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==September 23-24th, 2007 Princeton, New Jersey==
[[Category:GO Consortium Meetings]]
* [[GO 18th Consortium Meeting Minutes Day 1| Minutes Day 1]]
* [[GO 18th Consortium Meeting Minutes Day 2| Minutes Day 2]]
* [[Outstanding Action Items from 17th GOC Meeting, Cambridge UK]]
 
 
==Sept 23-24th, 2007 Princeton, New Jersey==


;Meeting Location: [http://www.princeton.edu/prospecthouse/ Prospect House] - Presidential Dining Room
;Meeting Location: [http://www.princeton.edu/prospecthouse/ Prospect House] - Presidential Dining Room
   Prospect House
   Prospect House ]]
   Washington St
   Washington St
   Princeton, NJ 08544
   Princeton, NJ 08544
Line 8: Line 14:
   www.princeton.edu/prospecthouse/
   www.princeton.edu/prospecthouse/


Lunch Location: Prospect House - Library
; Dinner on Sunday (9/23) @ 5.00 PM - Winbere's in Palmer Sq
 
; Dinner on Monday (9/24) @ 6.00 PM - Triump Brewery on Nassau St


;Accomodations:[http://www.nassauinn.com/ Nassau Inn]
;Accomodations:[http://www.nassauinn.com/ Nassau Inn]
Line 17: Line 25:
   (609) 921-7500
   (609) 921-7500
   www.nassauinn.com
   www.nassauinn.com
==Participants==
==Photo==
[[Image:GOC2007_Princeton2.jpg]]
==Draft Schedule==
----
=== ''Sunday morning, September 23, 2007''===
----
====Introduction====
#Introductions, especially new people
#Quick review of any outstanding [[2007 GOC 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.
#Ontology Development - Biological Content:::Midori Harris and David Hill reporting
#[[Ontology_Structure]] :::Chris Mungall reporting
#[[Ontology_Development]] wiki site.
#SO progress :::Karen Eilbeck reporting
===== Aim 2- Reference Genome Project =====
Judy Blake - Moderator/PI lead.
#Reference Genome Project :: Rex Chisholm and Pascale Gaudet reporting
#[[Reference Genome Annotation Project]] wiki site.
=====Aim 3- Annotation across all organisms=====
Michael Ashburner - Moderator/PI lead.
#[[Annotation Outreach]]:: Jen Deegan reporting
#[http://wiki.geneontology.org/index.php/OBO-Edit OBO-Edit working group]::John Day-Richter reporting
=====Aim 4- Providing annotations and tools to Users=====
Mike Cherry - Moderator/PI lead.
#[[User Advocacy]]::Eurie Hong reporting
#Production Systems :: Ben Hitz? reporting
#AmiGO and Web presence (Hub) working groups :: Amelia Ireland and Chris Mungall reporting.
#Report on [[SWUG:Database_changes_2007]]
#[[Reference_Genome_Database_Requirements_Discussion]]
#[[SWUG:AmiGO_Architecture_Roadmap]]
#[[AmiGO:_Prototypes]]
----
===''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.


== Brainstorming on Topics for upcoming 18th meeting ==
*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====
=====Updates and next steps=====
#Update on 'regulates' terms and relationships in GO (David)
#Plan for adding 'regulation of' relationship to GO (Chris)
##Will we maintain two copies of GO live at once?
##How will will notify users of timing and consequences of this (and other) changes?
#Completing is_a relations in the GO (Chris demo)
#Update on revamp of 'Sensu' terms. (David)
=====Cross-products=====
Background: [[Cross_Product_Guide]]
#Collaboration and cross-products with Cell Ontology
#Taxon-GO links
#The intersection of SO and CC (Chris and Karen E)
 
=====Discussions=====
#Incorporation or synchronization with the SAO (sub-cellular anatomical ontology)
#How can we confer micro-credit to experts who contribute to the content?
#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)
# Delineating, and isolating, the different categories of "slims" and their usage. See [[Taxon_Main_Page]] for more discussion.
# 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:
# The scope of 'binding' terms in the function ontology:
## How granular should terms be?
## 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].
## 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 how we are going to handle regulates and relationships between regulation terms (DPH)
## Does regulates always mean the same thing in GO?
## Can/should regulation be broken down into parts, or should it be a collection of types?
# What is the plan for implementing 'regulates' relationship in live GO?
## Will we have two GO implementations operating at once?
## How will we notify and time the change-over?...this is a big deal
# Discuss whether GO can add a has_part relationship (mah, krc)
# Discuss whether GO can add a has_part relationship (mah, krc)
# Annotation: Discuss situations where the 'contributes_to' qualifier should and should not be used (mah for vw)
# Taxon-GO links.
# Discuss the disjoint relationships/tags in the GO BP ontology.(dph)
# annotation of protein complexes; "use" of IPI protein binding to track physical interactions; collab. with Reactome
## This needs to be scheduled for Sunday afternoon as Peter D'Eustachio can attend then.
# Discuss ISS evidence code extensions from orthology


==GOC and Staff issues==
----
 
===''Morning, Monday, September 24, 2007''===
----
 
====Topics related to Annotation====
# 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.
# Ontology versioning proposal for keeping annotations up-to-date (John and Chris)
 
