GO 18th Consortium Meeting: Difference between revisions

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==Draft Schedule==
==Draft Schedule==
[[User:Judy|Judy]] 05:38, 12 September 2007 (PDT)Sept. 12, 2007
[[User:Judy|Judy]] 05:38, 12 September 2007 (PDT)Sept. 12, 2007
 
----
=== ''Sunday morning, September 23, 2007''===
=== ''Sunday morning, September 23, 2007''===
----
----
====Introduction====
====Introduction====
#Introductions, especially new people
#Introductions, especially new people
#Quick review of any outstanding [[Action Items]] from last GOC meeting.
#Quick review of any outstanding [[Action Items]] from Jan 2007GOC meeting held in Cambridge, UK http://www.geneontology.org/GO.meetings.shtml?all#consort


====Progress Reports====
====Progress Reports====
[[2007 Progress Report]] for NHGRI due Jan. 1, 2008
::These reports will review accomplishments to date.  
::These reports will review accomplishments to date.  
::We could use the itemized list of sub-aims from the grant to organize these
::We are using the itemized list of sub-aims from the grant to organize these


   Aim1: We will maintain comprehensive, logically rigorous and biologically accurate ontologies.
   Aim1: We will maintain comprehensive, logically rigorous and biologically accurate ontologies.
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#Report on [[SWUG:Database_changes_2007]]
#Report on [[SWUG:Database_changes_2007]]


----
===''Afternoon, Sunday, Sept 23, 2007''===
===''Afternoon, Sunday, Sept 23, 2007''===
----
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:: We especially have agreed to discuss protein complexes and the intersection with Reactome annotationsPeter D'Eustachio (Reactome) will be able to join us only for the afternoon.
====Discuss protein complexes and the intersection with Reactome annotations====
 
Peter D'Eustachio (Reactome) will be able to join us only for the afternoon.


These are some other topics that Ewan Birney brought up at the Interactome meeting:
These are some other topics that Ewan Birney brought up at the Interactome meeting:
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====Topics related to Ontology Development-1====
====Topics related to Ontology Development====
#Update on 'regulates' terms and relationships in GO (David)
#Update on 'regulates' terms and relationships in GO (David)
#Plan for adding 'regulation of' relationship to GO (Chris)
#Plan for adding 'regulation of' relationship to GO (Chris)
Line 87: Line 91:
#The intersection of SO and CC (Chris and Karen E)
#The intersection of SO and CC (Chris and Karen E)
#Creating Complex terms in the component ontology-when do two interacting proteins become a complex? How long should the interaction last for it to be called a complex? (Rama)
#Creating Complex terms in the component ontology-when do two interacting proteins become a complex? How long should the interaction last for it to be called a complex? (Rama)
#How will we notify users about nature and time of change-over ?
# Delineating, and isolating, the different categories of "slims" and their usage. See [[Taxon_Main_Page]] for more discussion.
# The scope of 'binding' terms in the function ontology:
## How granular should terms be?
## Should there be terms for substrate origin (e.g. "viral protein binding")? See [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1674020&group_id=36855| SF 1674020].
# Discuss whether GO can add a has_part relationship (mah, krc)
----
===''Morning, Monday, September 24, 2007''===
----


====Topics related to Annotation====
====Topics related to Annotation====
# Annotation of protein complexes; "use" of IPI protein binding to track physical interactions; collab. with Reactome
# Annotation of protein complexes
# Finalizing the format for cross-product information for the new column 16 of the gene association file - could this column also include information on the 'target' of a protein's activity?
# Issue with taxon/dual taxon usage to capture strains and cultivars etc, for which taxon IDs do not exist in NCBI.
====Annotation Evidence Codes====
# Summary of evidence code proposals* ([[see also summary email]])
# Summary of evidence code proposals* ([[see also summary email]])
#* Proposed evidence code documentation: http://www.ebi.ac.uk/~aji/web/GO.evidence.new.shtml
#* [[Use cases for evidence codes]]
# "use" of IPI protein binding to track physical interactions
# Discuss use of RCA evidence code* *see [[Email sum up on RCA]].
# Discuss use of RCA evidence code* *see [[Email sum up on RCA]].
# Discuss ISS evidence code* extensions from orthology ([[email discussions]])
# Discuss ISS evidence code* extensions from orthology ([[email discussions]])
# Discuss boundary between IMP and IGI ([[Email synopsis]] and [[further comment]])
# Discuss boundary between IMP and IGI ([[Email synopsis]] and [[further comment]])
# Discuss use of NAS evidence code (see [[summary Email thread on NAS]]).
# Discuss use of NAS evidence code (see [[summary Email thread on NAS]]).
# Finalizing the format for cross-product information for the new column 16 of the gene association file - could this column also include information on the 'target' of a protein's activity?
5.Issue with taxon/dual taxon usage to capture strains and cultivars etc, for which taxon IDs do not exist in NCBI.
6. Suggestion by PAMGO community to propose the use of GO terms as keywords in journals.
* Proposed evidence code documentation: http://www.ebi.ac.uk/~aji/web/GO.evidence.new.shtml
* [[Use cases for evidence codes]]
====Gene Association file ====
====Gene Association file ====
(Rama and MikeC)
(Rama and MikeC)
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* The HTML annotation table (http://www.geneontology.org/GO.current.annotations.shtml) should be sorted by kingdom.  The HTML table is currently sorted by genus name.
* The HTML annotation table (http://www.geneontology.org/GO.current.annotations.shtml) should be sorted by kingdom.  The HTML table is currently sorted by genus name.


