen 500 MG Oral Powder\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2374361\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5383962\",\n", + " \"label\": \"acetaminophen 500 MG Oral Powder [Tylenol]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2480095\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5442203\",\n", + " \"label\": \"50 ML acetaminophen 10 MG/ML Injection\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2588210\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5563790\",\n", + " \"label\": \"acetaminophen 6.67 MG/ML\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2639348\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5816528\",\n", + " \"label\": \"acetaminophen 32 MG/ML [Feverall]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2639349\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5816571\",\n", + " \"label\": \"Feverall Oral Liquid Product\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2639350\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5816549\",\n", + " \"label\": \"acetaminophen Oral Suspension [Feverall]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2639351\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5816285\",\n", + " \"label\": \"acetaminophen 32 MG/ML Oral Suspension [Feverall]\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2668205\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5854245\",\n", + " \"label\": \"acetaminophen Granules for Oral Solution\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2668206\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5854246\",\n", + " \"label\": \"acetaminophen 500 MG Granules for Oral Solution\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2683419\"\n", + " },\n", + " {\n", + " \"identifier\": \"UMLS:C5919757\",\n", + " \"label\": \"acetaminophen 250 MG Chewable Tablet\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1100002\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1100003\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1100004\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1100005\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1171657\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:1171658\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2705806\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2705807\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2705808\"\n", + " },\n", + " {\n", + " \"identifier\": \"RXCUI:2715604\"\n", + " }\n", + " ],\n", + " \"type\": [\n", + " \"biolink:SmallMolecule\",\n", + " \"biolink:MolecularEntity\",\n", + " \"biolink:ChemicalEntity\",\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:ChemicalOrDrugOrTreatment\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", + " \"biolink:NamedThing\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\",\n", + " \"biolink:Drug\",\n", + " \"biolink:OntologyClass\",\n", + " \"biolink:MolecularMixture\",\n", + " \"biolink:ChemicalMixture\"\n", + " ]\n", + " }\n", + "}\n" + ] + } + ], + "source": [ + "result = requests.post('https://nodenormalization-sri.renci.org/get_normalized_nodes',\n", + " json={\"curies\":[\"UniProtKB:P05503\", \"UMLS:C0704942\"],\n", + " \"conflate\": True,\n", + " \"drug_chemical_conflate\": True})\n", + "print( json.dumps( result.json(), indent = 2))" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "slideshow": { + "slide_type": "slide" + } + }, + "source": [ + "## Metadata\n", + "\n", + "There are two metadata services that can be used to find out what sorts of results have been incorporated into the Node Normalization service. These return the semantic types that are included, and the prefixes included for each type." + ] + }, + { + "cell_type": "markdown", + "metadata": { + "slideshow": { + "slide_type": "slide" + } + }, + "source": [ + "#### Which types have been normalized?" