Difference between revisions of "WormBase-Caltech Weekly Calls"
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LEGO (Logical extensions to GO) | LEGO (Logical extensions to GO) | ||
| − | *Try to use GO annotations to make more expressive | + | *Try to use GO annotations to make more expressive statements about gene function, pathways and processes |
*Prior to this, curators took gene or gene product to describe subcellular localization, molecular function, and processes the product involved in | *Prior to this, curators took gene or gene product to describe subcellular localization, molecular function, and processes the product involved in | ||
| − | *Looking to create much bigger picture of the | + | *Looking to create much bigger picture of the biology |
*LEGO annotations: adding info to typical GO annotation, such as regulation targets | *LEGO annotations: adding info to typical GO annotation, such as regulation targets | ||
**TF has sequence-specific DNA binding activity; now add what the targets are | **TF has sequence-specific DNA binding activity; now add what the targets are | ||
**If TF in nucleus, what cell types? | **If TF in nucleus, what cell types? | ||
| − | **Now we could start to create pathways and describe processes in more | + | **Now we could start to create pathways and describe processes in more detail |
*Being done with OWL, web ontology language | *Being done with OWL, web ontology language | ||
*Example, the dauer pathway; do more examples to see where the holes are | *Example, the dauer pathway; do more examples to see where the holes are | ||
| Line 58: | Line 58: | ||
*Filling in annotation gaps or inconsistencies | *Filling in annotation gaps or inconsistencies | ||
*Start to build annotation models | *Start to build annotation models | ||
| − | + | *Can we integrate with Wikipathways? | |
| − | + | *Community annotations? | |
| − | |||
| − | |||
Revision as of 18:43, 12 July 2012
2012 Meetings
July 12, 2012
Grant Renewal
- Like to have rough draft by end of July
- Including things we are doing now that are obvious
- 30 pages total
- 10 pages for Caltech, likely
- Focus on: Gene function, transcriptional networks, pathways
- How much have we curated? What is our rate of curation?
- What is the backlog? How much left to curate?
- Not caught up on RNAi and allele curation by end of this term
- Logical extensions to GO (we will discuss next week)
- How are we going to measure quality? Metrics?
- Coverage?
- Accuracy?
- What is a/the gold standard? These things aren't generally well defined
- Other species
- Automated triage for papers
- Use nematode Textpresso to estimate what's out there?
LEGO (Logical extensions to GO)
- Try to use GO annotations to make more expressive statements about gene function, pathways and processes
- Prior to this, curators took gene or gene product to describe subcellular localization, molecular function, and processes the product involved in
- Looking to create much bigger picture of the biology
- LEGO annotations: adding info to typical GO annotation, such as regulation targets
- TF has sequence-specific DNA binding activity; now add what the targets are
- If TF in nucleus, what cell types?
- Now we could start to create pathways and describe processes in more detail
- Being done with OWL, web ontology language
- Example, the dauer pathway; do more examples to see where the holes are
- 8 examples from C. elegans: involving cell types, signal transduction pathways, etc.
- Build much broader picture of the biology of the worm
- Filling in annotation gaps or inconsistencies
- Start to build annotation models
- Can we integrate with Wikipathways?
- Community annotations?