===''Morning, Monday, September 24, 2007''===
----
----
====Topics relevant to Ontology Development-2====
catch-up?
#How will we notify users about nature and time of change-over ?
# Delineating, and isolating, the different categories of "slims" and their usage. See [[Taxon_Main_Page]] for more discussion.
# The scope of 'binding' terms in the function ontology:
## How granular should terms be?
## Should there be terms for substrate origin (e.g. "viral protein binding")? See [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1674020&group_id=36855| SF 1674020].
# Discuss whether GO can add a has_part relationship (mah, krc)
===''Afternoon, Monday, September 24, 2007''===
===''Afternoon, Monday, September 24, 2007''===
----
----
====Our Public Face====
#AmiGO Architecture
#ORB and AmiGO
# Suggestion by PAMGO community to propose the use of GO terms as keywords in journals.
====Topics relevant to GO intersection with other ontologies====
====Topics relevant to GO intersection with other ontologies====
#Collaboration and cross-products with Cell Ontology
#Collaboration and cross-products with Cell Ontology
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*#Would it be a good idea to merge user advocacy and annotation outreach as these have a lot in common? <br>
*#Would it be a good idea to merge user advocacy and annotation outreach as these have a lot in common? <br>
*#Would it be possible to make a general annotation working group to deal with all issues surrounding annotation? This group could include sub-groups such as the reference genomes group, the evidence code groups and the annotation standard operating procedure group. The main annotation group could have two annotators to chair, or perhaps a rolling chair.
*#Would it be possible to make a general annotation working group to deal with all issues surrounding annotation? This group could include sub-groups such as the reference genomes group, the evidence code groups and the annotation standard operating procedure group. The main annotation group could have two annotators to chair, or perhaps a rolling chair.
==Resources==
===Action Items from last GOC meeting ===
[[Action Items]] from Jan 2007GOC meeting held in Cambridge, UK http://www.geneontology.org/GO.meetings.shtml?all#consort
===2007 Progress Report===
[[2007 Progress Report]]for NHGRI due Jan. 1, 2008

Revision as of 17:50, 20 September 2007

Sept 23-24th, 2007 Princeton, New Jersey

Meeting Location
Prospect House - Presidential Dining Room
 Prospect House ]] 
 Washington St
 Princeton, NJ 08544
 (609) 258-3455
 www.princeton.edu/prospecthouse/
Lunch Location: Prospect House - Library 
Dinner - dinner reservations at Mediterra
 Mediterra
 29 Hulfish St 
 Princeton, NJ 08542
 (609) 252-9680
Accomodations
Nassau Inn
 Nassau Inn
 10 Palmer Sq E
 Princeton, NJ 08542
 (609) 921-7500
 www.nassauinn.com

Draft Schedule

Judy 05:38, 12 September 2007 (PDT)Sept. 12, 2007


Sunday morning, September 23, 2007


Introduction

  1. Introductions, especially new people
  2. Quick review of any outstanding Action Items from Jan 2007GOC meeting held in Cambridge, UK http://www.geneontology.org/GO.meetings.shtml?all#consort

Progress Reports

2007 Progress Report for NHGRI due Jan. 1, 2008

These reports will review accomplishments to date.
We are using the itemized list of sub-aims from the grant to organize these
 Aim1: We will maintain comprehensive, logically rigorous and biologically accurate ontologies.
 Aim2: We will comprehensively annotate reference genomes in as complete detail as possible.
 Aim3: We will support annotation across all organisms.
 Aim4: We will provide our annotations and tools to the research community.
Aim 1- Ontology Development

Suzi Lewis - Moderator/PI Lead.

  1. Ontology Development - Biological Content:::Midori Harris and David Hill reporting
  2. Ontology structure :::Chris Mungall reporting
  3. Ontology_Development wiki site.
  4. SO progress :::Karen Eilbeck reporting
Aim 2- Reference Genome Project

Judy Blake - Moderator/PI lead.

  1. Reference Genome Project :: Rex Chisholm and Pascale Gaudet reporting
  2. Reference Genome Annotation Project wiki site.
Aim 3- Annotation across all organisms

Michael Ashburner - Moderator/PI lead.

  1. Annotation Outreach:: Jen Deegan reporting
  2. OBO-Edit working group::John Day-Richter reporting
Aim 4- Providing annotations and tools to Users

Mike Cherry - Moderator/PI lead.

  1. User Advocacy::Eurie Hong reporting
  2. Production Systems :: Ben Hitz? reporting
  3. AmiGO and Web presence (Hub) working groups :: Amelia Ireland and Chris Mungall reporting.
  4. Report on SWUG:Database_changes_2007

Afternoon, Sunday, Sept 23, 2007


Discuss protein complexes and the intersection with Reactome annotations

Peter D'Eustachio (Reactome) will be able to join us only for the afternoon.