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": { + "scrolled": true, + "slideshow": { + "slide_type": "subslide" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"semantic_types\": {\n", + " \"types\": [\n", + " \"biolink:Procedure\",\n", + " \"biolink:Agent\",\n", + " \"biolink:Phenomenon\",\n", + " \"biolink:CellLine\",\n", + " \"biolink:Cell\",\n", + " \"biolink:OntologyClass\",\n", + " \"biolink:GrossAnatomicalStructure\",\n", + " \"biolink:Cohort\",\n", + " \"biolink:MolecularEntity\",\n", + " \"biolink:NucleicAcidEntity\",\n", + " \"biolink:AnatomicalEntity\",\n", + " \"biolink:PhenotypicFeature\",\n", + " \"biolink:GeneProductMixin\",\n", + " \"biolink:ComplexMolecularMixture\",\n", + " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", + " \"biolink:GeneGroupingMixin\",\n", + " \"biolink:InformationContentEntity\",\n", + " \"biolink:MolecularMixture\",\n", + " \"biolink:Drug\",\n", + " \"biolink:Pathway\",\n", + " \"biolink:DiseaseOrPhenotypicFeature\",\n", + " \"biolink:OrganismTaxon\",\n", + " \"biolink:BiologicalProcessOrActivity\",\n", + " \"biolink:MacromolecularMachineMixin\",\n", + " \"biolink:OrganismalEntity\",\n", + " \"biolink:SubjectOfInvestigation\",\n", + " \"biolink:ChemicalMixture\",\n", + " \"biolink:Polypeptide\",\n", + " \"biolink:Entity\",\n", + " \"biolink:ThingWithTaxon\",\n", + " \"biolink:Gene\",\n", + " \"biolink:AdministrativeEntity\",\n", + " \"biolink:ChemicalEntity\",\n", + " \"biolink:Disease\",\n", + " \"biolink:BiologicalProcess\",\n", + " \"biolink:MolecularActivity\",\n", + " \"biolink:Publication\",\n", + " \"biolink:GeneFamily\",\n", + " \"biolink:StudyPopulation\",\n", + " \"biolink:Attribute\",\n", + " \"biolink:Activity\",\n", + " \"biolink:Mammal\",\n", + " \"biolink:PhysicalEntity\",\n", + " \"biolink:NamedThing\",\n", + " \"biolink:ActivityAndBehavior\",\n", + " \"biolink:MacromolecularComplex\",\n", + " \"biolink:SmallMolecule\",\n", + " \"biolink:GenomicEntity\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\",\n", + " \"biolink:ClinicalAttribute\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:GeographicLocation\",\n", + " \"biolink:Protein\",\n", + " \"biolink:Behavior\",\n", + " \"biolink:BiologicalEntity\",\n", + " \"biolink:PopulationOfIndividualOrganisms\",\n", + " \"biolink:Occurrent\",\n", + " \"biolink:Human\",\n", + " \"biolink:PhysiologicalProcess\",\n", + " \"biolink:CellularOrganism\",\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:GeneOrGeneProduct\",\n", + " \"biolink:CellularComponent\",\n", + " \"biolink:Event\",\n", + " \"biolink:Device\",\n", + " \"biolink:ChemicalOrDrugOrTreatment\",\n", + " \"biolink:PlanetaryEntity\"\n", + " ]\n", + " }\n", + "}\n" + ] + } + ], + "source": [ + "import json \n", + "import requests\n", + "\n", + "result = requests.get('https://nodenormalization-sri.renci.org/get_semantic_types')\n", + "print( json.dumps( result.json(), indent = 2))" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "slideshow": { + "slide_type": "slide" + } + }, + "source": [ + "#### Which prefixes are supported?