The States 8
Proposal for common reference ontologies/vocabularies (The States 8)
(To go back to the top page of the NCBC Scientific Ontologies discussion click http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies)
As a starting list of established standards we can/need to live with:
NCBI taxonomy
Gene names and symbols
Human - HGNC Mouse - JAX/MGI Drosophila - flybase C. elegans - wormbase Saccharomyces cerevisiae - SGDB
Protein names derived from gene names
Primary molecular sequence data
IUPAC single letter
Genomic sequence coordinates
NCBI genome builds
Gene/Protein sequences
NCBI RefSeq
I would like to add:
MeSH headings Gene Ontology
But MeSH and GO overlap in numerous areas and mapping between them is non-trivial. de facto, GO => model organism annotation while MeSH => literature indexing, but that does not tell us which to use in describing our own findings. My vote is for MeSH because it covers disease states, provides useful synonym data, and the links to literature are important, but there are lots of areas where specialized ontologies like GO offer useful detail not present in MeSH.
David States