Extension of Protein2GO to non-UniProtKB Identifiers
Conference Call Agenda
Google Spreadsheet
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
- Examples
- 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
- Examples
- 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
- capable_of relations