2008-10 SAB Meeting: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
m (Pascale moved page Oct 2008 SAB Meeting to 2008-10 SAB Meeting)
 
(48 intermediate revisions by 7 users not shown)
Line 1: Line 1:
[[Category:GO_SAB_Meetings]]
=Logistics=
=Logistics=
[[Instructions_for_Registration]]
[[October 2008 Meeting Logistics]]


=Agenda=
==Ontology Development - Blake ==
===Aims and Key accomplishments===
* [[Ontology_Quality_Control|Ontology Quality control]]
* [[:Category:Cross Products | Logic-based cross-product definitions]]
Progress reported at current GOC meeting, plus items reported at SLC GOC meeting (April):
* The [[Regulation_Main_Page|regulates relationships]] have been incorporated into the biological process (BP) ontology.
* New relationship types : spatial relations, etc
*Changes stemming from two content meetings have gone live
**[[Cardiovascular physiology/development]]
**[[Muscle Biology]]
*[[Sensu_Main_Page|Sensu terms]] renamed and rationalized
* New OBO-Edit features (video)
Also see Progress Reports from [[Meeting_Progress_Report_April_2008#Ontology_Development|April]] and [[Ontology_Development_progress_report_for_October_2008_meetings|October]] 2008.


=Agenda=
===Questions for SAB===
*We are committed to creating links between MF and BP, and know that it will facilitate annotation.
**Initially we plan to work on area XY ; does that make sense and are there other suggestions?
*Update on metrics: Are the metrics for ontology development that we now provide useful? What additional metrics should we gather, and how? Are we getting better at providing metrics? And (off on a bit of a tangent) are there any use cases for metrics other than our internal monitoring, SAB reporting, and funding agency reporting (not that we'd stop measuring if there aren't!)?
*Essentially the same questions about quality control measures - are our existing QC practices good; what others can we add; etc.
*Are we getting ontology content submissions/suggestions from a broad enough segment of our users? If not, which other groups (or even individuals) should we target? How can we motivate them to get involved?
*Maybe: ask SAB the questions about content development priorities on GOC meeting agenda.


==User Advocacy - Ashburner ==
==User Advocacy - Ashburner ==
===Key accomplishments===
===Key accomplishments===
* AmiGO 1.6
* AmiGO 1.6
* GOOSE? (Have they seen this already?)
* Help desk report
* Help desk report
* Newsletter
* Newsletter
Line 15: Line 36:


==Annotation - Cherry==
==Annotation - Cherry==
===Key accomplishments===
===Aims and Key accomplishments===
Good annotation outreach efforts have been organized by AgBase, TAIR and PAMGO.   
* Good annotation outreach efforts have been organized by AgBase, TAIR and PAMGO.   
* Changes to GAF
* Annotation camps
* Annotation IRC
* Evidence Code Ontology
* Swiss-Prot committed to start doing GO annotation which will help getting more gene proteins annotated, including proteins from species not currently being annotated. (4 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/PhotosynthesisAnnotationJDeegan.ppt Slides] from Jennifer to explain why other organisms also need to be annotated, leading in to Michael's talk on SwissProt.)
 
===Questions for SAB===
===Questions for SAB===
Due to the lack of available funding, no new annotation groups have been added in this recent period. It is proving to be very difficult for other species database groups to find funding for GO curators.<br>
To help other groups annotate:<br>
Our current approaches to work round this are:<br>
* Write better documentation to enable small community groups and individual users to make anntotations. (Docs by Reference Genome Group.)
* Write better documentation to enable small community groups and individual users to make anntotations. (Docs by Reference Genome Group.)
* Work on making the GO structure more intuitive for users so that when community annotation is made, it is more likely to be accurate. (Ontology Development Group)<br>
* Work on making the GO structure more intuitive for users so that when community annotation is made, it is more likely to be accurate. (Ontology Development Group)<br>
Do the SAB see any other approaches that might be better?
Do the SAB see any other approaches that might be better?
==Ontology Development-Blake ==
===Key accomplishments===
* [[:Category:Cross Products| Logic-based Quality Control: cross-product definitions]]
Progress reported at current GOC meeting, plus items reported at SLC GOC meeting (April):
*The [[Regulation_Main_Page|regulates relationships]] have been incorporated into the biological process (BP) ontology.
*Changes stemming from two content meetings have gone live
**[[Cardiovascular physiology/development]]
**[[Muscle Development]]
*[[Sensu_Main_Page|Sensu terms]] renamed and rationalized
* New OBO-Edit features (video)
*We now used reasoner-based reports for [[Ontology_Quality_Control|Ontology Quality control]].
Also see Progress Reports from [[Progress_Report_April_2008#Ontology_Development|April]] and [[Ontology_Development_progress_report_for_October_2008_meetings|October]] 2008.
===Questions for SAB===
*We are committed to creating links between MF and BP, and know that (e.g.) bacterial sequencing centers want to use them to facilitate annotation. We also know that they will be valuable when users cluster annotations that have only been annotated to the MF ontology. Can the SAB think of additional use cases?
*What is the best way to present new relationship types, such as has_part and regulates, to users? Should searches include or exclude them by default, should we offer users the choice, or try to make everything work somehow behind the scenes? Relationship composition is also relevant to this question.
*Update on metrics: Are the metrics for ontology development that we now provide useful? What additional metrics should we gather, and how? Are we getting better at providing metrics? And (off on a bit of a tangent) are there any use cases for metrics other than our internal monitoring, SAB reporting, and funding agency reporting (not that we'd stop measuring if there aren't!)?
*Essentially the same questions about quality control measures - are our existing QC practices good; what others can we add; etc.
*Are we getting ontology content submissions/suggestions from a broad enough segment of our users? If not, which other groups (or even individuals) should we target? How can we motivate them to get involved?
*Maybe: ask SAB the questions about content development priorities on GOC meeting agenda.


