RefGenome12Jun07 Phone Conference (Archived): Difference between revisions
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===3. How to assess the progress made towards curation of reference genome genes; strategies for improvement | ===3. How to assess the progress made towards curation of reference genome genes; strategies for improvement=== | ||
- We need to have a way to measure progress; right now it's rather crude. The data Rex sent last week was just counting how many genes each database has looked at. It included genes with no orthologs. <br> | - We need to have a way to measure progress; right now it's rather crude. The data Rex sent last week was just counting how many genes each database has looked at. It included genes with no orthologs. <br> | ||
- David: We leave the lines with no orthologs blank. <br> | - David: We leave the lines with no orthologs blank. <br> | ||
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- Rex: we discussed how many papers needs to be curated at the last GOC meeting (ie, we dont need to do everything)<br> | - Rex: we discussed how many papers needs to be curated at the last GOC meeting (ie, we dont need to do everything)<br> | ||
===4. Review of progress toward database and tool development (software group)=== | <pre> | ||
ACTION ITEM: Rex, Karen, Emily, Susan will write a list of information needed from curators to measure annotation progress | |||
</pre> | |||
===4. Discussions regarding metrics, including making a plan for how to use metrics=== | |||
<pre> | |||
ACTION ITEM: Rex, Judy, Ruth will summarize ideas on to how to capture breath and depth of annotations | |||
</pre> | |||
===5. Review of progress toward database and tool development (software group)=== | |||
<pre>ACTION ITEM: Mary, Sohel, Chris will send a summary of what is being done | |||
by the software group</pre> | |||
- See wiki page<br> | - See wiki page<br> | ||
===6. Annotation consistency discussion=== | ===6. Annotation consistency discussion=== |
Revision as of 13:23, 12 June 2007
Present
- Rex Chisholm (dictyBase)
- Petra Fey (dictyBase)
- Pascale Gaudet (dictyBase)
- Karen Christie (SGD)
- Eurie Hong (SGD)
- Ruth Lovering (HGNC)
- Fiona McCarthy (AgBase)
- Judy Blake (MGI)
- David Hill (MGI)
- Harold Drabkin (MGI)
- Mary Dolan (MGI)
- Emily Dimmer (GOA)
- Kimberly Van Auken (wormbase)
- Donghui Li(TAIR)
- Doug Howe (zfin)
- Susan Tweedie (flybase)
Agenda
Discuss agenda items for meeting
- We should be able to have the meeting at Princeton after the GOC meeting
1. Strategies for identifying orthologs
- now = YOGY, inparanoid, treefam
- one issue is about using consistent strategies
- we'd like to call in an expert at the meeting to help us, either Richard Durbin (pfam, treefam), Erik Sonnhammer (pfam, in paranoid), Paul Thomas (Panther)
- Judy: orthology analysis: we want to have tools but we need to make sure we dont inappropriately infer information from that
- Rex: it's about specificity
- KarenC: different tools give different results; I'd like to know why and understand how those tools work
- Judy: I completely agree. We need to have by the meeting a white paper about how those tools work to provide a basis for discussion
- Kimberley: also noticed different results with different tools
- Emily: GAO has started to transfer electronic annotations; it's hard to keep track of the orthology information with different genome versions, especially for multispecies databases
- MaryD/David: we'd like to to produce a tool that would help make ISS annotations
- Emily: if this is automated, it should be IEA
- Rex: I think we should look at the superset of all the ref genome species (and do what??)
ACTION ITEM: Judy, Petra, Karen, DongHui and Kimberley will write a write paper with an overview of how the different tools work, algorithm explanations, order of preference and pitfalls in identifying orthologs
2. How to prioritize disease genes
- Emily: will NCBI display that set of genes? This is a nice morbid map to provide and would give publicity
- Ruth: write a paper?
- Rex: important good addition
- Emily: do we have a target number of genes?
- Rex, Judy: all disease genes (~20,000)
- Emily: do the genes have to be in morbid map?
- Pascale: if there is a paper, then it's a good target gene. Data must be convincing (not just expression)
- Judy: Should we think of new ways to target new genes? including complex diseases
ACTION ITEM: Rex, Pascale, Emily will summarize the strategy used to identifying target genes and suggest possible improvements
3. How to assess the progress made towards curation of reference genome genes; strategies for improvement
- We need to have a way to measure progress; right now it's rather crude. The data Rex sent last week was just counting how many genes each database has looked at. It included genes with no orthologs.
- David: We leave the lines with no orthologs blank.
- Rex: We had agreed to write it down that we checked
- We should have a monthly meeting and everyone would provide stats
- Synchronicity of curation: it would be more helpful if we were all curating at the same time
- (a few) perhaps there are too many genes per month?
- Rex: we discussed how many papers needs to be curated at the last GOC meeting (ie, we dont need to do everything)
ACTION ITEM: Rex, Karen, Emily, Susan will write a list of information needed from curators to measure annotation progress
4. Discussions regarding metrics, including making a plan for how to use metrics
ACTION ITEM: Rex, Judy, Ruth will summarize ideas on to how to capture breath and depth of annotations
5. Review of progress toward database and tool development (software group)
ACTION ITEM: Mary, Sohel, Chris will send a summary of what is being done by the software group
- See wiki page
6. Annotation consistency discussion
- Karen: John Mullen annotation consistency study --we'll see if data is available
- Kim: maybe hard to compare across such different organisms
(Pascale, Donghui?)
7. Other points
- Karen E wants a gff3 file
- Judy: she wanted that for some tool development.
- inheriting annotations
- web presence
Review annotation stats
Regular monthly phone conference. Use to review stats, open ref genome source forge items
- Every second Tuesday of each month; alternate times: 8 AM/11AM Pacific time
- Next meeting: Tuesday July 10, 1 PM CDT (11 AM PDT, 7 PM BST)