Extension of Protein2GO to non-UniProtKB Identifiers

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Conference Call Agenda

Google Spreadsheet

https://docs.google.com/spreadsheet/ccc?key=0Aiei4RvoiQdqdHBFVEcwXzRvcW94V2JOLVFSNjJaTHc&usp=drive_web#gid=0


What types of entity identifiers might be needed?

  • Proteins not in UniProtKB
  • ncRNAs
    • Examples
      • C. elegans gene lin-4 encodes a miRNA that regulates gene expression during larval development - Currently annotations are made to the WB gene ID
  • Orphan genes
    • Examples
      • C. elegans gene abc-1 is an uncloned locus defined by a variation that results in defective chromosome segregation - Currently annotations are made to the WB gene ID
  • Protein complexes

Knowledge Representation

  • What kind of biological statements do we want to make?
  • Given these statements, what is the appropriate resource for the entity IDs?
  • How will this be represented in the GAFs/GPADs?

Practical Considerations

  • How many of each type?
  • ID stability - if there is churn, can IDs be mapped forward, not go stale?

Overview of representation of complexes in ontology