2011 USC Meeting Agenda: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
No edit summary
 
(195 intermediate revisions by 16 users not shown)
Line 1: Line 1:
[[Category:GO Consortium Meetings]]
Minutes: (By hosts of previous meeting: MGI)
Minutes: (By hosts of previous meeting: MGI)
== Welcome; Review of schedule and agenda ==
 
[[2011_USC_Meeting_Action_Items | Meeting action items]]
 
=Thursday May 19, Cardinal & Gold Room=
===8:30 Registration===
 
===9:00 Welcome; Review of schedule and agenda ===
* Introductions.
* Introductions.
* GO PI announcements
* GOC PI announcements
----
==9:15 - 5:30 Working Group Reports, plans through 2011, discussion of priorities==
 
===9:15 Annotation ===
(Rama, Emily, Pascale) [http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2011 Progress and Priorities]
 
To encompass:
# Annotation Outreach efforts (30 min)
# Development of  Annotation Guidelines (Geneva, Evidence codes). Suggestions for further guidelines.
# Draft on how external groups should display annotation.
# Focused annotation efforts by GO Consortium members (Emily)
# Proposed improvements to the Annotation web pages
# has_part relationship (Chris)
# Automated annotation support (QCs, Taxon GO, inferred annotations)
## XML encoding of QC checks: [http://geneontology.org/GO.annotation_qc.shtml http://geneontology.org/GO.annotation_qc.shtml]
## Demo of web-based GAF validator: [http://ladle.lbl.gov:8888/gaftools.html http://ladle.lbl.gov:8888/gaftools.html]  (Amelia)
[[AAC Discussion Questions]]
 
[[file:AAandC_presentation.pdf‎]]
 
===10:15 Community resources and Dissemination (Emily & Rama)===
# GO Help Rotation. (Rama) [[File:ECOtoGO.pdf]]
----
 
===10:30 Break===
----
 
 
===11:30 Evidence Code Ontology presentation===
# Marcus (25 minutes)
# Discussion on the appropriate usage of ECO identifiers in annotation (Rama)
 
===12:00 Annotation deliverables===
# Discussion of the distinction between annotations distributed by the GOC and those from the MODs. (Mike, 15 min)
# Discussion on changing the policy on restricting taxon to specific GAF files. (Mike, 15 min)
* Number of annotations removed from GOA files grouped by MOD  [[File:mod-taxon-removed-by-filter.pdf]]
* Number of annotations removed from GOA files GAF based on taxid [[File:gaf-taxon-removed-by-filter.pdf]]
----
 
===12:30 Lunch===
----
 
===1:30 Overview of the outreach efforts===
# Overview of the outreach efforts to specific scientific communities for community annotation by the BHF-UCL [[file:BHF_UCL_CommunityAnnotation.pdf]] and TAIR teams as well as the CACAO (Community Assessment of Community Annotation with Ontologies;  [[File:CACAO2011.pdf]]) course by EcoliWiki (Ruth, Tanya and Jim; 10 mins each and 15 mins discussion)
# RACE-PRO community submission/annotation tool for the Protein Ontology has a section for adding GO annotation.  http://pir.georgetown.edu/cgi-bin/pro/race_pro
 
===2:30 InterPro2GO presentation===
(Sarah Burge) (40 min presentation, 10 mins discussion)
# Brief summary of the revised guidelines for the GO mapping of InterPro entries.
# InterPro evidence requirements, new policy of mapping Domain, Site and Repeat entries, changes in coverage between the old and new approaches, occasions where InterPro is  unable to GO map an entry and finally, the automatic checks to prevent taxonomy violations and assignment of redundant terms.
----
 
===3:20 Break===
----
 
===3:30 Ontology development ===
(David)
# [http://wiki.geneontology.org/index.php/2011_Timeline Timeline: discuss progress and priorities] (10 mins)
# Recent projects - notes/accomplishments
#* Transcription factors (Karen; available any time Thursday or Friday morning before noon) (15 mins)
#* Signaling (Becky) (15 mins) [http://wiki.geneontology.org/images/6/62/Signaling_LA_May2011.pdf]
#* Chemicals (Tanya) (15 mins)
 
