The States 8

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Proposal for common reference ontologies/vocabularies (The States 8)

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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