RefGenome12Feb08 Phone Conference (Archived): Difference between revisions

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==ACTION ITEMSs==
==REVIEW ACTION ITEMS==
*  [ACTION ITEM] Go over the issues relating to quality control. Suzi will email the group, and we will set up a meeting with all those who want to participate.  
*  [ACTION ITEM] Go over the issues relating to quality control. Suzi will email the group, and we will set up a meeting with all those who want to participate.  


* [ACTION ITEM]: (Chris/AmiGO) Look into loading IEAs for reference genome set into AmiGO  
* [ACTION ITEM]: (Chris/AmiGO) Look into loading IEAs for reference genome set into AmiGO  
==ONGOING ACTION ITEMS==
(Pascale: Need to clean this up)
[ACTION ITEM]: (Amelia): Fix web page where the number of annotations are to give an estimated number of protein-coding genes; problems: unmapped genes; splice variants; etc. Maybe this should also be on the ref genome page. USE count from gp2protein file-- then it's all consistent.
in progress. Amelia had some questions: what should be taken as the correct number, the number of unique IDs in the first column [the db that produced the file], or the number in the second column [the UniProt or NCBI ID]? I just checked with Dan and he says that the mapping may not necessarily be one to one.
[ACTION ITEM]: all: look at Stan's error reports: http://www.geneontology.org/internal-reports/gp2protein/
[ACTION ITEM]: Chris: generate new report that would show errors that need fixing for the Orthology determination project
[ACTION ITEM]: Chris will provide date on the ISS outliers query so that we dont always review the same annotations.
[ACTION ITEM]: Mary will include IC in the graphs
* Would be nice if we had a report describing when genes are 'comprehensively' curated
in progress
[ACTION ITEM]: can Mary show the date completed on the index page? Possibly - she will try
in progress: Email communication:
Hi, Pascale.
I was in the process of implementing both things when my computer was hit with bad malware,
which I am still dealing with.
The IC part was simple and I posted graphs on a temporary site with the IC annotations but realized that some were incomplete because some groups were not putting in EntrezGene ids, which is now the only sure way to connect the orthologs. That led me to contact each groups to make corrections and to ask that they include all EntrezGene ids. At the point I was hit with the malware so I've been somewhat stalled. When I can get that resolved I will be able to update the graphs and include the
date on the index page.
Mary
[ACTION ITEM]: Discuss at the GOC meeting whether it would be useful to add the 'comprehensively annotated' tag to all genes, somehow? Either in the gene association file or in the database somehow
[ACTION ITEM]: Mike will set up 'annotation' calls?
[ACTION ITEM]: Mike(pascale) merge two email lists (reference genome and annotation) into  'annotation'
*Should we copy them to the SF tracker?
[ACTION ITEM] (Tanya Berardini, Emily Dimmer, Pascale Gaudet, David Hill, Chris Mungall, Kimberly Van Auken): Write up recommendations for usage of ISS, IEA, IC: Report by next meeting???
* Started, [[IEA%2C_ISS%2C_IC_Usage_Discussion]]


==Next conference call==
==Next conference call==

Revision as of 19:32, 8 February 2008

Tuesday February 12, 10 AM CDT (8 AM PDT, 4 PM BST)

Present

Next Reference Genome Meeting

April 20-21, Salt Lake City

This will be followed by a GO Consortium Meeting on April 22 and 23 in Salt Lake City.

Karen Eilbeck: host

Orthology determination

Kara: update


Curation tool update

Chris, Siddhartha, Seth, Mary, Pascale, David, Doug

Updated graphs

Mary

  • I have posted new refG graphs (temporarily) at:

http://proto.informatics.jax.org/prototypes/GOgraphEX/RefGenomeGraphs/ We will move them to the GO site when refG folks have had a chance to review them (some time next week?)

To simplify comparison of organism annotations (and following Chris' lead on detecting outliers) I have modified the comparison matrix to show only high order GO terms, e.g. PEX1 http://proto.informatics.jax.org/prototypes/GOgraphEX/RefGenomeGraphs/5189.html#Slim or POLA http://proto.informatics.jax.org/prototypes/GOgraphEX/RefGenomeGraphs/5422.html#Slim

Please review the graphs and let me know if you notice missing orthologs or annotations -- I am still doing a lot of data editing manually  :(


REVIEW ACTION ITEMS

  • [ACTION ITEM] Go over the issues relating to quality control. Suzi will email the group, and we will set up a meeting with all those who want to participate.
  • [ACTION ITEM]: (Chris/AmiGO) Look into loading IEAs for reference genome set into AmiGO

ONGOING ACTION ITEMS

(Pascale: Need to clean this up)

[ACTION ITEM]: (Amelia): Fix web page where the number of annotations are to give an estimated number of protein-coding genes; problems: unmapped genes; splice variants; etc. Maybe this should also be on the ref genome page. USE count from gp2protein file-- then it's all consistent.

in progress. Amelia had some questions: what should be taken as the correct number, the number of unique IDs in the first column [the db that produced the file], or the number in the second column [the UniProt or NCBI ID]? I just checked with Dan and he says that the mapping may not necessarily be one to one.

[ACTION ITEM]: all: look at Stan's error reports: http://www.geneontology.org/internal-reports/gp2protein/

[ACTION ITEM]: Chris: generate new report that would show errors that need fixing for the Orthology determination project

[ACTION ITEM]: Chris will provide date on the ISS outliers query so that we dont always review the same annotations.


[ACTION ITEM]: Mary will include IC in the graphs

  • Would be nice if we had a report describing when genes are 'comprehensively' curated

in progress

[ACTION ITEM]: can Mary show the date completed on the index page? Possibly - she will try

in progress: Email communication: Hi, Pascale. I was in the process of implementing both things when my computer was hit with bad malware, which I am still dealing with.

The IC part was simple and I posted graphs on a temporary site with the IC annotations but realized that some were incomplete because some groups were not putting in EntrezGene ids, which is now the only sure way to connect the orthologs. That led me to contact each groups to make corrections and to ask that they include all EntrezGene ids. At the point I was hit with the malware so I've been somewhat stalled. When I can get that resolved I will be able to update the graphs and include the date on the index page.

Mary

[ACTION ITEM]: Discuss at the GOC meeting whether it would be useful to add the 'comprehensively annotated' tag to all genes, somehow? Either in the gene association file or in the database somehow


[ACTION ITEM]: Mike will set up 'annotation' calls?

[ACTION ITEM]: Mike(pascale) merge two email lists (reference genome and annotation) into 'annotation'

  • Should we copy them to the SF tracker?


[ACTION ITEM] (Tanya Berardini, Emily Dimmer, Pascale Gaudet, David Hill, Chris Mungall, Kimberly Van Auken): Write up recommendations for usage of ISS, IEA, IC: Report by next meeting???


Next conference call

Tuesday March 11, 2008, 1 PM CDT, 11 AM PDT, 7 PM GMT

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