==Reference Genome Annotation Project - Lewis==
==Reference Genome Annotation Project - Lewis==
===Key accomplishments===
===Aims and Key accomplishments===
* Working on methods to establish curation sets (PANTHER, PPOD, Paul Thomas, Kara Dolinski)
* Since the last GOC meeting (and reference genome meeting), put a lot of emphasis on annotation consistency during the monthly conference calls and two electronic jamboree
* Publication submitted (I hope it will be)
* Publication submitted (I hope it will be)
* POGO demo
* Paul Thomas: gp2protein files issues; (link wiki page describing what we need to generate a proper gp2protein file) Chris/Stan/Paul to provide numerical profiles.
* Working on methods to establish curation sets (PANTHER, PPOD, Paul Thomas, Kara Dolinski).
* Pascale Gaudet: Development of shared GO curation guidelines that are being adopted by all ref. genome MODs. Since the last GOC meeting (and reference genome meeting), put a lot of emphasis on annotation consistency.
** Monthly conference calls
** two electronic jamboree
* Suzi Lewis: TCT demo and proposed data flow


===Questions for SAB===
===Questions for SAB===
* I have nothing specific right now; but general feedback would be greatly appreciated
# How do we obtain compliance in generating these protein files?
* One thought is: Should we solicit the advice of the SAB for expanding (or reducing) evidence codes, and in particular adding HTP?
# How do we obtain compliance in adhering to curation guidelines?
# Annotation consistency : do we need evidences codes other than EXP, NON-EXP and IEA? This is one major cause for inconsistent annotations.


Return to [[Consortium_Meetings]]
Return to [[Consortium_Meetings]]

Latest revision as of 08:53, 12 April 2019

Logistics

October 2008 Meeting Logistics

Agenda

Ontology Development - Blake

Aims and Key accomplishments

Progress reported at current GOC meeting, plus items reported at SLC GOC meeting (April):

Also see Progress Reports from April and October 2008.

Questions for SAB

  • We are committed to creating links between MF and BP, and know that it will facilitate annotation.
    • Initially we plan to work on area XY ; does that make sense and are there other suggestions?
  • Update on metrics: Are the metrics for ontology development that we now provide useful? What additional metrics should we gather, and how? Are we getting better at providing metrics? And (off on a bit of a tangent) are there any use cases for metrics other than our internal monitoring, SAB reporting, and funding agency reporting (not that we'd stop measuring if there aren't!)?
  • Essentially the same questions about quality control measures - are our existing QC practices good; what others can we add; etc.
  • Are we getting ontology content submissions/suggestions from a broad enough segment of our users? If not, which other groups (or even individuals) should we target? How can we motivate them to get involved?
  • Maybe: ask SAB the questions about content development priorities on GOC meeting agenda.

User Advocacy - Ashburner

Key accomplishments

  • AmiGO 1.6
  • Help desk report
  • Newsletter

Questions for SAB

Annotation - Cherry

Aims and Key accomplishments

  • Good annotation outreach efforts have been organized by AgBase, TAIR and PAMGO.
  • Changes to GAF
  • Annotation camps
  • Annotation IRC
  • Evidence Code Ontology
  • Swiss-Prot committed to start doing GO annotation which will help getting more gene proteins annotated, including proteins from species not currently being annotated. (4 Slides from Jennifer to explain why other organisms also need to be annotated, leading in to Michael's talk on SwissProt.)

Questions for SAB

To help other groups annotate:

  • Write better documentation to enable small community groups and individual users to make anntotations. (Docs by Reference Genome Group.)
  • Work on making the GO structure more intuitive for users so that when community annotation is made, it is more likely to be accurate. (Ontology Development Group)

Do the SAB see any other approaches that might be better?

Reference Genome Annotation Project - Lewis

Aims and Key accomplishments

  • Publication submitted (I hope it will be)
  • Paul Thomas: gp2protein files issues; (link wiki page describing what we need to generate a proper gp2protein file) Chris/Stan/Paul to provide numerical profiles.
  • Working on methods to establish curation sets (PANTHER, PPOD, Paul Thomas, Kara Dolinski).
  • Pascale Gaudet: Development of shared GO curation guidelines that are being adopted by all ref. genome MODs. Since the last GOC meeting (and reference genome meeting), put a lot of emphasis on annotation consistency.
    • Monthly conference calls
    • two electronic jamboree
  • Suzi Lewis: TCT demo and proposed data flow

Questions for SAB

  1. How do we obtain compliance in generating these protein files?
  2. How do we obtain compliance in adhering to curation guidelines?
  3. Annotation consistency : do we need evidences codes other than EXP, NON-EXP and IEA? This is one major cause for inconsistent annotations.

Return to Consortium_Meetings