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Wednesday, January 30, 2013

CHEMINF example #2: database identifiers

As a second example (see this first example), I will give a few pointers on how you can semantically link database identifiers to molecules with CHEMINF. The CHEMINF example page lists a number of databases, reproduced here:

ResourceLabel
CHEMINF_000405ChemSpider identifier
CHEMINF_000406DrugBank identifier
CHEMINF_000407ChEBI identifier
CHEMINF_000408HMDB identifier
CHEMINF_000409KEGG identifier
CHEMINF_000410Wikipedia identifier
CHEMINF_000411Reactome identifier
CHEMINF_000412PubChem identifier

The matching CHEMINF encoding structure looks identical to that for the InChI, by just replacing the CHEMINF_000113 for InChI by the resource for the database. For example, for HMDB and Wikipedia we get:

:Methane rdfs:subClassOf cheminf:CHEMINF_000000 ;
  rdfs:label "methane"@en ;
 cheminf:CHEMINF_000200 [
   a cheminf:CHEMINF_000408 ;
   cheminf:SIO_000300 "HMDB02714" . ] ;
  cheminf
:CHEMINF_000200 [     a cheminf:CHEMINF_000410 ;     cheminf:SIO_000300 "Methane" .   ] .

A full overview of database identifiers is, obviously, available from the ontology itself.