APIPlanning

API planning

Genes

Given an ID return useful basic information:

• symbol
• product
• transcript ID(s)
• protein ID(s)
• location (per transcript)
  • CDS start/stop
  • gene start/stop
  • exon cooords
• characterisation status
• type
• product size
• synonyms
• biological process overview (GO slim)
• number of annotations?
• viability status
• list of (systematic) allele IDs (issue 986)
• taxonomic conservation
• orthologs/paralogs with reference
• transcripts
  • IDs
  • coordination, introns, exons
• protein sequence
• mRNA sequence
• warnings / comments?
• external IDs?
  • UniProtKB
  • BioGRID
  • SPD / RIKEN

Gene ID mapper

This is probably the most useful API.

• example: submit some UniProt IDs and return pombe IDs (or vice versa)
• look up orthologs

GO annotation

• by gene ID?
• by reference

Phenotype annotation

• by gene ID or reference?

Ontology term lookup

Return:

• term name
• ontology name
• aspect
• descendents / ancestors?
• the IDs, evidence and references of the genes annotated with the term

References / PMIDs

Return:

• the genes for the publication
• annotation?