Reading Relations And Synonyms From Chebi Ontology
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Entering edit mode
11.6 years ago
Biesterfeld ▴ 30

Hey there,

I am trying to read relations from the ChEBI ontology using the ontoCAT R-package:

ontology <- getOntology( "ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo" )
getTermChildrenById( ontology, "CHEBI_24431" )
term <- getTermById( ontology, "CHEBI_36531" ) 
getTermParents( ontology, term )

The code above works absolutely fine. However, getOntologyRelationNames(ontology) gives an empty list as well as

getTermRelationNames( ontology, term )
getTermSynonyms( ontology, term )

will, although the term has relations and synonyms:

[Term]
id: CHEBI:36531
name: (2Z,4E)-5-carboxy-2,3,5-trichloropenta-2,4-dienoate
def: "A 2,3,5-trichloro-cis,cis-muconate(1-) that has formula C6H2Cl3O4." []
synonym: "(2Z,4E)-5-carboxy-2,3,5-trichloropenta-2,4-dienoate" EXACT IUPAC_NAME [IUPAC:]
synonym: "C6H2Cl3O4" RELATED FORMULA [ChEBI:]
synonym: "OC(=O)C(\\Cl)=C/C(Cl)=C(/Cl)C([O-])=O" RELATED SMILES [ChEBI:]
synonym: "InChI=1S/C6H3Cl3O4/c7-2(4(9)6(12)13)1-3(8)5(10)11/h1H,(H,10,11)(H,12,13)/p-1/b3-1+,4-2-" RELATED InChI [ChEBI:]
synonym: "InChIKey=AHDWVTPNJCBFTN-TZFCGSKZSA-M" RELATED InChIKey [ChEBI:]
is_a: CHEBI:35695
is_a: CHEBI:38427
relationship: is_tautomer_of CHEBI:38426

Any suggestions what I am doing wrong? Many thanks in advance.

r • 2.2k views
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