Managers 21Oct09: Difference between revisions

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[[Category:GO_Managers_Meetings]]
Participants: Judy, Suzi, Jane, Pascale, Jen, Midori, Chris, David
Participants: Judy, Suzi, Jane, Pascale, Jen, Midori, Chris, David


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*'''David, Chris''': organize the xp webex. (There has been a great tutorial by David OS at the Buffalo Ontology meeting)  
*'''David, Chris''': organize the xp webex. (There has been a great tutorial by David OS at the Buffalo Ontology meeting)  
*'''Jane:''' email Amelia to put xp documentation (for GO users): ongoing
*'''Jane:''' email Amelia to put xp documentation (for GO users): DONE  see [http://www.geneontology.org/GO.ontology.structure.shtml#xp GO Structure and XPs]
*'''Midori''' awaiting webex on XPs before sending announcement mail.  
*'''Midori''' awaiting webex on XPs before sending announcement mail.


==Action items from 09-09 Cambridge GO meeting ==
==Assign people to the Action items from 09-09 Cambridge GO meeting ==
# ACTION: [Judy, Chris, Darren, Suzi] Primary stake holders in GO and PRO need to agree on how GO components and PRO will relate to each other. Next PRO meeting end of April
# ACTION: [Judy, Chris, Darren, Suzi] Primary stake holders in GO and PRO need to agree on how GO components and PRO will relate to each other. Next PRO meeting end of April
# ACTION: [Pascale, Kara, Paul] Ref genome annotation groups need to get ISS annotations from PAINT into their databases this year. This includes having a repository to put the annotations.  
# ACTION: [Pascale, Kara, Paul] Ref genome annotation groups need to get ISS annotations from PAINT into their databases this year. This includes having a repository to put the annotations.  
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Function->Process inferred annotations by IC
Function->Process inferred annotations by IC
# ACTION: [Chris] MODS please look at the F->P IC annotations proposed for your species in http://geneontology.org/scratch/gaf-inference. If you have issues get back to Chris in the next 2 weeks. // there should be a discussion about what evidence code to use  IC-IEA?  
# ACTION: [Chris] MODS please look at the F->P IC annotations proposed for your species in http://geneontology.org/scratch/gaf-inference. If you have issues get back to Chris in the next 2 weeks. // there should be a discussion about what evidence code to use  IC-IEA?  
# ACTION: MODS will load these F->P IC annotations to their database.  
# ACTION: [Chris? ] MODS will load these F->P IC annotations to their database.  
This is related to the reference genome issues. Some  MODs can not integrate GAFs yet.  
This is related to the reference genome issue. Some  MODs can not integrate GAFs yet.  
# ACTION: Taxon constraint checks, report should be sent back to group but not filtered out..still load.
# ACTION: Taxon constraint checks, report should be sent back to group but not filtered out..still load.
# ACTION: Chris check that interontology inferred annotations limited to inference from experimental annotations only.
# ACTION: Chris check that interontology inferred annotations limited to inference from experimental annotations only.


Changes to GO Database management practices
Changes to GO Database management practices
# ACTION: use a more relaxed schedule for building GO Full (quarterly perhaps?)
# ACTION: [Chris] use a more relaxed schedule for building GO Full (quarterly perhaps?)
# ACTION: reduce load of go lite from 3 to 1 time per week.  
# ACTION: [Chris] reduce load of go lite from 3 to 1 time per week.  


XP term request template
XP term request template
# ACTION: implement a version like shown for curators to try before next GO meeting
# ACTION: [Chris] implement a version like shown for curators to try before next GO meeting
# Annotation Relationships (Chris/Jane): There is an implicit relation between an annotation and the gene to which it applies; an explicit relation between annotation and gene would be better. The relations may be like ‘extrinic to’ or ‘acted on during’ to relate annotation to gene  
# Annotation Relationships [Chris/Jane]: There is an implicit relation between an annotation and the gene to which it applies; an explicit relation between annotation and gene would be better. The relations may be like ‘extrinsic to’ or ‘acted on during’ to relate annotation to gene  
#UniPath:  
#UniPath:  
##ACTION:Pascale, Anne, Harold, Chris, Peter D’Eustachio, and Mary Dolan will work together to provide cross products b/t MFunction and Chebi to provide and report back to the group in the Spring meeting
## ACTION: [Pascale, Anne, Harold, Chris, Peter D’Eustachio, and Mary Dolan] will work together to provide cross products b/t MFunction and Chebi to provide and report back to the group in the Spring meeting