 
----
 
===Dinner on your own===
----
 
=Friday May 20, Alumni Room=
 
== 8:15-12:30 Working Group Reports (cont), plans through 2011, discussion of priorities ==
 
===8:15 ontology group (cont'd)===
 
# Protein complexes (Harold) (15 mins, [[File:Complexes_in_GO_and_PRO.pdf‎]])
#* The scope of GO relative to that of PRO?
#* Should GO capture gene product specific protein complexes, or species-specific protein complexes?
#* Should protein complexes be defined based on function or component information? (Becky and Peter D'E)
#* Notifications of change (Becky) (15-20 mins).
#* Large-scale changes to the ontology.
#** When a development project is starting up, and when their key changes are released
#** Process for discussion and release of proposed term obsoletions.
 
===9:00 Reference Genomes===
# Report from the Reference Genomes project (Pascale) [[File:2011-05-USC-RefGenome-Report-Pascale.pdf]]
# [http://wiki.geneontology.org/index.php/Reference_Genome_Timeline-Jul-Dec2011 Timeline: discuss progress and priorities]  20 min
# [http://pantree.org PanTree website] for tree annotations and evidence trail for inferred annotations from PAINT (Paul T) 15 min
 
 
----
 
===10:00 Break===
----
===10:30  annotation===
# BHF-UCL team involved in annotating specific genes identified through GWAS or microarray (Ruth; 15 mins) [[file:BHF_UCL_FocusedAnnotation.pdf]]
 
=== 10:45 Software ===
# Report from the Working Group (Chris)
#* Software utilities (Reasoners, QC - Chris; TG - Heiko)
# OBO/OWL migration (Chris)
# [http://wiki.geneontology.org/index.php/SWUG_Timeline_2010-2011 Timeline: discuss progress and priorities]
# Software status (AmiGO, GOOSE, GOLD, etc. - Seth) [[File:goSW-USC-CM.pdf]]
 
===11:30 Annotation Extension information ===
# Annotation Extension information (Column 16) (MGI / Chris / Val/Emily 30 min)
[[File: Go-c16-roles-USC.pdf]]<br>
Other related slides:([[File: Annotation_extension_tableVal.pdf‎]], [[File:UniProtKB_col16.pdf]], [[File:MGI_GO_Notes_demo.pdf]])
 
===12:00 Review Action items from Bar Harbor meeting===
<font color = "Red">see [[2010 Bar Harbor Action items]]</font>
----
 
===12:30 Lunch===
----
 
==1:30-5:30 Discussion of the Vision defined in the GOC NIH grant application==
(Friday afternoon, Saturday Morning)
(This includes presentations of our current efforts and how this vision can become a reality.  Also what goals are needed to reach the aims stated in the application.)
===1:30 Literature-based annotations (Mike)===
(chair of session Rama)
# Vision (i.e. efficiency, quality and consistency goals)
# Implementation: what will be necessary to accomplish this goal?
#* Prioritization of which organisms and genes to be curated
# Current status/accomplishments
# Possible metrics
 
===2:00 Biological focus-group annotations (Judy)===
(chair of session Emily)
# vision (and entire text-book TOC)
# Implementation: what will be necessary to accomplish this goal?
# Current status/accomplishments
#* New ontologies terms added at recent meetings.
# Possible metrics/milestones
 
===2:45 Phylogenetically-based annotations (Paul T)===
# Vision (comprehensive annotations)
# Implementation (scalability)
# Pilot project, including possible metrics
----
 