\n", + "\n", + "Even if a semantic type has some identifier equivalence, not every vocabulary has been included. To see which vocabularies are likely to give useful results for a specific Biolink class, call:" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "slideshow": { + "slide_type": "skip" + } + }, + "source": [ + "More than one type can be queried:" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": { + "scrolled": true, + "slideshow": { + "slide_type": "skip" + } + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"biolink:ChemicalEntity\": {\n", + " \"curie_prefix\": {\n", + " \"PUBCHEM.COMPOUND\": \"123887334\",\n", + " \"INCHIKEY\": \"115975484\",\n", + " \"CAS\": \"4112274\",\n", + " \"HMDB\": \"217920\",\n", + " \"CHEMBL.COMPOUND\": \"2479770\",\n", + " \"UNII\": \"138975\",\n", + " \"CHEBI\": \"218762\",\n", + " \"MESH\": \"256235\",\n", + " \"UMLS\": \"603550\",\n", + " \"DrugCentral\": \"4995\",\n", + " \"GTOPDB\": \"13265\",\n", + " \"RXCUI\": \"124800\",\n", + " \"DRUGBANK\": \"15274\",\n", + " \"KEGG.COMPOUND\": \"16039\"\n", + " }\n", + " },\n", + " \"biolink:Disease\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"353693\",\n", + " \"SNOMEDCT\": \"98214\",\n", + " \"NCIT\": \"25975\",\n", + " \"MONDO\": \"26294\",\n", + " \"orphanet\": \"11048\",\n", + " \"MESH\": \"11255\",\n", + " \"medgen\": \"21044\",\n", + " \"icd11.foundation\": \"4056\",\n", + " \"MEDDRA\": \"47094\",\n", + " \"DOID\": \"11951\",\n", + " \"ICD10\": \"2520\",\n", + " \"ICD9\": \"2233\",\n", + " \"OMIM\": \"10210\",\n", + " \"EFO\": \"3760\",\n", + " \"HP\": \"2361\",\n", + " \"OMIM.PS\": \"573\",\n", + " \"KEGG.DISEASE\": \"40\",\n", + " \"icd11\": \"5\",\n", + " \"MP\": \"4\"\n", + " }\n", + " }\n", + "}\n" + ] + } + ], + "source": [ + "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes/',\n", + " params={'semantic_type':[\"biolink:ChemicalEntity\",\"biolink:Disease\"]})\n", + "print( json.dumps( result.json(), indent = 2))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Or you can just ask for all the prefix counts for every type:" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{\n", + " \"biolink:CellLine\": {\n", + " \"curie_prefix\": {\n", + " \"CLO\": \"38810\"\n", + " }\n", + " },\n", + " \"biolink:Pathway\": {\n", + " \"curie_prefix\": {\n", + " \"SMPDB\": \"30248\",\n", + " \"REACT\": \"22114\",\n", + " \"PANTHER.PATHWAY\": \"175\",\n", + " \"GO\": \"588\"\n", + " }\n", + " },\n", + " \"biolink:PhysiologicalProcess\": {\n", + " \"curie_prefix\": {\n", + " \"UMLS\": \"112\"\n", + " }\n", + " }\n", + "}\n" + ] + } + ], + "source": [ + "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes')\n", + "responses = result.json()\n", + "\n", + "# Display only the first three responses. \n", + "print( json.dumps( dict(list(responses.items())[:3]), indent = 2))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## TRAPI" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**Warning**: the NodeNorm TRAPI API endpoints have been deprecated, and will be removed from a future NodeNorm release.\n", + "\n", + "NodeNorm can normalize entire TRAPI messages. Here we have a message in terms of HGNC and DOID, and the normalizer returns a message using NCBIGene and MONDO." + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [], + "source": [ + "trapi_message = {\n", + " \"message\": {\n", + " \"query_graph\": {\n", + " \"nodes\": {\n", + " \"n1\": {\n", + " \"id\": \"HGNC:11603\",\n", + " \"categories\": [\n", + " \"biolink:Gene\"\n", + " ]\n", " },\n", " \"n2\": {\n", " \"categories\": [\n", @@ -717,7 +3686,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 