RefGenome12Jun07 Phone Conference (Archived): Difference between revisions
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*'''Strategies for identifying orthologs: Judy, Petra, Karen, DongHui and Kimberley''' | *'''Strategies for identifying orthologs: Judy, Petra, Karen, DongHui and Kimberley''' | ||
- now = YOGY, inparanoid, treefam | - now = YOGY, inparanoid, treefam <br> | ||
- one issue is about using consistent strategies | - one issue is about using consistent strategies<br> | ||
- we'd like to call in an expert at the meeting to help us | - we'd like to call in an expert at the meeting to help us<br> | ||
- Judy: orthology analysis: we want to have tools but we need to make sure we dont user-infer from that | - Judy: orthology analysis: we want to have tools but we need to make sure we dont user-infer from that <br> | ||
- Rex: it's about specificity | - Rex: it's about specificity<br> | ||
- KarenC: different tools give different results; I'd like to know why and understand how those tools work | - KarenC: different tools give different results; I'd like to know why and understand how those tools work<br> | ||
- 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 | - 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 <br> | ||
- Kimberley: also noticed different results with different tools | - Kimberley: also noticed different results with different tools<br> | ||
- 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 | - 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<br> | ||
- MaryD/David: we'd like to to produce a tool that would help make ISS annotations | - MaryD/David: we'd like to to produce a tool that would help make ISS annotations<br> | ||
- Emily: if this is automated, it should be IEA | - Emily: if this is automated, it should be IEA<br> | ||
- Rex: I think we should look at the superset of all the ref genome species (and do what??) | - Rex: I think we should look at the superset of all the ref genome species (and do what??)<br> | ||
*'''How to prioritize disease genes: Rex, Pascale, Emily''' | *'''How to prioritize disease genes: Rex, Pascale, Emily''' | ||
- Emily: will NCBI display that set of genes? This is a nice morbid map to provide and would give publicity | - Emily: will NCBI display that set of genes? This is a nice morbid map to provide and would give publicity<br> | ||
- Ruth: write a paper? | - Ruth: write a paper?<br> | ||
- Rex: important good addition | - Rex: important good addition<br> | ||
- Emily: do we have a target number of genes? | - Emily: do we have a target number of genes? <br> | ||
- Rex, Judy: all disease genes? | - Rex, Judy: all disease genes?<br> | ||
- Emily: do the genes have to be in morbid map? | - Emily: do the genes have to be in morbid map?<br> | ||
- Pascale: if there is a paper, then it's a good target gene. Data must be convincing (not just expression) | - Pascale: if there is a paper, then it's a good target gene. Data must be convincing (not just expression)<br> | ||
- Judy: new ways to target new genes? | - Judy: new ways to target new genes?<br> | ||
*'''How to assess the progress made towards curation of reference genome genes; strategies for improvement (Rex, Emily, Susan''' | *'''How to assess the progress made towards curation of reference genome genes; strategies for improvement (Rex, Emily, Susan''' | ||
- 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. | - 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. | - David: We leave the lines with no orthologs blank. <br> | ||
- Rex: We had agreed to write it down that we checked | - Rex: We had agreed to write it down that we checked <br> | ||
- We should have a monthly meeting and everyone would provide stats | - We should have a monthly meeting and everyone would provide stats<br> | ||
# Review annotation stats. | # Review annotation stats. |
Revision as of 11:33, 12 June 2007
Attendees
- 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
- Plan to develop proposals for main issues on agenda
- We should be able to have the meeting at Princeton after the GOC meeting
- Strategies for identifying orthologs: Judy, Petra, Karen, DongHui and Kimberley
- 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
- Judy: orthology analysis: we want to have tools but we need to make sure we dont user-infer 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??)
- How to prioritize disease genes: Rex, Pascale, Emily
- 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?
- 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: new ways to target new genes?
- How to assess the progress made towards curation of reference genome genes; strategies for improvement (Rex, Emily, Susan
- 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
- Review annotation stats.
- Regular monthly phone conference. Use to review stats, open ref genome source forge items
- Other issues? (no other issues)