Difference between revisions of "20th GO Consortium Meeting"

From GO Wiki
Jump to: navigation, search
(8:45 progress on homology sets and homology inference)
m (Logistics)
 
(23 intermediate revisions by 7 users not shown)
Line 1: Line 1:
 +
[[Category:GO Consortium Meetings]]
 
=Logistics=
 
=Logistics=
[[Instructions_for_Registration]]
+
[[October 2008 Meeting Logistics]]
 
 
  
 
=Agenda=
 
=Agenda=
Line 20: Line 20:
 
** Manually curated links - pilot projects (Jennifer, Harold)
 
** Manually curated links - pilot projects (Jennifer, Harold)
 
:The electron transport working group have been discussing this issue in depth. We present our conclusions. In brief, our proposal is that links between function and process should only be made when we can use part_of (rather than has_part) or when there is a single step process term. (Jennifer presenting 29 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/FunctionProcessLinksPhotosynthesisJDeegan.ppt Slides])
 
:The electron transport working group have been discussing this issue in depth. We present our conclusions. In brief, our proposal is that links between function and process should only be made when we can use part_of (rather than has_part) or when there is a single step process term. (Jennifer presenting 29 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/FunctionProcessLinksPhotosynthesisJDeegan.ppt Slides])
 +
: Various intermediary Metabolism MF-BPs (Harold [20 slides http://wiki.geneontology.org/index.php/Image:FXP-HJD-GOC_Montreal-reduced.pdf])
 
:*Plans to add regulates relationships within the molecular function (MF) ontology, and between MF and BP (David, Tanya, Chris) -- this is now covered
 
:*Plans to add regulates relationships within the molecular function (MF) ontology, and between MF and BP (David, Tanya, Chris) -- this is now covered
 
*[[Ontology_Quality_Control|Ontology content QC]]
 
*[[Ontology_Quality_Control|Ontology content QC]]
Line 57: Line 58:
 
* Using the ECO as the primary source (and definition) for evidence codes. The documentation should <em>reflect</em> (not define) the evidence codes found in the ontology. Also, need to make sure that there is a tracker for this.
 
* Using the ECO as the primary source (and definition) for evidence codes. The documentation should <em>reflect</em> (not define) the evidence codes found in the ontology. Also, need to make sure that there is a tracker for this.
 
Plan to get some people together to work on it for 2-3 days and fix it (somewhat)
 
Plan to get some people together to work on it for 2-3 days and fix it (somewhat)
 +
* Michelle will be ECO editor
 +
* HTP evidence code? (Eurie)
 
* [[Electronically curated flag]] in GAF proposal
 
* [[Electronically curated flag]] in GAF proposal
 +
* New subcodes of IGC will be going into ECO:  inferred from system reconstruction (ISR) and inferred from genome cluster (ICL).  Currently IGC encompasses more than one type of evidence - it includes both pathway reconstruction/protein complex reconstruction and also operon structure/synteny.  In order to be able to more precisely describe which was used we want to have the two new codes.  These are currently being used by the Bioinformatics Resource Centers (BRCs).  This was discussed on the evidence code mail list and there was no objection. (Michelle)
  
 
===Annotation and ontologies===
 
===Annotation and ontologies===
Line 71: Line 75:
 
* New way of calculating the [[Transitive_closure]]
 
* New way of calculating the [[Transitive_closure]]
  
===Taxa===
+
===PAMGO report on successes and some problem annotations from consortium members===
* How to address the problem that comes up in trying to do dual taxon annotations when one of the partners has no taxon ID number at NCBI [e.g. when a microbe is interacting with a plant which has no taxon ID number (and this also is a problem because different cultivars of a plant also do not have different ID numbers)]Can we discuss how to handle the requirement for a taxon ID (especially the second one in the Dual Taxon situation) when one has not yet been assigned by NCBI?  -Candace Collmer
+
* PAMGO terms are in wide use, however they are sometimes being used incorrectly by consortium members.  Candace will outline the way the terms should be used, Michelle will outline the problems and suggest some solutionsAlso will touch on alternate taxon id resources that we might want to incoroporate. (Candace and Michelle)
* Update on loading dual taxon into database/AmiGO
+
 
 +
* Update on loading dual taxon into database/AmiGO.  Also will touch on alternate taxon id resources that we might want to incoroporate. (Michelle and Chris?)
  
