Table 1 The prefixes and corresponding namespaces of PubChem subdomains and standardized ontologies

PubChemRDF subdomains

 compound

http://rdf.ncbi.nlm.nih.gov/pubchem/compound/

 substance

http://rdf.ncbi.nlm.nih.gov/pubchem/substance/

 descr

http://rdf.ncbi.nlm.nih.gov/pubchem/descriptor/

 inchikey

http://rdf.ncbi.nlm.nih.gov/pubchem/inchikey/

 syno

http://rdf.ncbi.nlm.nih.gov/pubchem/synonym/

 concept

http://rdf.ncbi.nlm.nih.gov/pubchem/concept/

 reference

http://rdf.ncbi.nlm.nih.gov/pubchem/reference/

 nbr

http://rdf.ncbi.nlm.nih.gov/pubchem/neighbor/

 source

http://rdf.ncbi.nlm.nih.gov/pubchem/source/

 vocab

http://rdf.ncbi.nlm.nih.gov/pubchem/vocabulary#

External RDF resources

 pdbr

http://rdf.wwpdb.org/pdb/

 mesh

http://id.nlm.nih.gov/mesh/

 chembl

http://rdf.ebi.ac.uk/resource/chembl/molecule/

 linkedchem

http://linkedchemistry.info/chembl/chemblid/

Existing ontologies

 rdfs

http://www.w3.org/2000/01/rdf-schema#

RDF schema [55]

 rdf

http://www.w3.org/1999/02/22-rdf-syntax-ns#

RDF [56]

 xsd

http://www.w3.org/2001/XMLSchema#

XML schema [57]

 obo

http://purl.obolibrary.org/obo/

ChEBI [29–31] and UO [34]

 sio/cheminf

http://semanticscience.org/resource/ ^b

CHEMINF [32] and SIO [33]

 cito

http://purl.org/spar/cito/

CiTO [36]

 pdbo

http://rdf.wwpdb.org/schema/pdbx-v40.owl#

PDB ontology

 skos

http://www.w3.org/2004/02/skos/core#

SKOS [37]

 dcterms

http://purl.org/dc/terms/

DCMI terms [35]