These are some other topics that Ewan Birney brought up at the Interactome meeting:

  • Reactome has a lot of function annotations with the connections to the complex that has the function. These are for very small complexes like homodimers. He says can we accept these? Also he says that he understands that this is a bit granular for us and that we have a lot of similar information for larger complexes. He suggests that there might be better way to store all the data for the functions of all sizes of complexes if we pooled out data and thought of a good system to make it available.
  • Ewan Birney and the people at the Interactome meeting felt strongly that the more complicated annotations such as those with a NOT or colocalizes_with qualifier, and those with annotations to the root should be in a separate file from the straightforward annotations. The users felt that many people do not know about these more complicated annotations and it would be better to make them an added extra that people must specifically go to download. They were particularly concerned that users may not know that it is important to parse the qualifier column and so may miss vital information.
  • Reactome would like to have a new evidence code to show where an IEA has been transferred from a known orthologue. Such transfers tend to produce more granular annotations. (This has been discussed before but Ewan asked me to bring it up while Peter is there to back the proposal.)


Topics related to Ontology Development

  1. Update on 'regulates' terms and relationships in GO (David)
  2. Plan for adding 'regulation of' relationship to GO (Chris)
    1. Will we maintain two copies of GO live at once?
    2. How will will notify users of timing and consequences of this change?
  3. Update on revamp of 'Sensu' terms. (David)
  4. The intersection of SO and CC (Chris and Karen E)
  5. Creating Complex terms in the component ontology-when do two interacting proteins become a complex? How long should the interaction last for it to be called a complex? (Rama)
  6. How will we notify users about nature and time of change-over ?
  7. Delineating, and isolating, the different categories of "slims" and their usage. See Taxon_Main_Page for more discussion.
  8. The scope of 'binding' terms in the function ontology:
    1. How granular should terms be?
    2. Should there be terms for substrate origin (e.g. "viral protein binding")? See SF 1674020.
  9. Discuss whether GO can add a has_part relationship (mah, krc)

Morning, Monday, September 24, 2007


Topics related to Annotation

  1. Annotation of protein complexes
  2. Finalizing the format for cross-product information for the new column 16 of the gene association file - could this column also include information on the 'target' of a protein's activity?
  3. Issue with taxon/dual taxon usage to capture strains and cultivars etc, for which taxon IDs do not exist in NCBI.

Annotation Evidence Codes

  1. Summary of evidence code proposals* (see also summary email)
  2. "use" of IPI protein binding to track physical interactions
  3. Discuss use of RCA evidence code* *see Email sum up on RCA.
  4. Discuss ISS evidence code* extensions from orthology (email discussions)
  5. Discuss boundary between IMP and IGI (Email synopsis and further comment)
  6. Discuss use of NAS evidence code (see summary Email thread on NAS).

Gene Association file

(Rama and MikeC)

  • We have previously discussed the interest of some groups in having two gene association files. This will allow users to easily download a subset of the annotations. The GO database will load all annotations files. We propose a discussion on the naming convention that should be used for these second (or third) files. The HTML table would have all GA files listed. This proposal comes from SGD as we have now incorporated all S. cerevisiae annotations from the GOA UniProt file. The manual annotations from this file are included in our gene_association.sgd file with UniProt (or MGI) as source. We would like to use a second file for the IEA annotations. This is to allow users to easily use the curated annotations or the computationally predicted set. The worry is that many do not look inside the file before they use it for analysis or as a training set. If developers include the computationally predicted annotations within their training sets the overall quality of there annotations will suffer.

Afternoon, Monday, September 24, 2007


Our Public Face

  1. AmiGO Architecture
  2. ORB and AmiGO
  3. Suggestion by PAMGO community to propose the use of GO terms as keywords in journals.

Topics relevant to GO intersection with other ontologies

  1. Collaboration and cross-products with Cell Ontology
  2. Taxon-GO links

Background: Cross_Product_Guide

GOC and Staff issues (this is largely go-top stuff, perhaps a breakfast?)

  • Considering sending in a proposal to ESF Research Conferences 2007 RFA
  • The PIs should consider options for the future of the GO Editorial Office (GOEO). Affiliation with EBI has numerous advantages (for both GO and EBI), but all four GOEO staff will reach the 9-year limit by the end of the current NIH grant period.
(added at Michael's request)
  • Currently we have several working groups including:
    1. Ontology content - to work on the content of the ontology
    2. Annotation-Outreach - to encourage new groups to start annotating
    3. User Advocacy - to help users to learn how to use the GO and to represent user's need to the consortium.
    4. Reference Genomes - to choose genes lists for everyone to work on.

So the questions are:

    1. Would it be a good idea to merge user advocacy and annotation outreach as these have a lot in common?
    2. Would it be possible to make a general annotation working group to deal with all issues surrounding annotation? This group could include sub-groups such as the reference genomes group, the evidence code groups and the annotation standard operating procedure group. The main annotation group could have two annotators to chair, or perhaps a rolling chair.