Binding terms:  
Binding terms:  
# ACTION:more work needed to iron out HOW to transfer binding term annotations properly to retain all information
# ACTION [Binding term WG]: more work needed to iron out HOW to transfer binding term annotations properly to retain all information
#* Paul NEEDS us to be able to do this for PAINT tree annotation  
#* Paul NEEDS us to be able to do this for PAINT tree annotation  
# ACTION: Current working group will edit the binding term annotation gielines in line with the comments from discussion and distribute to PI’s for approval and then include in guidelines.
# ACTION: Current working group will edit the binding term annotation guidelines in line with the comments from discussion and distribute to PI’s for approval and then include in guidelines.
# ACTION: Paul and Emily interested in joining new working group discussion on ISS/IC topic


(Rex) ACTION:actin-dependent ATPase activity and tubulin-dependent GTPase activity terms are incorrect
 
Other topics:
# ACTION: [Emily] Paul and Emily interested in joining new working group discussion on ISS/IC topic
# ChEBI(Marcus Ennis): Increase effort to get GO and ChEBI aligned
# ChEBI(Marcus Ennis): Increase effort to get GO and ChEBI aligned
# ACTION:Have another annotation camp, perhaps just for current GO curators
# ACTION: [Judy, GO-tops] Have another annotation camp, perhaps just for current GO curators [Geneva?]


==Discussion items==
==Discussion items==


*Function-process proposal [David and Jane]
*Function-process proposal [David, Tanya, Chris and Jane] - in progress.
*GOC meeting - dates fixed? will be last week of March at Stanford, SAB on April 2.
*GOC meeting - dates fixed? will be last week of March at Stanford, SAB on April 2. To be discussed : would the GOC meeting be Tues- Wed or Fri, Sat.  
*After going to the Cardiovascular meeting, Yasmin and David Hill were very interested in carrying out a similar meeting for renal development. However the Kidney research charity's grant could not support travel costs etc. associated with such a meeting. I had a vague recollection that Judy might have some funds to support content meetings (although I may have just dreamt this up!), if so would there be any possibility of financial support coming from GOC for a renal development content meeting? [Emily]
*After going to the Cardiovascular meeting, Yasmin and David Hill were very interested in carrying out a similar meeting for renal development. However the Kidney research charity's grant could not support travel costs etc. associated with such a meeting. I had a vague recollection that Judy might have some funds to support content meetings (although I may have just dreamt this up!), if so would there be any possibility of financial support coming from GOC for a renal development content meeting? [Emily]
**Judy - yes there are funds for content meetings.
**Judy - yes there are funds for content meetings.

Latest revision as of 12:44, 30 June 2014

Participants: Judy, Suzi, Jane, Pascale, Jen, Midori, Chris, David

Agenda: Jane

Minutes: Pascale

Action items from previous calls

  • David, Chris: organize the xp webex. (There has been a great tutorial by David OS at the Buffalo Ontology meeting)
  • Jane: email Amelia to put xp documentation (for GO users): DONE see GO Structure and XPs
  • Midori awaiting webex on XPs before sending announcement mail.

Assign people to the Action items from 09-09 Cambridge GO meeting

  1. ACTION: [Judy, Chris, Darren, Suzi] Primary stake holders in GO and PRO need to agree on how GO components and PRO will relate to each other. Next PRO meeting end of April
  2. ACTION: [Pascale, Kara, Paul] Ref genome annotation groups need to get ISS annotations from PAINT into their databases this year. This includes having a repository to put the annotations.
  3. ACTION: [Pascale, Kara, Paul] Ref genome participating groups need to provide a file of their comprehensively annotated genes. To be discussed - how to do this
  4. ACTION: [Pascale, Kara, Paul, Dan] Keep working on getting the gene indices from the MODs
  5. Species to consider outreach to:
    1. daphnia (Indiana)has GO annotations (Judy: Michael Lynch)
    2. Xenopus : ask Erik Segerdell
    3. Sea Urchin (Judy will investigate: Andy Cameron)
    4. plasmodium (in progress - Suzi, Pascale)
  6. ACTION: [Judy, Pascale] MODs-make an effort to highlight Ref Genome annotation; eventually we need to see high-quality ISS annotations in the MODs
  7. ACTION ITEM: [Pascale, ref genome] Community interaction and outreach: Val presented the form where users annotated their papers : http://www.sanger.ac.uk/Projects/S_pombe/community_curation.shtml . Should we try extending the experiment to other groups? We can try using it when we work with experts on 'annotation projects' such as lung development.
  8. ACTION: [Jane] Build a survey for grant update (Val, Jane, Jen), determine where to send it. (Mike has subscription to SurveyMonkey). Jane will send an email she wrote about that
  9. ACTION: provide two survey urls and compare responses from a targeted list like the submitters to GO help list with responses from a random list of biologists

