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
Minutes
In attendance: Chris, Fiona, Harold, Judy, Kimberly, Paul S., Petra, Rama, Sandra
Unfortunately, people from the UK were not able to call in to the conference line, so we were missing Rachael, Tony, Claire, Susan, amongst others.
- Summary of issue: some entities that curators would like to use for GO annotation cannot currently be used with Protein2GO
- Examples:
- Proteins that don't have UniProtKB IDs
- Gene IDs
- ncRNA IDs
- Protein Complex IDs
- Examples:
- There are two parallel issues here wrt curation:
- What entities are needed and how to use them in Protein2GO
- How to consistently represent annotations to other entities (e.g. protein complexes) across the consortium
- Issue #1
- It seems that there is agreement on which database IDs would be helpful to start:
- MOD gene IDs
- NCBI RefSeq IDs
- Note that UniProt is willing to add protein IDs for proteins not currently represented
- Protein complex IDs - IntAct, RACE-PRO
- IntAct is in discussion/development with UniProt about using web services to annotate to protein complex IDs
- MOD protein IDs
- RNA Central
- It seems that there is agreement on which database IDs would be helpful to start:
Action Item: Kimberly will follow up with an email to ask Tony what would be most helpful for groups to provide wrt external IDs.
- Issue #2
- Representing annotations to entities like protein complexes in the GAFs/GPADs
- This issue will also be discussed on the Tuesday, GO annotation calls
- We want to make sure we're consistent across GO about propagating BP, MF, and CC annotations to complex members
- Annotations to protein complex identifiers - should these be in a separate GAF?