24, "metadata": {}, "outputs": [ { @@ -735,7 +3704,7 @@ }, { "cell_type": "code", - "execution_count": 26, + "execution_count": 25, "metadata": {}, "outputs": [ { @@ -773,21 +3742,21 @@ " \"nodes\": {\n", " \"NCBIGene:9496\": {\n", " \"categories\": [\n", - " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", + " \"biolink:PhysicalEssenceOrOccurrent\",\n", + " \"biolink:GeneProductMixin\",\n", + " \"biolink:ThingWithTaxon\",\n", " \"biolink:MacromolecularMachineMixin\",\n", - " \"biolink:OntologyClass\",\n", " \"biolink:GeneOrGeneProduct\",\n", + " \"biolink:GenomicEntity\",\n", " \"biolink:NamedThing\",\n", " \"biolink:BiologicalEntity\",\n", - " \"biolink:PhysicalEssenceOrOccurrent\",\n", + " \"biolink:Gene\",\n", " \"biolink:Protein\",\n", - " \"biolink:GenomicEntity\",\n", - " \"biolink:ThingWithTaxon\",\n", - " \"biolink:PhysicalEssence\",\n", " \"biolink:Polypeptide\",\n", - " \"biolink:GeneProductMixin\",\n", + " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", - " \"biolink:Gene\"\n", + " \"biolink:PhysicalEssence\",\n", + " \"biolink:OntologyClass\"\n", " ],\n", " \"name\": \"TBX4\",\n", " \"attributes\": [\n", @@ -801,7 +3770,9 @@ " \"UMLS:C1420614\",\n", " \"UniProtKB:P57082\",\n", " \"PR:P57082\",\n", - " \"UMLS:C3815898\"\n", + " \"UMLS:C1455491\",\n", + " \"UMLS:C3815898\",\n", + " \"MESH:C491193\"\n", " ],\n", " \"value_type_id\": \"EDAM:data_0006\",\n", " \"original_attribute_name\": \"equivalent_identifiers\"\n", @@ -810,11 +3781,11 @@ " },\n", " \"MONDO:0005002\": {\n", " \"categories\": [\n", + " \"biolink:Disease\",\n", + " \"biolink:ThingWithTaxon\",\n", " \"biolink:DiseaseOrPhenotypicFeature\",\n", " \"biolink:NamedThing\",\n", - " \"biolink:BiologicalEntity\",\n", - " \"biolink:Disease\",\n", - " \"biolink:ThingWithTaxon\"\n", + " \"biolink:BiologicalEntity\"\n", " ],\n", " \"name\": \"chronic obstructive pulmonary disease\",\n", " \"attributes\": [\n", @@ -827,9 +3798,7 @@ " \"EFO:0000341\",\n", " \"UMLS:C0024117\",\n", " \"UMLS:C1527303\",\n", - " \"UMLS:C1847014\",\n", " \"UMLS:C2751329\",\n", - " \"MESH:C564641\",\n", " \"MESH:D029424\",\n", " \"MEDDRA:10008828\",\n", " \"MEDDRA:10009025\",\n", @@ -842,6 +3811,8 @@ " \"MEDDRA:10070975\",\n", " \"NCIT:C3199\",\n", " \"SNOMEDCT:13645005\",\n", + " \"medgen:9818\",\n", + " \"icd11.foundation:133207228\",\n", " \"ICD10:J44.9\",\n", " \"HP:0006510\"\n", " ],\n", @@ -869,7 +3840,7 @@ " \"attributes\": [\n", " {\n", " \"attribute_type_id\": \"biolink:has_numeric_value\",\n", - " \"value\": 100.0,\n", + " \"value\": 90.9,\n", " \"value_type_id\": \"EDAM:data_0006\",\n", " \"original_attribute_name\": \"information_content\"\n", " }\n", @@ -882,7 +3853,7 @@ " \"attributes\": [\n", " {\n", " \"attribute_type_id\": \"biolink:has_numeric_value\",\n", - " \"value\": 100.0,\n", + " \"value\": 81.7,\n", " \"value_type_id\": \"EDAM:data_0006\",\n", " \"original_attribute_name\": \"information_content\"\n", " }\n", @@ -914,313 +3885,6 @@ "source": [ "print(json.dumps(result.json(), indent=2))" ] - }, - { - "cell_type": "markdown", - "metadata": { - "slideshow": { - "slide_type": "slide" - } - }, - "source": [ - "## Metadata\n", - "\n", - "There are two metadata services that can be used to find out what sorts of results have been incorporated into the Node Normalization service. These return the semantic types that are included, and the prefixes included for each type." - ] - }, - { - "cell_type": "markdown", - "metadata": { - "slideshow": { - "slide_type": "slide" - } - }, - "source": [ - "#### Which types have been normalized?" