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RTXteam / RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
MIT License
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liver diseases subtypes of liver? Chemical returned as phenotype #212

Open cbizon opened 2 years ago

cbizon commented 2 years ago

https://arax.ncats.io/?r=06f9907b-bc1b-45e5-a21b-e71bc6d7869c

This query is (?DiseaseOrPhenotypicFeature)-[related_to]->(Liver).

The results look good, but many also contain an edge like (Hepatitis)-[subclass of]->liver, which I don't think makes sense.

Also, acetylcarnitine is returned as a result, which is not a disease or phenotype.

ecwood commented 1 year ago

This result no longer exists at that URL. However, I was able to reproduce the issue here: https://arax.ncats.io/?r=148548.

It appears the problematic categorization of acetylcarnitine is coming from LOINC:

Identifier Label Original Label Category
UMLS:C0087163 levocarnitine levocarnitine biolink:ChemicalEntity
ATC:A16AA01 levocarnitine levocarnitine biolink:ChemicalEntity
UMLS:C0001040 acetylcarnitine acetylcarnitine biolink:ChemicalEntity
ATC:N06BX12 acetylcarnitine acetylcarnitine biolink:ChemicalEntity
DRUGBANK:DB08842 Acetylcarnitine Acetylcarnitine biolink:ChemicalEntity
DRUGBANK:DB00583 Levocarnitine Levocarnitine biolink:ChemicalEntity
UMLS:C0007258 carnitine carnitine biolink:NamedThing
LOINC:MTHU001931 Carnitine Carnitine biolink:NamedThing
LOINC:LP14482-1 Carnitine Carnitine biolink:NamedThing
LOINC:LA16918-7 Carnitine Carnitine biolink:DiseaseOrPhenotypicFeature
UMLS:C0600146 Alcar Alcar biolink:ChemicalEntity
UMLS:C0887516 Acetylcarnitine, (R)-Isomer Acetylcarnitine, (R)-Isomer biolink:ChemicalEntity
UMLS:C0633601 Medosan Medosan biolink:ChemicalEntity
MESH:D000108 Acetylcarnitine Acetylcarnitine biolink:ChemicalEntity
MESH:D002331 Carnitine Carnitine biolink:NamedThing
UMLS:C0206800 L-propionylcarnitine L-propionylcarnitine biolink:ChemicalEntity
UMLS:C0894393 propionylcarnitine, (R)-isomer propionylcarnitine, (R)-isomer biolink:ChemicalEntity
UMLS:C0072196 propionylcarnitine propionylcarnitine biolink:ChemicalEntity
MESH:C003223 propionylcarnitine propionylcarnitine biolink:ChemicalEntity
NCIT:C26657 Levocarnitine Levocarnitine biolink:NamedThing
NCIT:C87329 Acetylcarnitine Acetylcarnitine biolink:ChemicalEntity
NCIT:C82599 Carnitine Carnitine biolink:NamedThing
NDDF:000932 carnitine carnitine biolink:NamedThing
NDDF:003576 levocarnitine levocarnitine biolink:ChemicalEntity
NDDF:006988 acetylcarnitine acetylcarnitine biolink:ChemicalEntity
UMLS:C5440668 levocarnitine propionate levocarnitine propionate biolink:ChemicalEntity
NDDF:018603 levocarnitine propionate levocarnitine propionate biolink:ChemicalEntity
PDQ:CDR0000301896 levocarnitine levocarnitine biolink:NamedThing
RXNORM:42955 levocarnitine levocarnitine biolink:Drug
RXNORM:193 acetylcarnitine acetylcarnitine biolink:Drug
RXNORM:2106 carnitine carnitine biolink:Drug
VANDF:4018934 Levocarnitine Levocarnitine biolink:ChemicalEntity
VANDF:4020953 Carnitine Carnitine biolink:NamedThing
VANDF:4020870 L-carnitine L-carnitine biolink:ChemicalEntity
VANDF:4029065 Acetylcarnitine Acetylcarnitine biolink:ChemicalEntity
CHEBI:28867 O-propanoylcarnitine O-propanoylcarnitine biolink:MolecularEntity
CHEBI:73024 O-acetylcarnitine O-acetylcarnitine biolink:MolecularEntity
CHEBI:53210 O-propanoyl-L-carnitine O-propanoyl-L-carnitine biolink:MolecularEntity
CHEBI:15960 O-acetylcarnitinium O-acetylcarnitinium biolink:MolecularEntity
CHEBI:3424 carnitinium carnitinium biolink:MolecularEntity
CHEBI:16347 (R)-carnitine (R)-carnitine biolink:MolecularEntity
CHEBI:17126 carnitine carnitine biolink:MolecularEntity
CHEBI:57589 O-acetyl-L-carnitine O-acetyl-L-carnitine biolink:MolecularEntity
CHEBI:39547 (R)-carnitinium (R)-carnitinium biolink:MolecularEntity
