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OpenBEL / resource-generator

Python modules to generate BEL resource documents.
Apache License 2.0
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Use identifiers.org URIs for ConceptScheme and Concept resources #58

Open abargnesi opened 9 years ago

abargnesi commented 9 years ago

If we can create our resources using the http://identifiers.org/... URI / URL values then our SKOS RDF becomes more convenient to consumers.

We could then link BEL RDF to identifiers.org Concept resources through the hasConcept property. See OpenBEL/bel.rb#65.

ncatlett commented 8 years ago

short term plan - provide owl:sameAs mappings for bel concept URIs to identifiers.org in separate file

ncatlett commented 8 years ago
prefix type openbel uri miriam collection identifiers.org notes
EGID namespace http://www.openbel.org/bel/namespace/entrez-gene/ MIR:00000069 http://identifiers.org/ncbigene/
SP namespace http://www.openbel.org/bel/namespace/swissprot/ MIR:00000005 http://identifiers.org/uniprot/ uniprot includes swissprot
HGNC namespace http://www.openbel.org/bel/namespace/hgnc-human-genes/ MIR:00000080 http://identifiers.org/hgnc/
RGD namespace http://www.openbel.org/bel/namespace/rgd-rat-genes/ MIR:00000047 http://identifiers.org/rgd/
MGI namespace http://www.openbel.org/bel/namespace/mgi-mouse-genes/ MIR:00000037 http://identifiers.org/mgd/
AFFX namespace http://www.openbel.org/bel/namespace/affy-probeset/ MIR:00000394 http://identifiers.org/affy.probeset/ site requires registration and user login
SFAM namespace http://www.openbel.org/bel/namespace/selventa-protein-families/ N/A N/A
GOBP namespace http://www.openbel.org/bel/namespace/go-biological-process/ MIR:00000022 http://identifiers.org/go/
GOCC namespace http://www.openbel.org/bel/namespace/go-cellular-component/ MIR:00000022 http://identifiers.org/go/
MESHC namespace http://www.openbel.org/bel/namespace/mesh-chemicals/ MIR:00000473 http://identifiers.org/mesh.2013/ most recent MeSH not available
MESHCS namespace; annotation http://www.openbel.org/bel/namespace/mesh-cellular-structures/ MIR:00000473 http://identifiers.org/mesh.2013/ most recent MeSH not available
MESHD namespace; annotation http://www.openbel.org/bel/namespace/mesh-diseases/ MIR:00000473 http://identifiers.org/mesh.2013/ most recent MeSH not available
MESHPP namespace http://www.openbel.org/bel/namespace/mesh-processes/ MIR:00000473 http://identifiers.org/mesh.2013/ most recent MeSH not available
MESHA annotation http://www.openbel.org/bel/namespace/mesh-anatomy/ MIR:00000473 http://identifiers.org/mesh.2013/ most recent MeSH not available
CL annotation http://www.openbel.org/bel/namespace/cell-ontology/ MIR:00000110 http://identifiers.org/cl/
CLO annotation http://www.openbel.org/bel/namespace/cell-line-ontology/ can't find in MIRIAM?
DO namespace; annotation http://www.openbel.org/bel/namespace/disease-ontology/ MIR:00000233 http://identifiers.org/doid/
CHEBI namespace http://www.openbel.org/bel/namespace/chebi/ MIR:00000002 http://identifiers.org/chebi/
TAXON annotation http://www.openbel.org/bel/namespace/ncbi-taxonomy/ MIR:00000006 http://identifiers.org/taxonomy/
UBERON annotation http://www.openbel.org/bel/namespace/uberon/ MIR:00000446 http://identifiers.org/uberon/
SDIS namespace http://www.openbel.org/bel/namespace/selventa-legacy-diseases/ N/A
SCOMP namespace http://www.openbel.org/bel/namespace/selventa-named-complexes/ N/A
SCHEM namespace http://www.openbel.org/bel/namespace/selventa-legacy-chemicals/ N/A
EFO annotation http://www.openbel.org/bel/namespace/experimental-factor-ontology MIR:00000391 http://identifiers.org/efo/ using for cell line annotations