Difference between revisions of "2012 GOC Meeting Caltech"

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= Biological relevance - Paul S =
+
[[Category:GO Consortium Meetings]]
* GO as a biological reference (critique?)
+
= [[2012 Caltech GOC Meeting Logistics]] =
** Strategy for prioritization of ontology development topics
+
Follow Link to [https://docs.google.com/document/d/1h85nGcAFs2qzhslpuxDpj06V1y84GwVJ7l2TJA_PmSE/edit meeting minutes as a Google Doc]
*** Information content approach aka Gil
+
 
*** Emily summation of needed areas aka textbook
+
Today's wireless:
 +
* name: NETGEAR49(-5G)
 +
* pass: rockyrabbit990
 +
 
 +
MONDAY:  Millikin Library; coffee at 0830; snack at 1500; lunch on your own (Chandler Cafeteria)
 +
 
 +
= Biological relevance - Paul S - Sunday 10:30 =  
 +
024 Beckman Behavioral Biology Building; [coffee at 09:30; lunch 1at 1230]
 +
* GO as a biological reference (critique?) [[File: GOC12-slidesPaulSternberg.pdf]]
 +
** Biological utility survey (Rama, Ranjana) [[File: GOCwebsiteCaltech12.pdf‎]]
 
* Objectives for this meeting
 
* Objectives for this meeting
 
** set quarterly objectives process
 
** set quarterly objectives process
  
= Biological Representation - Paul T =
+
= Web - Cherry - Sunday afternoon =
 +
* GO Website and user interfaces
 +
** AmiGO 2 status (Seth) [[File:A2-update.pdf]]
 +
** QuickGO (Tony)
 +
** GOMine InterMine for GO (Mike/Rama) ([http://celis.stanford.edu:8080/gomine-dev/template.do?name=DataSouce_GOAnnot&scope=global GoMine])
 +
** Switch to Drupal (Seth) [[File:Drupal-community.pdf]]
 +
*** dynamic monitoring of discussions (biostars, Tweets, etc.)
 +
*** [http://fork.lbl.gov/ demo site]
 +
** New logo (contest is happening : [http://www.logomyway.com/9400/friends/Gene_Ontology.php Rate the logos you like at LogoMyWay])
 +
** Need a webmaster?
 +
* GO Help (Judy)
 +
** any new approaches?
 +
** %of questions we can answer with available tools?
 +
* Dissemination
 +
** Publication plans
 +
** Meetings to attend
 +
** New training material
 +
* Licensing issues (Seth) [[File:Licenses.pdf]]
 +
 
 +
= Biological Representation - Paul T - Sunday aft - Monday morning=
 
* Management of Ontology Development
 
* Management of Ontology Development
 
** Jira tracking system (Jane)
 
** Jira tracking system (Jane)
** Automated ontology checks [[Jenkins]] (Chris)
+
** Automated ontology checks [[Jenkins]] (Chris) [http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/meeting/consortium/Pasadena2012/GO-Jenkins-for-ontologies-2012.pptx pptx]
** Term Genie Demo (Heiko)
+
*** ontology publishing pipeline
 +
** Term Genie status (Heiko - ~6 slides + demo) [[File:GOC-Meeting-2012-Oct-TermGenie_Status_Update.pdf]]
 
* Incorporation of External ontologies (David and Jane)
 
* Incorporation of External ontologies (David and Jane)
 +
** CHEBI  (David)  [[file:Chemicals_Caltech.pdf]]  done Sunday afternoon
 
** Report on migration of NIF subcellular AO to GO-CC (Jane)
 
** Report on migration of NIF subcellular AO to GO-CC (Jane)
** BFO 2.0 - do we comply with BFO and split part_of into 2 relations? (Chris)
+
** Rhea - importing enzymatic reactions (Jane)
** CHEBI  (David)
+
** BFO 2.0 - (Chris)
* LEGO status: current model and how it relates to col. 16 extensions
+
*** do we comply with BFO and split part_of into 2 relations? Need 'official' signoff of GO's stance
** 'annoton' data model (Chris and Paul)
+
* Extensions to the GO annotation model
** Protege plug-in for annotation (Heiko)
+
** LEGO data model, an 'annoton' (Chris and Paul) [http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/meeting/consortium/Pasadena2012/GO-lego-20121007.pptx pptx]
** Current examples (Kimberly and David)
+
*** For prototyping: Protege plug-in for annotation (Heiko)
** col. 16 extensions and LEGO (Paul, Chris, Jane, Rachael)
+
*** Current examples (Kimberly and David)
 +
** col. 16 extensions (Paul, Chris, Jane, Rachael)
 +
*** GPAD releases
 +
*** relationship to LEGO
  