===3:30 Break===
----
===3:45 Common Annotation Framework (Paul S)===
# Vision
#* Goals:
#**        More efficient curation
#**        Support annotation by volunteers
#* Plan:
#**      Specify Requirements    2011  including minimal functional system and common GOC database
#**      Make it so    2012 onwards
#* Pieces:  Curation Form (ontology viewer, autocomplete with synonyms, multi-value fields, QC checks [GAF validator], etc.)
#**Paper Viewer (view markup on HTML, XML, PDF;)
#**NLP modules (run algorithms, see results on Paper (entity recognition;  and auto-fill into Curation Form).
#**PAINT (web) [interPro etc. window] PAINT viewer? with pictures of organisms…
#**Term Genie
#**Control Panel
 
# implementation: what will be necessary to accomplish this goal?
# Current Efforts
#* PomBase community annotation tool (Val; [[File:Curation tool.pdf]])
#* Textpresso, Phenote, PAINT-web, and all the rest...
#**Introduction to GO Curation using Textpresso (Kimberly, 10-15 mins.)
# metrics and milestones
----
 
===Group dinner at Rosa Mexicano at LA Live (Downtown LA) at 6pm===
----
 
=Saturday May 21, Davidson Center, Board Room=
==9:00-10:45 Discussion of the Vision defined in the GOC NIH grant application==
=== 9:00 group photo===
=== 9:05 Annotation File Format proposals ===
 
Proposal for annotation submission in GPAD and GPI formats - see [[Annotation File Format Proposal]]
 
 
=== 9:15 Ontology development (David)===
# Vision
# Implementation: what will be necessary to accomplish this goal.
# Metrics and milestones


== Action Items from Bar Harbor GOC meeting ==
=== 10:00 Community resources and Dissemination (Mike, co-chairs: Emily & Rama)===
# Vision
# Implementation: what will be necessary to accomplish this goal.
# Monitoring customer satisfaction
----


== Working plans for deliverables over the next 4 & 12 months ==
===10:45 Coffee break===
# Annotation (Rama and Emily)
----
#* [http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2011 Timeline: discuss progress and priorities]
===11 to 11:45 Wrap up, action items===
#* [http://wiki.geneontology.org/index.php/Annotation_Quality_Control_Checks#Proposed_Soft_QC_checks New annotation sanity checks being proposed]
----
#** mention QC checks? How groups should be kept up-to-date? See Managers discussion [http://wiki.geneontology.org/index.php/Manager_23March11 here]
===11:45 fresh air break===
#* '''ECO presentation'''.
#** Would be nice to establish how the ECO project should be used by GOC, now that the first draft has been published. [[User:Edimmer|Edimmer]] 17:14, 28 February 2011 (UTC) (Marcus will present ECO update)
#* '''Pre- vs post-composition of GO terms, and use of column 16.''' Should we be adding in terms for E.g. apoptosis of individual cell types (if they have no other parent in a different node), or should we be capturing this at the annotation stage using column 16? What is the time-scale of using column 16 and what data types can be included? (Becky)
#* Biological focus-group annotations (Emily)
#** Transcription factor workshop?
#** Working in a research environment and the impact on annotation targets? (Ruth)
#*** BHF-UCL team involved in annotating specific genes identified through GWAS or microarray (Ruth)
# Reference Genome (Pascale)
#* [http://wiki.geneontology.org/index.php/Reference_Genome_Timeline-Jan-Jun2011 Timeline: discuss progress and priorities]
#* Enhancements to PAINT & DB (Suzi)
#* Incorporating InterPro motifs into PAINT''
# Software (Chris)
#* [http://wiki.geneontology.org/index.php/SWUG_Timeline_2010-2011 Timeline: discuss progress and priorities]
#* software status update (AmiGO, GOOSE, GOLD, etc. - Seth)
# Ontology development (David)
#* [http://wiki.geneontology.org/index.php/2011_Timeline Timeline: discuss progress and priorities]
#* recent projects - notes/accomplishments
#** Transcription factors (Karen C; available Thursday or Friday morning)
#** Signaling (Becky)
#** Chemicals (David or Tanya)
#** software utilities (Reasoners, QC - Chris)
#* OBO/OWL migration (Chris)
#* Notifying a wider audience about large-scale changes to the ontology: when a project is starting up, and when key changes have been done (Becky)
#* Notifying a wider audience about proposed term obsoletions.
#* '''Protein complexes'''(Harold)
#** What is within the scope of GO, and what is in the scope of PRO?
#** Should GO capture gene product specific protein complexes, or species-specific protein complexes?
#** Should protein complexes be defined based on function or component information? (Becky and Peter D'E)
# Community resources and Dissemination (Emily & Rama)
#* GO Help Rotation/designated person to deal with GO help (Rama)
#* '''InterPro2GO presentation'''
#** Sarah Burge, InterPro. Time requested: 40 min presentation, 20 mins discussion.
#** Contents: Brief summary of the revised guidelines for the GO mapping of InterPro entries. To include: InterPro evidence requirements, new policy of mapping Domain, Site and Repeat entries, changes in coverage between the old and new approaches, occasions where InterPro is  unable to GO map an entry and finally, the automatic checks to prevent taxonomy violations and assignment of redundant terms.


