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liver diseases subtypes of liver? Chemical returned as phenotype
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.
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).
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.