 
+
= Project infrastructure - Suzi - Monday afternoon =
= Project infrastructure - Suzi  =
 
 
* CAT
 
* CAT
** Architecture, services (Chris)
+
** Architecture, services (Suzi) [[File: CAT-webservices.pdf‎]]
 +
** protein2go introduction (Rachael)  
 
** WormBase experience with protein2go (Kimberly)
 
** WormBase experience with protein2go (Kimberly)
 
** Wormbase CC tool (Kimberly)
 
** Wormbase CC tool (Kimberly)
* PAINT
+
** Migration plans (Suzi) [[File: p2go transition.pdf]]
** PAINT annotation progress
+
*** Short term: towards protein2go
* Enrichment tool improvement plans
+
*** Longer term: capabilities to support LEGO
** Standardize interface to tools & allow plug in play eg via [[Galaxy]]
+
* Enrichment (and other) tool improvement plans (Chris)
 +
** Standardize interface to tools & allow plug in play eg via [[Galaxy]] [http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/meeting/consortium/Pasadena2012/GO-Galaxy.pptx pptx]
 
** Promote tools that provide access to latest GO, work with those that don't. See [[GO Tools Registry]]
 
** Promote tools that provide access to latest GO, work with those that don't. See [[GO Tools Registry]]
 
** Getting enrichment tools to leverage ontology and annotation improvements
 
** Getting enrichment tools to leverage ontology and annotation improvements
*** other relationship types
+
* PAINT (Paul T)
*** CHEBI, CL etc
+
** SwissProt strategy for protein family annotation (Alan)
*** LEGO (Paul)
+
** PAINT user guide (Huaiyu) at http://wiki.geneontology.org/index.php/PAINT_User_Guide
*** [[Annotation Extension]]
+
** PAINT annotation progress
  
= Annotation Production - Judy =
+
= Annotation Production - Judy Tuesday morning=
* Annotation Production
+
==Annotation==
** volume of annotations
+
* Annotation Measurement of Success(Mike)
** backlog of papers selected
+
** [[File:GO-annotations.201201008-2.pdf | Measures 2012]]
*Term requests
+
** "Quality" aka Reproducibility
** Current rate of additions & rate of clearance
+
* Annotation Hard Checks. (Mike)
** TermGenie
+
** Have removed IEAs from JCVI, Gramene, GeneDB P. falciparum, GeneDB tsetse, Pseudocap because > 2yr out of date
* GO Help
+
** Propose to remove IEAs from CGD, AspDB, GeneDB L. major, GeneDB T. brucei, and include up to date IEAs from GOA
** Move to JIRA
+
*** General rule: this will be done for any other projects that *DO NOT* include annotations from GOA.
** any new approaches?  
+
** We filter out IEA annotations that are older than 1 year.  Should we be filtering out ISS say after 2 years?
** biostars etc
+
* Standard processing of uploaded annotations
** Tweeting?
+
** [http://www.geneontology.org/GO.annotation_qc.shtml Automated annotation QC] (Chris/Heiko ~5 slides + demo) [[File:GOC-Meeting-2012-Oct-Automated_QC_for_annotations.pdf]]
** %of questions we can answer with available tools?
+
* Redundant/non-redundant annotations (Rama) [[File:RedundantCaltech2012.pdf‎]]
* Submissions from outside groups
+
* Provenance of evidence (Rama)
 +
* Submissions and outreach to outside groups
 
** Web page with instructions (Rama)
 
** Web page with instructions (Rama)
** Future work here... (who has been in contact? any active outreach?)
+
** Pulling in external annotations
* Automated annotation production
+
 
** [http://www.geneontology.org/GO.annotation_qc.shtml QC rules]
+
==Annotation via Ontology: Production and Priorities==
** [[Jenkins]]
+
[[File:OverviewOntologyAnnotation.pdf]]
* Project-led GOC annotation efforts (Paul S)
+
* Current ontology development and annotation topics on the table
** New reporting page
+
** ONE: Term requests (Jane)
** Observations/Comments
+
***Current rate of additions & rate of clearance
* Move to SVN
+
** TWO: topic oriented via community interest
* Current ontology development and annotation topics on the table (one slide each)
+
*** cardio conduction (Ruth)
*** cardio (Ruth)
 
 
*** apoptosis (Paola)
 
*** apoptosis (Paola)
*** cell cycle (Val or Judy)
+
*** cell cycle (Val)
 
*** tRNA Modification (Harold)
 
*** tRNA Modification (Harold)
 +
** THREE global review of coverage
 +
* Priority of Ontology development workflow and coordination
 +
** Strategy for prioritization of ontology development topics
 +
*** Emily summation of needed areas aka textbook
 +
*** Information content approac
  