== Discussion of the Vision defined in the GOC NIH grant application ==
=== 12:00 lunch and departures or Satellite meeting ===
(This includes presentations of our current efforts and how these will map into the vision.  Also what goals are needed to reach the aims stated in the application.)
# Literature-based annotations (Rama)
#* vision (i.e. efficiency, quality and consistency goals)
#* implementation: what will be necessary to accomplish this goal?
#* current status/accomplishments
#* possible metrics
# Biological focus-group annotations (Emily)
#* vision (and entire text-book TOC?)
#* implementation: what will be necessary to accomplish this goal?
#* current status/accomplishments
#** New ontologies terms added at recent meetings?
#* possible metrics/milestones
# Phylogenetically-based annotations (Paul T)
#* vision (e.g. dynamically adding a new protein to the right family, versioning with stable IDs for ancestral nodes)
#* implementation: what will be necessary to accomplish this goal?
#* current status/accomplishments
#* possible metrics
# Common Annotation Framework (Suzi and Paul S)
#* vision
#* implementation: what will be necessary to accomplish this goal?
#* ''Current Efforts''
#** PomBase community annotation tool (Val?)
#** Textpresso, Phenote, PAINT-web, and all the rest...
#* metrics and milestones
# Ontology development (David)
#* Vision
#* implementation: what will be necessary to accomplish this goal?
#* metrics and milestones
# Community resources and Dissemination (Emily & Rama)
#* vision
#* implementation: what will be necessary to accomplish this goal?
#** '''Current Efforts in Community GO Annotation''' (Emily)
#*** BHF-UCL team training programs for MSc students and staff training at UCL. How productive are UCL students and staff at annotating? (Ruth)
#*** Texas A&M annotation competition? (CACAO)
#*** TAIR GO annotations from submitted publications?
#* Monitoring customer satisfaction


== Satellite meetings ==
== Satellite meetings ==
# Cardiac Conduction ontology development workshop (Ruth&David) [http://wiki.geneontology.org/index.php/Cardiac_conduction]
# Cardiac Conduction ontology development workshop (Ruth & David) [http://wiki.geneontology.org/index.php/Cardiac_conduction]
#* pre-workshop discussion (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
#* pre-workshop discussion (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
#* probably straight after main meeting closes on 19th May
#* probably straight after main meeting closes on 19th May
#* workshop date not yet set, aiming for Sept-Nov 2011
#* workshop date not yet set, aiming for Sept-Nov 2011
#* Please let Ruth know if interested in attending workshop/pre-meeting
#* Please let Ruth know if interested in attending workshop/pre-meeting

Latest revision as of 12:34, 8 April 2014

Minutes: (By hosts of previous meeting: MGI)

Meeting action items

Thursday May 19, Cardinal & Gold Room

8:30 Registration

9:00 Welcome; Review of schedule and agenda

  • Introductions.
  • GOC PI announcements

9:15 - 5:30 Working Group Reports, plans through 2011, discussion of priorities

9:15 Annotation

(Rama, Emily, Pascale) Progress and Priorities

To encompass:

