Extension of Protein2GO to non-UniProtKB Identifiers: Difference between revisions
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Conference Call Agenda | =Conference Call Agenda= | ||
=What types of entity identifiers might be needed?= | ==What types of entity identifiers might be needed?== | ||
*Proteins not in UniProtKB | |||
*ncRNAs | |||
**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) | |||
**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 | |||
See Google spreadsheet: | See Google spreadsheet: | ||
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https://docs.google.com/spreadsheet/ccc?key=0Aiei4RvoiQdqdHBFVEcwXzRvcW94V2JOLVFSNjJaTHc&usp=drive_web#gid=0 | https://docs.google.com/spreadsheet/ccc?key=0Aiei4RvoiQdqdHBFVEcwXzRvcW94V2JOLVFSNjJaTHc&usp=drive_web#gid=0 | ||
=Knowledge Representation= | ==Knowledge Representation== | ||
*What kind of biological statements do we want to make? | *What kind of biological statements do we want to make? | ||
*Given these statements, what is the appropriate resource for the entity IDs? | *Given these statements, what is the appropriate resource for the entity IDs? | ||
*How will this be represented in the GAFs/GPADs? | *How will this be represented in the GAFs/GPADs? | ||
=Practical Considerations= | ==Practical Considerations== | ||
*How many of each type? | *How many of each type? | ||
*ID stability - if there is churn, can IDs be mapped forward, not go stale? | *ID stability - if there is churn, can IDs be mapped forward, not go stale? | ||
Revision as of 16:16, 5 December 2013
Conference Call Agenda
What types of entity identifiers might be needed?
- Proteins not in UniProtKB
- ncRNAs
- 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
- 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
- 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
- Protein complexes
See Google spreadsheet:
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?