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": { - "slideshow": { - "slide_type": "subslide" - } - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"semantic_types\": {\n", - " \"types\": [\n", - " \"biolink:BiologicalProcess\",\n", - " \"biolink:BiologicalEntity\",\n", - " \"biolink:OrganismTaxon\",\n", - " \"biolink:Device\",\n", - " \"biolink:PlanetaryEntity\",\n", - " \"biolink:GeneOrGeneProduct\",\n", - " \"biolink:ChemicalMixture\",\n", - " \"biolink:ComplexMolecularMixture\",\n", - " \"biolink:StudyPopulation\",\n", - " \"biolink:Phenomenon\",\n", - " \"biolink:ClinicalAttribute\",\n", - " \"biolink:MolecularActivity\",\n", - " \"biolink:Food\",\n", - " \"biolink:Publication\",\n", - " \"biolink:ChemicalEntity\",\n", - " \"biolink:NamedThing\",\n", - " \"biolink:MolecularMixture\",\n", - " \"biolink:GeneGroupingMixin\",\n", - " \"biolink:BiologicalProcessOrActivity\",\n", - " \"biolink:Gene\",\n", - " \"biolink:Disease\",\n", - " \"biolink:OntologyClass\",\n", - " \"biolink:Cohort\",\n", - " \"biolink:GrossAnatomicalStructure\",\n", - " \"biolink:Drug\",\n", - " \"biolink:SubjectOfInvestigation\",\n", - " \"biolink:PhenotypicFeature\",\n", - " \"biolink:MacromolecularComplex\",\n", - " \"biolink:Event\",\n", - " \"biolink:ActivityAndBehavior\",\n", - " \"biolink:PopulationOfIndividualOrganisms\",\n", - " \"biolink:NucleicAcidEntity\",\n", - " \"biolink:OrganismalEntity\",\n", - " \"biolink:Protein\",\n", - " \"biolink:Human\",\n", - " \"biolink:Agent\",\n", - " \"biolink:GeneFamily\",\n", - " \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n", - " \"biolink:Attribute\",\n", - " \"biolink:SmallMolecule\",\n", - " \"biolink:CellularComponent\",\n", - " \"biolink:ChemicalOrDrugOrTreatment\",\n", - " \"biolink:MolecularEntity\",\n", - " \"biolink:InformationContentEntity\",\n", - " \"biolink:PhysicalEssenceOrOccurrent\",\n", - " \"biolink:Cell\",\n", - " \"biolink:GenomicEntity\",\n", - " \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n", - " \"biolink:GeneProductMixin\",\n", - " \"biolink:Polypeptide\",\n", - " \"biolink:PhysicalEssence\",\n", - " \"biolink:PhysiologicalProcess\",\n", - " \"biolink:Occurrent\",\n", - " \"biolink:Procedure\",\n", - " \"biolink:PhysicalEntity\",\n", - " \"biolink:Entity\",\n", - " \"biolink:OrganismAttribute\",\n", - " \"biolink:Behavior\",\n", - " \"biolink:Activity\",\n", - " \"biolink:AdministrativeEntity\",\n", - " \"biolink:GeographicLocation\",\n", - " \"biolink:AnatomicalEntity\",\n", - " \"biolink:MacromolecularMachineMixin\",\n", - " \"biolink:ThingWithTaxon\",\n", - " \"biolink:DiseaseOrPhenotypicFeature\",\n", - " \"biolink:Pathway\"\n", - " ]\n", - " }\n", - "}\n" - ] - } - ], - "source": [ - "import json \n", - "import requests\n", - "\n", - "result = requests.get('https://nodenormalization-sri.renci.org/get_semantic_types')\n", - "print( json.dumps( result.json(), indent = 2))" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "slideshow": { - "slide_type": "slide" - } - }, - "source": [ - "#### Which prefixes are supported?