  1. Annotation Outreach efforts (30 min)
  2. Development of Annotation Guidelines (Geneva, Evidence codes). Suggestions for further guidelines.
  3. Draft on how external groups should display annotation.
  4. Focused annotation efforts by GO Consortium members (Emily)
  5. Proposed improvements to the Annotation web pages
  6. has_part relationship (Chris)
  7. Automated annotation support (QCs, Taxon GO, inferred annotations)
    1. XML encoding of QC checks: http://geneontology.org/GO.annotation_qc.shtml
    2. Demo of web-based GAF validator: http://ladle.lbl.gov:8888/gaftools.html (Amelia)

AAC Discussion Questions

File:AAandC presentation.pdf

10:15 Community resources and Dissemination (Emily & Rama)

  1. GO Help Rotation. (Rama) File:ECOtoGO.pdf

10:30 Break



11:30 Evidence Code Ontology presentation

  1. Marcus (25 minutes)
  2. Discussion on the appropriate usage of ECO identifiers in annotation (Rama)

12:00 Annotation deliverables

  1. Discussion of the distinction between annotations distributed by the GOC and those from the MODs. (Mike, 15 min)
  2. Discussion on changing the policy on restricting taxon to specific GAF files. (Mike, 15 min)

12:30 Lunch


1:30 Overview of the outreach efforts

  1. Overview of the outreach efforts to specific scientific communities for community annotation by the BHF-UCL File:BHF UCL CommunityAnnotation.pdf and TAIR teams as well as the CACAO (Community Assessment of Community Annotation with Ontologies; File:CACAO2011.pdf) course by EcoliWiki (Ruth, Tanya and Jim; 10 mins each and 15 mins discussion)
  2. RACE-PRO community submission/annotation tool for the Protein Ontology has a section for adding GO annotation. http://pir.georgetown.edu/cgi-bin/pro/race_pro

2:30 InterPro2GO presentation

(Sarah Burge) (40 min presentation, 10 mins discussion)

  1. Brief summary of the revised guidelines for the GO mapping of InterPro entries.
  2. InterPro evidence requirements, new policy of mapping Domain, Site and Repeat entries, changes in coverage between the old and new approaches, occasions where InterPro is unable to GO map an entry and finally, the automatic checks to prevent taxonomy violations and assignment of redundant terms.

3:20 Break


3:30 Ontology development

(David)

  1. Timeline: discuss progress and priorities (10 mins)
  2. Recent projects - notes/accomplishments
    • Transcription factors (Karen; available any time Thursday or Friday morning before noon) (15 mins)
    • Signaling (Becky) (15 mins) [1]
    • Chemicals (Tanya) (15 mins)



Dinner on your own


Friday May 20, Alumni Room

8:15-12:30 Working Group Reports (cont), plans through 2011, discussion of priorities

8:15 ontology group (cont'd)

  1. Protein complexes (Harold) (15 mins, File:Complexes in GO and PRO.pdf)
    • The scope of GO relative to that of PRO?
    • Should GO capture gene product specific protein complexes, or species-specific protein complexes?
    • Should protein complexes be defined based on function or component information? (Becky and Peter D'E)
    • Notifications of change (Becky) (15-20 mins).
    • Large-scale changes to the ontology.
      • When a development project is starting up, and when their key changes are released
      • Process for discussion and release of proposed term obsoletions.