= Web - Cherry =
+
= Wrap-Up (Paul S) Tuesday 1140 =
* Licensing issues
+
* Review Action Items
* User interfaces
+
* Set objectives for next period
** GO-Mine/Enrichment
+
* Discuss / decide on tag for Logo competition
** AmiGO
+
* Wrap-up
** QuickGO
+
* Group Photos
** Galaxy?
+
[[File:GOC Caltech-1..JPG|200px|thumb|left|Photo 1]] [[File:GOC-Caltech-2.JPG|200px|thumb|center|Photo 2]]
** New logo (just tell us)
 
* GO Website
 
** Need a webmaster?
 
** Switch to Drupal? (Seth)
 
* Dissemination
 
** Publication plans
 
** Meetings to attend
 
** New training material
 
* [[GO Tools Registry]]
 
* GO & Linked Data
 
 
 
= Set objectives for next period (Paul S) =
 

Latest revision as of 09:25, 8 April 2014

2012 Caltech GOC Meeting Logistics

Follow Link to meeting minutes as a Google Doc

Today's wireless:

  • name: NETGEAR49(-5G)
  • pass: rockyrabbit990

MONDAY: Millikin Library; coffee at 0830; snack at 1500; lunch on your own (Chandler Cafeteria)

Biological relevance - Paul S - Sunday 10:30

024 Beckman Behavioral Biology Building; [coffee at 09:30; lunch 1at 1230]

Web - Cherry - Sunday afternoon

Biological Representation - Paul T - Sunday aft - Monday morning

  • Management of Ontology Development
  • Incorporation of External ontologies (David and Jane)
    • CHEBI (David) File:Chemicals Caltech.pdf done Sunday afternoon
    • Report on migration of NIF subcellular AO to GO-CC (Jane)
    • Rhea - importing enzymatic reactions (Jane)
    • BFO 2.0 - (Chris)
      • do we comply with BFO and split part_of into 2 relations? Need 'official' signoff of GO's stance
  • Extensions to the GO annotation model
    • LEGO data model, an 'annoton' (Chris and Paul) pptx
      • For prototyping: Protege plug-in for annotation (Heiko)
      • Current examples (Kimberly and David)
    • col. 16 extensions (Paul, Chris, Jane, Rachael)
      • GPAD releases
      • relationship to LEGO

Project infrastructure - Suzi - Monday afternoon

  • CAT
    • Architecture, services (Suzi) File:CAT-webservices.pdf
    • protein2go introduction (Rachael)
    • WormBase experience with protein2go (Kimberly)
    • Wormbase CC tool (Kimberly)
    • Migration plans (Suzi) File:P2go transition.pdf
      • Short term: towards protein2go
      • Longer term: capabilities to support LEGO
  • Enrichment (and other) tool improvement plans (Chris)
    • Standardize interface to tools & allow plug in play eg via Galaxy pptx
    • Promote tools that provide access to latest GO, work with those that don't. See GO Tools Registry
    • Getting enrichment tools to leverage ontology and annotation improvements
  • PAINT (Paul T)

Annotation Production - Judy Tuesday morning

Annotation

  • Annotation Measurement of Success(Mike)
  • Annotation Hard Checks. (Mike)
    • Have removed IEAs from JCVI, Gramene, GeneDB P. falciparum, GeneDB tsetse, Pseudocap because > 2yr out of date
    • Propose to remove IEAs from CGD, AspDB, GeneDB L. major, GeneDB T. brucei, and include up to date IEAs from GOA
      • General rule: this will be done for any other projects that *DO NOT* include annotations from GOA.
    • We filter out IEA annotations that are older than 1 year. Should we be filtering out ISS say after 2 years?
  • Standard processing of uploaded annotations
  • Redundant/non-redundant annotations (Rama) File:RedundantCaltech2012.pdf
  • Provenance of evidence (Rama)
  • Submissions and outreach to outside groups
    • Web page with instructions (Rama)
    • Pulling in external annotations

Annotation via Ontology: Production and Priorities

File:OverviewOntologyAnnotation.pdf

  • Current ontology development and annotation topics on the table
    • ONE: Term requests (Jane)
      • Current rate of additions & rate of clearance
    • TWO: topic oriented via community interest
      • cardio conduction (Ruth)
      • apoptosis (Paola)
      • cell cycle (Val)
      • tRNA Modification (Harold)
    • THREE global review of coverage
  • Priority of Ontology development workflow and coordination
    • Strategy for prioritization of ontology development topics
      • Emily summation of needed areas aka textbook
      • Information content approac

Wrap-Up (Paul S) Tuesday 1140

  • Review Action Items
  • Set objectives for next period
  • Discuss / decide on tag for Logo competition
  • Wrap-up
  • Group Photos
Photo 1
Photo 2