\n", - "\n", - "Even if a semantic type has some identifier equivalence, not every vocabulary has been included. To see which vocabularies are likely to give useful results for a specific Biolink class, call:" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "slideshow": { - "slide_type": "skip" - } - }, - "source": [ - "More than one type can be queried:" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": { - "collapsed": true, - "jupyter": { - "outputs_hidden": true - }, - "scrolled": true, - "slideshow": { - "slide_type": "skip" - } - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"biolink:ChemicalEntity\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"124460882\",\n", - " \"INCHIKEY\": \"110336273\",\n", - " \"CHEMBL.COMPOUND\": \"2399641\",\n", - " \"CHEBI\": \"196937\",\n", - " \"CAS\": \"3556698\",\n", - " \"HMDB\": \"217920\",\n", - " \"UNII\": \"126327\",\n", - " \"MESH\": \"258102\",\n", - " \"KEGG.COMPOUND\": \"16020\",\n", - " \"UMLS\": \"549120\",\n", - " \"DRUGBANK\": \"15179\",\n", - " \"DrugCentral\": \"4995\",\n", - " \"GTOPDB\": \"12347\",\n", - " \"RXCUI\": \"123395\"\n", - " }\n", - " },\n", - " \"biolink:Disease\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"336767\",\n", - " \"SNOMEDCT\": \"94514\",\n", - " \"MEDDRA\": \"46033\",\n", - " \"MONDO\": \"24012\",\n", - " \"DOID\": \"11498\",\n", - " \"NCIT\": \"25540\",\n", - " \"HP\": \"2182\",\n", - " \"EFO\": \"3711\",\n", - " \"orphanet\": \"10780\",\n", - " \"MESH\": \"11238\",\n", - " \"OMIM\": \"10314\",\n", - " \"ICD10\": \"2429\",\n", - " \"ICD9\": \"2218\",\n", - " \"OMIM.PS\": \"556\",\n", - " \"KEGG.DISEASE\": \"40\",\n", - " \"MP\": \"1\"\n", - " }\n", - " }\n", - "}\n" - ] - } - ], - "source": [ - "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes/',\n", - " params={'semantic_type':[\"biolink:ChemicalEntity\",\"biolink:Disease\"]})\n", - "print( json.dumps( result.json(), indent = 2))" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "jupyter": { - "source_hidden": true - } - }, - "source": [ - "Or you can just ask for all the prefix counts for every type:" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"biolink:Pathway\": {\n", - " \"curie_prefix\": {\n", - " \"REACT\": \"21784\",\n", - " \"SMPDB\": \"30248\",\n", - " \"GO\": \"642\",\n", - " \"PANTHER.PATHWAY\": \"175\"\n", - " }\n", - " },\n", - " \"biolink:OrganismTaxon\": {\n", - " \"curie_prefix\": {\n", - " \"UMLS\": \"749649\",\n", - " \"NCBITaxon\": \"2546095\",\n", - " \"MESH\": \"70628\"\n", - " }\n", - " },\n", - " \"biolink:GeneFamily\": {\n", - " \"curie_prefix\": {\n", - " \"PANTHER.FAMILY\": \"26138\",\n", - " \"HGNC.FAMILY\": \"1807\"\n", - " }\n", - " }\n", - "}\n" - ] - } - ], - "source": [ - "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes')\n", - "responses = result.json()\n", - "\n", - "# Display only the first three responses. \n", - "print( json.dumps( dict(list(responses.items())[:3]), indent = 2))" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": { - "slideshow": { - "slide_type": "subslide" - } - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"biolink:ChemicalEntity\": {\n", - " \"curie_prefix\": {\n", - " \"PUBCHEM.COMPOUND\": \"124460882\",\n", - " \"INCHIKEY\": \"110336273\",\n", - " \"CHEMBL.COMPOUND\": \"2399641\",\n", - " \"CHEBI\": \"196937\",\n", - " \"CAS\": \"3556698\",\n", - " \"HMDB\": \"217920\",\n", - " \"UNII\": \"126327\",\n", - " \"MESH\": \"258102\",\n", - " \"KEGG.COMPOUND\": \"16020\",\n", - " \"UMLS\": \"549120\",\n", - " \"DRUGBANK\": \"15179\",\n", - " \"DrugCentral\": \"4995\",\n", - " \"GTOPDB\": \"12347\",\n", - " \"RXCUI\": \"123395\"\n", - " }\n", - " }\n", - "}\n" - ] - } - ], - "source": [ - "result = requests.get('https://nodenormalization-sri.renci.org/get_curie_prefixes/',\n", - " params={'semantic_type':\"biolink:ChemicalEntity\"})\n", - "print( json.dumps( result.json(), indent = 2))" - ] } ], "metadata": {