CHEMBL.COMPOUND:CHEMBL1149 LEVOCARNITINE LEVOCARNITINE biolink:SmallMolecule
CHEMBL.COMPOUND:CHEMBL172513 CARNITINE CARNITINE biolink:SmallMolecule
CHEMBL.COMPOUND:CHEMBL1229656 DEXTROCARNITINE DEXTROCARNITINE biolink:SmallMolecule
CHEMBL.COMPOUND:CHEMBL1358846     biolink:SmallMolecule
CHEMBL.COMPOUND:CHEMBL1516469 LEVOCARNITINE PROPIONATE LEVOCARNITINE PROPIONATE biolink:SmallMolecule
CHEMBL.COMPOUND:CHEMBL1620698 3-carboxy-2-hydroxy-N,N,N-trimethylpropan-1-aminium 3-carboxy-2-hydroxy-N,N,N-trimethylpropan-1-aminium biolink:SmallMolecule
CHEMBL.COMPOUND:CHEMBL1697733 ACETYLCARNITINE ACETYLCARNITINE biolink:SmallMolecule
CHEMBL.COMPOUND:CHEMBL2074916 Propionyl-Carnitine Propionyl-Carnitine biolink:SmallMolecule
CHEMBL.COMPOUND:CHEMBL2107420 LEVOCARNITINE PROPIONATE HYDROCHLORIDE LEVOCARNITINE PROPIONATE HYDROCHLORIDE biolink:SmallMolecule
CHEMBL.COMPOUND:CHEMBL3392074 SID11113598 SID11113598 biolink:SmallMolecule
PathWhiz.Compound:44 L-Carnitine L-Carnitine biolink:SmallMolecule
PathWhiz.Compound:129 L-Acetylcarnitine L-Acetylcarnitine biolink:SmallMolecule
PathWhiz.Compound:658 Propionylcarnitine Propionylcarnitine biolink:SmallMolecule
DRUGBANK:DB02648 (3-Carboxy-2-(R)-Hydroxy-Propyl)-Trimethyl-Ammonium (3-Carboxy-2-(R)-Hydroxy-Propyl)-Trimethyl-Ammonium biolink:SmallMolecule
DRUGBANK:DB15980 Levocarnitine propionate Levocarnitine propionate biolink:SmallMolecule
HMDB:HMDB0000062 L-Carnitine L-Carnitine biolink:SmallMolecule
HMDB:HMDB0000201 L-Acetylcarnitine L-Acetylcarnitine biolink:SmallMolecule
HMDB:HMDB0000824 Propionylcarnitine Propionylcarnitine biolink:SmallMolecule
HMDB:HMDB0240773 DL-Acetylcarnitine DL-Acetylcarnitine biolink:SmallMolecule
REACT:R-ALL-390274 Propionylcarnitine [peroxisomal matrix] Propionylcarnitine [peroxisomal matrix] biolink:BiologicalEntity
REACT:R-ALL-390287 ACAR [peroxisomal matrix] ACAR [peroxisomal matrix] biolink:BiologicalEntity
REACT:R-ALL-390294 CAR [peroxisomal matrix] CAR [peroxisomal matrix] biolink:BiologicalEntity
REACT:R-ALL-201023 CAR [mitochondrial matrix] CAR [mitochondrial matrix] biolink:BiologicalEntity
REACT:R-ALL-164988 CAR [extracellular region] CAR [extracellular region] biolink:BiologicalEntity
REACT:R-ALL-30235 CAR [cytosol] CAR [cytosol] biolink:BiologicalEntity
REACT:R-ALL-549207 CAR [mitochondrial intermembrane space] CAR [mitochondrial intermembrane space] biolink:BiologicalEntity
DrugCentral:513 (-)-Carnitine (-)-Carnitine biolink:ChemicalEntity
DrugCentral:64 acetylcarnitine acetylcarnitine biolink:ChemicalEntity
DrugCentral:4040 levocarnitine propionate HCl levocarnitine propionate HCl biolink:ChemicalEntity
KEGG.COMPOUND:C00318     biolink:SmallMolecule
KEGG.COMPOUND:C00487     biolink:SmallMolecule
KEGG.COMPOUND:C02571     biolink:SmallMolecule
KEGG.COMPOUND:C03017     biolink:SmallMolecule
KEGG.DRUG:D02176     biolink:Drug
KEGG.DRUG:D04713 Levocarnitine propionate hydrochloride (USAN) Levocarnitine propionate hydrochloride (USAN) biolink:Drug

This might want to be considered when thinking about #307. This also reminds me of #277 and #256.

The (Hepatitis)-[subclass of]->liver edge is from OMIM:

OMIM:MTHU046633---rdfs:subClassOf---None---None---None---OMIM:MTHU000220---umls_source:OMIM
OMIM:MTHU038293---rdfs:subClassOf---None---None---None---OMIM:MTHU000220---umls_source:OMIM
OMIM:MTHU067436---rdfs:subClassOf---None---None---None---OMIM:MTHU000220---umls_source:OMIM

All of these OMIM nodes (OMIM:MTHU000220, OMIM:MTHU046633, OMIM:MTHU038293, and OMIM:MTHU067436) are deprecated. This ties into #129 (regarding deprecated nodes).

ecwood commented 1 year ago

Per https://bioportal.bioontology.org/ontologies/OMIM?p=classes&conceptid=MTHU000220, hepatitis is stored as a subclass of liver. We may need to change how we import OMIM if this is important, because this seems to be exactly how OMIM is structured. There are a lot of disease subclasses of liver.