Difference between revisions of "WormBase-Caltech Weekly Calls"
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*Like to have rough draft by end of July | *Like to have rough draft by end of July | ||
*Including things we are doing now that are obvious | *Including things we are doing now that are obvious | ||
| − | * | + | *30 pages total |
*10 pages for Caltech, likely | *10 pages for Caltech, likely | ||
*Focus on: Gene function, transcriptional networks, pathways | *Focus on: Gene function, transcriptional networks, pathways | ||
| Line 35: | Line 35: | ||
*Not caught up on RNAi and allele curation by end of this term | *Not caught up on RNAi and allele curation by end of this term | ||
*Logical extensions to GO (we will discuss next week) | *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 statemetns 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 biolgy | ||
| + | *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 detali | ||
| + | *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 | ||
| + | |||
| + | |||
| + | |||
| + | Wikipathways | ||
Revision as of 18:42, 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 statemetns 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 biolgy
- 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 detali
- 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
Wikipathways
