Extension of Protein2GO to non-UniProtKB Identifiers: Difference between revisions
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*Proteins not in UniProtKB | *Proteins not in UniProtKB | ||
*ncRNAs | *ncRNAs | ||
**C. elegans gene lin-4 encodes a miRNA that regulates gene expression during larval development | **Examples | ||
***Currently annotations are made to the WB gene ID | ***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 (variations not associated with a specific gene) | *Orphan genes (variations not associated with a specific gene) | ||
**C. elegans gene abc-1 is defined by a variation that results in defective chromosome segregation | **Examples | ||
***Currently annotations are made to the WB gene ID | ***C. elegans gene abc-1 is defined by a variation that results in defective chromosome segregation | ||
****Currently annotations are made to the WB gene ID | |||
*Protein complexes | *Protein complexes | ||
Revision as of 16:50, 5 December 2013
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
- C. elegans gene lin-4 encodes a miRNA that regulates gene expression during larval development
- Examples
- Orphan genes (variations not associated with a specific gene)
- Examples
- C. elegans gene abc-1 is defined by a variation that results in defective chromosome segregation
- Currently annotations are made to the WB gene ID
- C. elegans gene abc-1 is defined by a variation that results in defective chromosome segregation
- 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?