Issue/How and whether to indicate what records are about
What has been done before:
LSRN primary types: DNA, article, chemical compound, chemical substance, cluster of nucleotide sequences, concept, drug, enzyme, gene, nucleotide sequence, pathway, protein
GO 'objects': AGRICOLA call number, Accession, Accession (for reference), Accession ID, Accession Number, Accession number, Cluster identifier, EC enzyme identifier, ECK accession number (E. coli K-12 gene identifier), EcoGene Accession Number, EcoGene Primary Gene Name, Enzyme identifier, Enzyme or Compound, Gene Identifier, Gene identifier, Gene name (gene symbol in mammalian nomenclature), Gene symbol, Gene/protein identifier, Identifier, Identifier (any), Identifier for CGD Loci, Identifier for SGD Loci, Interaction identifier, Literature Reference Identifier, Locus, Maize gene name, MaizeGDB Object ID Number, MeSH heading, NASC code Identifier, Pathway, Pathway identifier, Peptidase family identifier, Prefix, Protein identifier, Protein modification identifier, QTL identifier, Receptor code, Reference, Restriction enzyme name, Sequence accession number, TC accession, cDNA clone identifier, mRNA identifier, ontology term, prediction tool, reference locator
Uniprot categories: 2D gel databases, 3D structure databases, Enzyme and pathway databases, Family and domain databases, Gene expression databases, Genome annotation databases, Ontologies, Organism-specific databases, Other, PTM databases, Phylogenomic databases, Polymorphism databases, Protein family/group databases, Protein-protein interaction databases, Proteomic databases, Proteomics databases, Sequence databases
Miriam tags: annotation, bibliography, chemical, clustering, disease, disorder, domain, drug, enzyme, eukaryotic, expression, gene, genome, human, interaction, kinetics, lipid, mammalian, mass_spectrometry, microarray, model, nucleotide, ontology, pathway, phenotype, protein, reaction, registry, sequence, structure, taxonomy
Proposal:
- We allow multiple indications of what the records are about.
- Subjects are considered in union and are recorded at the databank level, since databanks can have records about different things and we don't necessarily know this information at a record level.
- We use (at least) the foaf:topic property to record these. Vocabularies used here are either from: MeSH, NCBI Taxonomy, OBO Foundry