Infrastructure

  1. ACTION: OBO format 1.3 tags (creation date, etc.) is already in gene ontology ext. Chris will add it to the main GO file.
  2. ACTION: OBO version number added to all OBO files . DONE

GAF publishing pipelines

  1. ACTION: [Suzi] GAF files from PAINT will need to be GAF 2.0 format
  2. ACTION: [Chris] Switch to GAF 2.0 in publishing pipeline with substantially long (3 Months) public notice to this change.
  3. ACTION: [Jane] add notices like this change to GAF 2.0 to GO News Feeds

Unannotated genes and GAFs

  1. ACTION: [Amelia, Chris, in progress] post a clear spec of the desired format for gp2protein files for all MODs-include 1 row for every gene? 1 protein ID per row? No protein ID is OK if no protein is available?
  2. ACTION: [Amelia, Chris, in progress] keep GAF file as is. Provide a new file (gpfile?) to describe gene products. Provide a detailed spec of the contents of this new file. This file may subsume gp2protein

Function->Process inferred annotations by IC

  1. ACTION: [Chris] MODS please look at the F->P IC annotations proposed for your species in http://geneontology.org/scratch/gaf-inference. If you have issues get back to Chris in the next 2 weeks. // there should be a discussion about what evidence code to use IC-IEA?
  2. ACTION: [Chris? ] MODS will load these F->P IC annotations to their database.

This is related to the reference genome issue. Some MODs can not integrate GAFs yet.

  1. ACTION: Taxon constraint checks, report should be sent back to group but not filtered out..still load.
  2. ACTION: Chris check that interontology inferred annotations limited to inference from experimental annotations only.

Changes to GO Database management practices

  1. ACTION: [Chris] use a more relaxed schedule for building GO Full (quarterly perhaps?)
  2. ACTION: [Chris] reduce load of go lite from 3 to 1 time per week.

XP term request template

  1. ACTION: [Chris] implement a version like shown for curators to try before next GO meeting
  2. Annotation Relationships [Chris/Jane]: There is an implicit relation between an annotation and the gene to which it applies; an explicit relation between annotation and gene would be better. The relations may be like ‘extrinsic to’ or ‘acted on during’ to relate annotation to gene
  3. UniPath:
    1. ACTION: [Pascale, Anne, Harold, Chris, Peter D’Eustachio, and Mary Dolan] will work together to provide cross products b/t MFunction and Chebi to provide and report back to the group in the Spring meeting

Binding terms:

  1. ACTION [Binding term WG]: more work needed to iron out HOW to transfer binding term annotations properly to retain all information
    • Paul NEEDS us to be able to do this for PAINT tree annotation
  2. ACTION: Current working group will edit the binding term annotation guidelines in line with the comments from discussion and distribute to PI’s for approval and then include in guidelines.


Other topics:

  1. ACTION: [Emily] Paul and Emily interested in joining new working group discussion on ISS/IC topic
  2. ChEBI(Marcus Ennis): Increase effort to get GO and ChEBI aligned
  3. ACTION: [Judy, GO-tops] Have another annotation camp, perhaps just for current GO curators [Geneva?]

Discussion items

  • Function-process proposal [David, Tanya, Chris and Jane] - in progress.
  • GOC meeting - dates fixed? will be last week of March at Stanford, SAB on April 2. To be discussed : would the GOC meeting be Tues- Wed or Fri, Sat.
  • After going to the Cardiovascular meeting, Yasmin and David Hill were very interested in carrying out a similar meeting for renal development. However the Kidney research charity's grant could not support travel costs etc. associated with such a meeting. I had a vague recollection that Judy might have some funds to support content meetings (although I may have just dreamt this up!), if so would there be any possibility of financial support coming from GOC for a renal development content meeting? [Emily]
    • Judy - yes there are funds for content meetings.
    • I suspect the cast of people coming from the states would be the same as for the heart meeting: Doug, David, Tanya.

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