 
==22 OCT AM: Reference Genome 1/2 day==
 
==22 OCT AM: Reference Genome 1/2 day==
  
 +
===Proposed Process: Paul and Kara===
  
 
===8:30 Progress Report===
 
 
==Improvements in annotation depth and breadth ==
 
(Chris and Mike's data)
 
 
==Improvement in ontology structure==
 
*Examples of ontology changes stemming from Reference Genome annotation (David?)
 
 
===8:45 progress on homology sets and homology inference===
 
Paul and Kara
 
 
# generating homology sets, including protein set generation
 
# generating homology sets, including protein set generation
# process for making ISS inferences  
+
# new paradigm for making homology inferences  
# implementation and merging with PPOD data
+
# process and implementation for homology set selection, and homology inferences
  
===Discussion about protein set generation===
+
====Discussion about protein set generation====
Paul
 
 
* Issues:  
 
* Issues:  
** augmentation
+
** incompleteness
** isoforms vs canonical protein  
+
** splice forms vs canonical protein  
 
** complete proteome; partial gene predictions
 
** complete proteome; partial gene predictions
 
** possible solution:  try to work with Swiss Prot?
 
** possible solution:  try to work with Swiss Prot?
  
* Paul will present a table of problems for each genome
 
* We will add documentation as to how to generate files and protein sequences
 
 
* Regarding gp2protein files: The original aim was to support BLAST server.  
 
* Regarding gp2protein files: The original aim was to support BLAST server.  
 
** Do we need another file? g2protein? predicted_non_redundant_protein? this file would have just protein??
 
** Do we need another file? g2protein? predicted_non_redundant_protein? this file would have just protein??
  
 +
====new paradigm for making homology inferences====
 +
 +
===Literature-baseed Annotation Consistency and Quality Issues: Pascale===
 +
# How to improve documentation
 +
# How to address the QC issue
 +
# Make working groups for recurrent problems:
 +
#* binding
 +
#* regulation
 +
#* most evidence codes
  
 +
===Improvement in ontology structure: David===
 +
*Examples of ontology changes stemming from Reference Genome annotation
  
===Annotation Consistency and Quality Issues===
+
=== Improvements in annotation depth and breadth: Mike===
Pascale
 
# HTP evidence code?
 
# Discuss use of binding/regulation terms (GOC meeting)
 
# Establish guidelines for annotation to a process versus regulation of that process
 
# Process IC or IDA? (from [[Jamboree 18 July 2008-minutes]]; example : GCH1)
 
# There will likely be several other topics to discuss from the two electronic jamborees; so far: [[Reference_Genome_Annotation_Project#Annotation_Consistency_Issues]]
 
  
 
==Web presence, Outreach and User Advocacy==
 
==Web presence, Outreach and User Advocacy==
Line 125: Line 122:
 
===AmiGO 1.6 for Reference Genome (Seth & Amelia)===
 
===AmiGO 1.6 for Reference Genome (Seth & Amelia)===
 
# Present progress on AmiGO graphical views
 
# Present progress on AmiGO graphical views
 +
 +
===Michael Schroeder will report on new OBO-Edit plugin===
 +
 
===Resource Usage statistics (Mike)===
 
===Resource Usage statistics (Mike)===
  

Latest revision as of 05:52, 12 April 2019

Logistics

October 2008 Meeting Logistics

Agenda

ALERT: GO Top needs to sign off on agenda prior to these meetings. If there is no action item, or discussion point proposed in advance, the meeting is not the forum for first initiating a discussion.

Action Items

http://wiki.geneontology.org/index.php/SLC_GO_Consortium_Meeting_Minutes_April_2008#ACTION_ITEMS

Ontology Content Development

Work in progress

The electron transport working group have been discussing this issue in depth. We present our conclusions. In brief, our proposal is that links between function and process should only be made when we can use part_of (rather than has_part) or when there is a single step process term. (Jennifer presenting 29 Slides)
Various intermediary Metabolism MF-BPs (Harold [20 slides http://wiki.geneontology.org/index.php/Image:FXP-HJD-GOC_Montreal-reduced.pdf])
  • Plans to add regulates relationships within the molecular function (MF) ontology, and between MF and BP (David, Tanya, Chris) -- this is now covered
Jennifer and David have been working on a proposal for a new set of high level signaling terms. The new terms are ready to go live and we present them for comment. (~5 min talk) Slides

Ontology development discussion topics

  • Setting priorities across different types of content development task
    • How to allocate effort among (a) overall logical enhancements (e.g. improving genus-differentia aspects of definitions or adding new relationship types); (b) keeping up with SF submissions; (c) content meeting changes; anything else
    • More generally, what's the right balance between retrofitting the existing ontology (definition style, relationship types just two examples) versus new additions?