9:00 Reference Genomes

  1. Report from the Reference Genomes project (Pascale) File:2011-05-USC-RefGenome-Report-Pascale.pdf
  2. Timeline: discuss progress and priorities 20 min
  3. PanTree website for tree annotations and evidence trail for inferred annotations from PAINT (Paul T) 15 min



10:00 Break


10:30 annotation

  1. BHF-UCL team involved in annotating specific genes identified through GWAS or microarray (Ruth; 15 mins) File:BHF UCL FocusedAnnotation.pdf

10:45 Software

  1. Report from the Working Group (Chris)
    • Software utilities (Reasoners, QC - Chris; TG - Heiko)
  2. OBO/OWL migration (Chris)
  3. Timeline: discuss progress and priorities
  4. Software status (AmiGO, GOOSE, GOLD, etc. - Seth) File:GoSW-USC-CM.pdf

11:30 Annotation Extension information

  1. Annotation Extension information (Column 16) (MGI / Chris / Val/Emily 30 min)

File:Go-c16-roles-USC.pdf
Other related slides:(File:Annotation extension tableVal.pdf, File:UniProtKB col16.pdf, File:MGI GO Notes demo.pdf)

12:00 Review Action items from Bar Harbor meeting

see 2010 Bar Harbor Action items


12:30 Lunch


1:30-5:30 Discussion of the Vision defined in the GOC NIH grant application

(Friday afternoon, Saturday Morning) (This includes presentations of our current efforts and how this vision can become a reality. Also what goals are needed to reach the aims stated in the application.)

1:30 Literature-based annotations (Mike)

(chair of session Rama)

  1. Vision (i.e. efficiency, quality and consistency goals)
  2. Implementation: what will be necessary to accomplish this goal?
    • Prioritization of which organisms and genes to be curated
  3. Current status/accomplishments
  4. Possible metrics

2:00 Biological focus-group annotations (Judy)

(chair of session Emily)

  1. vision (and entire text-book TOC)
  2. Implementation: what will be necessary to accomplish this goal?
  3. Current status/accomplishments
    • New ontologies terms added at recent meetings.
  4. Possible metrics/milestones

2:45 Phylogenetically-based annotations (Paul T)

  1. Vision (comprehensive annotations)
  2. Implementation (scalability)
  3. Pilot project, including possible metrics

3:30 Break


3:45 Common Annotation Framework (Paul S)

  1. Vision
    • Goals:
      • More efficient curation
      • Support annotation by volunteers
    • Plan:
      • Specify Requirements 2011 including minimal functional system and common GOC database
      • Make it so 2012 onwards
    • Pieces: Curation Form (ontology viewer, autocomplete with synonyms, multi-value fields, QC checks [GAF validator], etc.)
      • Paper Viewer (view markup on HTML, XML, PDF;)
      • NLP modules (run algorithms, see results on Paper (entity recognition; and auto-fill into Curation Form).
      • PAINT (web) [interPro etc. window] PAINT viewer? with pictures of organisms…
      • Term Genie
      • Control Panel
  1. implementation: what will be necessary to accomplish this goal?
  2. Current Efforts
    • PomBase community annotation tool (Val; File:Curation tool.pdf)
    • Textpresso, Phenote, PAINT-web, and all the rest...
      • Introduction to GO Curation using Textpresso (Kimberly, 10-15 mins.)
  3. metrics and milestones

Group dinner at Rosa Mexicano at LA Live (Downtown LA) at 6pm


Saturday May 21, Davidson Center, Board Room

9:00-10:45 Discussion of the Vision defined in the GOC NIH grant application

9:00 group photo

9:05 Annotation File Format proposals

Proposal for annotation submission in GPAD and GPI formats - see Annotation File Format Proposal


9:15 Ontology development (David)

  1. Vision
  2. Implementation: what will be necessary to accomplish this goal.
  3. Metrics and milestones

10:00 Community resources and Dissemination (Mike, co-chairs: Emily & Rama)

  1. Vision
  2. Implementation: what will be necessary to accomplish this goal.
  3. Monitoring customer satisfaction

10:45 Coffee break


11 to 11:45 Wrap up, action items


11:45 fresh air break

12:00 lunch and departures or Satellite meeting

Satellite meetings

  1. Cardiac Conduction ontology development workshop (Ruth & David) [2]
    • pre-workshop discussion (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
    • probably straight after main meeting closes on 19th May
    • workshop date not yet set, aiming for Sept-Nov 2011
    • Please let Ruth know if interested in attending workshop/pre-meeting