Revision as of 16:54, 10 July 2007

Agenda

Tuesday July 10, 1 PM CDT (11 AM PDT, 7 PM BST)

Present

Rex Chisholm (dictyBase)
Petra Fey (dictyBase)
Pascale Gaudet (dictyBase)
Sohel Merchant (dictyBase)
Karen Christie (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)
Ranjana Kishore(wormbase)
Tanya Berardini (TAIR)
Donghui Li(TAIR)
Doug Howe (zfin)
Susan Tweedie (flybase)
Val Wood (Sanger- pombe)
Victoria Petri (RGD)
Chris Mungall (NCBO)

Reference Genome meeting update

Judy: will be held 26 and the morning of the 27th in Princeton. Accommodations yet to be organized.

Announcement

We will not have new targets for August. Use that time to catch up with annotations.

Review Action Items

1. ACTION ITEM: Judy, Petra, Karen, DongHui and Kimberley summarize how the different Tools for identifying orthologs work, algorithm explanations, order of preference and pitfalls in identifying orthologs

Judy was away last week, this will be done for the next meeting

2. ACTION ITEM: Rex, Pascale, Emily will summarize the Strategy used to identifying target genes and suggest possible improvements

Current strategy is to use gene from the OMIM morbid map
There was a list of common genes between human, fly and worm that was being used as a test case for PATO annotations; most of these genes were not used as they were not in the OMIM morbid map list
Suggestions: David, Emily others: it would be nice to focus on certain diseases rather than randomly pick genes involved in more or less medically important diseases
Victoria: RGD has several lists of genes implicated in various types of disease, such as cardiovascular, neurological diseases
Ruth: focusing on specific diseases would give more direction to the project and make it easier to justify doing this
Judy: we could chose a disease and one person could read a review and send a list of all relevant genes
Rex: let's do that for the next few months and see how it works

3. ACTION ITEM: Rex, Karen, Emily, Susan will write a list of information needed from curators to measure Annotation progress

Curators feel that 'completely' curating a gene is often impossible (when there is too much literature). We will now refer to 'curation status = comprehensive' rather than complete. This means that the curator feels the annotations for that gene represent well the status of the knowledge regarding the gene's function, process, component.
The column currently labeled 'Date completed' in the individual spreadsheets should be renamed "Curation comprehensive as of (MM-DD-YYYY)
Other stats can be derived from the total number of publications, number of publications chosen for GO, and number of papers curated

4. ACTION ITEM: Rex, Judy, Ruth will summarize ideas on to how to capture Metrics: breath and depth of annotations
5. ACTION ITEM: Mary, Sohel, Chris will send a summary of what is being done by the RG Software group

There is a test server available since this morning

http://rails-dev.bioinformatics.northwestern.edu:24000/curator http://rails-dev.bioinformatics.northwestern.edu:24000/admin

Chris, Sohel and interested curators will have a separate conference call to discuss the tool

Karen wanted to know where the reference genome database was to be held; we don't know that yet

6. ACTION ITEM: Pascale, Donghui will provide a framework for discussing Consistency of annotations across genomes
7. ACTION ITEM: Susan and Rex will present suggestions for Outreach: publicizing the project and developing a web presence

Annotation Progress

How many of the human genes have orthologs identified ?
How many of these have papers associated (are published genes) ?
How many papers associated in total ?
How many papers have been considered for GO curation ?
How many papers provided GO terms ?
How many genes which have papers associated are considered complete/comprehensive ?

Issues with target genes

pombe (Val): takes a long time to triage papers
GOA, pombe: too many genes per month
If too many groups are falling behind, we should consider skipping August
not enough coordination between annotation efforts
pombe/dictyBase: We would like to know when other databases have completed annotation

- Judy suggestion: Change from 'complete' to 'comprehensive'
- Pascale: did we not have a wiki for doing that?

Next meeting

Tuesday August 14, 10 AM CDT (8 AM PDT, 4 PM BST)

@@ Line 43: / Line 43: @@
 . ACTION ITEM: Rex, Karen, Emily, Susan will write a list of information needed from curators to measure [[Annotation progress]] <br>
+* Curators feel that 'completely' curating a gene is often impossible (when there is too much literature). We will now refer to 'curation status = comprehensive' rather than complete. This means that the curator feels the annotations for that gene represent well the status of the knowledge regarding the gene's function, process, component.
+* The column currently labeled 'Date completed' in the individual spreadsheets should be renamed "Curation comprehensive as of (MM-DD-YYYY)
+* Other stats can be derived from the total number of publications, number of publications chosen for GO, and number of papers curated
 . ACTION ITEM: Rex, Judy, Ruth will summarize ideas on to how to capture [[Metrics: breath and depth of annotations]]<br>
@@ Line 52: / Line 54: @@
 * Chris, Sohel and interested curators will have a separate conference call to discuss the tool
 <br>
+* Karen wanted to know where the reference genome database was to be held; we don't know that yet
 . ACTION ITEM: Pascale, Donghui will provide a framework for discussing [[Consistency of annotations across genomes]]<br>
 . ACTION ITEM: Susan and Rex will present suggestions for [[Outreach: publicizing the project and developing a web presence]]<br>

RefGenome10July07 Phone Conference (Archived): Difference between revisions