OBO-Edit

Organization/Management

  • SourceForge clearout done
  • Possible forthcoming changes to day-to-day editing practices (David, Midori, Chris?)
    • Creating and using cross-products
    • Using new relationship types
    • Integrating QC into editing pipeline

General Annotation

Evidence Codes

  • Using the ECO as the primary source (and definition) for evidence codes. The documentation should reflect (not define) the evidence codes found in the ontology. Also, need to make sure that there is a tracker for this.

Plan to get some people together to work on it for 2-3 days and fix it (somewhat)

  • Michelle will be ECO editor
  • HTP evidence code? (Eurie)
  • Electronically curated flag in GAF proposal
  • New subcodes of IGC will be going into ECO: inferred from system reconstruction (ISR) and inferred from genome cluster (ICL). Currently IGC encompasses more than one type of evidence - it includes both pathway reconstruction/protein complex reconstruction and also operon structure/synteny. In order to be able to more precisely describe which was used we want to have the two new codes. These are currently being used by the Bioinformatics Resource Centers (BRCs). This was discussed on the evidence code mail list and there was no objection. (Michelle)

Annotation and ontologies

  • A (re-)introduction to the new column 16, Annotation_Cross_Products
  • Ontological relationships between gene products and functions, processes and components

GO Database

  • APIs
    • GHOUL GO Hibernate Object Utility Layer. An API to the GO database for Java programmers
    • Lucene indexing
  • Regular reporting of statistics, sanity checks, and such on the GO database.
  • New way of calculating the Transitive_closure

PAMGO report on successes and some problem annotations from consortium members

  • PAMGO terms are in wide use, however they are sometimes being used incorrectly by consortium members. Candace will outline the way the terms should be used, Michelle will outline the problems and suggest some solutions. Also will touch on alternate taxon id resources that we might want to incoroporate. (Candace and Michelle)
  • Update on loading dual taxon into database/AmiGO. Also will touch on alternate taxon id resources that we might want to incoroporate. (Michelle and Chris?)

22 OCT AM: Reference Genome 1/2 day

Proposed Process: Paul and Kara

  1. generating homology sets, including protein set generation
  2. new paradigm for making homology inferences
  3. process and implementation for homology set selection, and homology inferences

Discussion about protein set generation

  • Issues:
    • incompleteness
    • splice forms vs canonical protein
    • complete proteome; partial gene predictions
    • possible solution: try to work with Swiss Prot?
  • Regarding gp2protein files: The original aim was to support BLAST server.
    • Do we need another file? g2protein? predicted_non_redundant_protein? this file would have just protein??

new paradigm for making homology inferences

Literature-baseed Annotation Consistency and Quality Issues: Pascale

  1. How to improve documentation
  2. How to address the QC issue
  3. Make working groups for recurrent problems:
    • binding
    • regulation
    • most evidence codes

Improvement in ontology structure: David

  • Examples of ontology changes stemming from Reference Genome annotation

Improvements in annotation depth and breadth: Mike

Web presence, Outreach and User Advocacy

Outreach

  • Short update on Outreach going on throughout the Consortium. Highlights presented by Tanya Berardini (Author submission of annotations - 3 Slides) and Michelle Gwinn-Giglio (PAMGO outreach and University of Maryland Annotation courses - 6 Slides).
  • Swiss-Prot to do GO annotations (Michael)

AmiGO 1.6 for Reference Genome (Seth & Amelia)

  1. Present progress on AmiGO graphical views

Michael Schroeder will report on new OBO-Edit plugin

Resource Usage statistics (Mike)

User Support

  1. Evaluation of helpdesk performance

GO Papers, Publications and Presentations

  1. Ref Genome paper status report
  2. AmiGO app. note
  3. News letter impact

Other items

Consortium meetings

Breakout sessions to fit in somehow

  • Final preparations for SAB meeting
  • Amina, Chris and OBO-Edit users (including cross-products)
  • Pascale, Suzi and reference genome curators

Return to Consortium_Meetings