====Annotation Evidence Codes====
# Evidence code proposals from Evidence Code Committee
## Finalizing Proposed evidence code documentation  (need someone to oversee completion of final details; [[see also summary email]] and [http://www-dev.yeastgenome.org/draftGO/go/www/GO.evidence.new.shtml Proposed evidence code documentation])
## Boundary between ISS & RCA and scope of RCA evidence code (Michelle and Rama (filling in for KarenC); see [http://genetics.stanford.edu/~kchris/go/evCodeIssues/RCAvsISStxpt.html Evidence Code Committee discussion on ISS vs RCA] and [[Email sum up on RCA]] (contains link to RCA example papers)).
## Use of with column for ISS, pending decision on ISS vs RCA boundary  (?; see [[summary of ISS with (blank) proposal]] (contains link to ISS with '____' sample papers) and some [[further comments on filling with field for ISS]]).
## Boundary between IMP and IGI (Val; [[Email synopsis]] and [[further comment]])
## Use of with column for NAS evidence code (David; see [[summary Email thread on NAS]]).
## Annotations to root nodes (Rama; see [[Email sum up on ND]] and probable conclusion of [[use of ND for root annotations]]).
## Thoughts from MGI [[See this document]] and some [[responses to MGI from Karen]]
## Karen's [http://genetics.stanford.edu/~kchris/go/evCodeIssues/EvCodeFlowChart.html draft of an Evidence Code Decision tree] (and John's [http://www.fruitfly.org/~jrichter/decisiontree/ html implementation])
# [[Use cases for evidence codes]]
# "use" of IPI protein binding to track physical interactions
 
====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.
 
* 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.
 
----
===''Afternoon, Monday, September 24, 2007''===
----
====Our Public Face====
=====AmiGO=====
#AmiGO Architecture
#ORB and AmiGO
#GOOSE
#Changes to AmiGO to improve visualization when there are multiple relationships linking terms
=====And the rest=====
#Wiki
# Suggestion by PAMGO community to propose the use of GO terms as keywords in journals.
 
----
----
==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.
*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)
:(added at Michael's request)
* Annotation Outreach and User Support have been, at least temporarily, combined
* Currently we have several working groups including:
*#Ontology content - to work on the content of the ontology<br>
*#Annotation-Outreach - to encourage new groups to start annotating <br>
*#User Advocacy - to help users to learn how to use the GO and to represent user's need to the consortium.<br>
*#Reference Genomes - to choose genes lists for everyone to work on.


==Resources==
So the questions are:
[[Action Items]] from Jan 2007 GOC meeting held in Cambridge, UK http://www.geneontology.org/GO.meetings.shtml?all#consort
*#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.

Latest revision as of 20:26, 8 April 2014


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/
Dinner on Sunday (9/23) @ 5.00 PM - Winbere's in Palmer Sq
Dinner on Monday (9/24) @ 6.00 PM - Triump Brewery on Nassau St
Accomodations
Nassau Inn
 Nassau Inn
 10 Palmer Sq E
 Princeton, NJ 08542
 (609) 921-7500
 www.nassauinn.com

Participants

Photo

Draft Schedule


Sunday morning, September 23, 2007


Introduction

  1. Introductions, especially new people
  2. Quick review of any outstanding 2007 GOC 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
  5. Reference_Genome_Database_Requirements_Discussion
  6. SWUG:AmiGO_Architecture_Roadmap
  7. AmiGO:_Prototypes

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

Updates and next steps
  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 (and other) changes?
  3. Completing is_a relations in the GO (Chris demo)
  4. Update on revamp of 'Sensu' terms. (David)
Cross-products

Background: Cross_Product_Guide

  1. Collaboration and cross-products with Cell Ontology
  2. Taxon-GO links
  3. The intersection of SO and CC (Chris and Karen E)
Discussions
  1. Incorporation or synchronization with the SAO (sub-cellular anatomical ontology)
  2. How can we confer micro-credit to experts who contribute to the content?
  3. 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)
  4. Delineating, and isolating, the different categories of "slims" and their usage. See Taxon_Main_Page for more discussion.
  5. 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.
  6. 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.
  4. Ontology versioning proposal for keeping annotations up-to-date (John and Chris)

Annotation Evidence Codes

  1. Evidence code proposals from Evidence Code Committee
    1. Finalizing Proposed evidence code documentation (need someone to oversee completion of final details; see also summary email and Proposed evidence code documentation)
    2. Boundary between ISS & RCA and scope of RCA evidence code (Michelle and Rama (filling in for KarenC); see Evidence Code Committee discussion on ISS vs RCA and Email sum up on RCA (contains link to RCA example papers)).
    3. Use of with column for ISS, pending decision on ISS vs RCA boundary (?; see summary of ISS with (blank) proposal (contains link to ISS with '____' sample papers) and some further comments on filling with field for ISS).
    4. Boundary between IMP and IGI (Val; Email synopsis and further comment)
    5. Use of with column for NAS evidence code (David; see summary Email thread on NAS).
    6. Annotations to root nodes (Rama; see Email sum up on ND and probable conclusion of use of ND for root annotations).
    7. Thoughts from MGI See this document and some responses to MGI from Karen
    8. Karen's draft of an Evidence Code Decision tree (and John's html implementation)
  2. Use cases for evidence codes
  3. "use" of IPI protein binding to track physical interactions

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

AmiGO
  1. AmiGO Architecture
  2. ORB and AmiGO
  3. GOOSE
  4. Changes to AmiGO to improve visualization when there are multiple relationships linking terms
And the rest
  1. Wiki
  2. Suggestion by PAMGO community to propose the use of GO terms as keywords in journals.


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.