2012 GOC Meeting Caltech: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
|||
(106 intermediate revisions by 15 users not shown) | |||
Line 1: | Line 1: | ||
[[Category:GO Consortium Meetings]] | |||
= [[2012 Caltech GOC Meeting Logistics]] = | = [[2012 Caltech GOC Meeting Logistics]] = | ||
Follow Link to [https://docs.google.com/document/d/1h85nGcAFs2qzhslpuxDpj06V1y84GwVJ7l2TJA_PmSE/edit meeting minutes as a Google Doc] | |||
= Biological relevance - Paul S - Sunday 10:30 = [coffee at | Today's wireless: | ||
* GO as a biological reference (critique?) | * name: NETGEAR49(-5G) | ||
** Biological utility survey (Rama, Ranjana) | * 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 | ||
Line 12: | Line 18: | ||
= Web - Cherry - Sunday afternoon = | = Web - Cherry - Sunday afternoon = | ||
* GO Website and user interfaces | * GO Website and user interfaces | ||
** AmiGO 2 | ** AmiGO 2 status (Seth) [[File:A2-update.pdf]] | ||
** QuickGO (Tony) | ** QuickGO (Tony) | ||
** GO- | ** 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) | ** Switch to Drupal (Seth) [[File:Drupal-community.pdf]] | ||
*** dynamic monitoring of discussions (biostars, Tweets, etc.) | *** dynamic monitoring of discussions (biostars, Tweets, etc.) | ||
** New logo ( | *** [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? | ** Need a webmaster? | ||
* GO Help (Judy) | * GO Help (Judy) | ||
Line 26: | Line 33: | ||
** Meetings to attend | ** Meetings to attend | ||
** New training material | ** New training material | ||
* Licensing issues (Seth) | * Licensing issues (Seth) [[File:Licenses.pdf]] | ||
= Biological Representation - Paul T - Monday morning | = 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] | ||
*** ontology publishing pipeline | *** ontology publishing pipeline | ||
** Term Genie status (Heiko) | ** 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) | ||
** | ** Rhea - importing enzymatic reactions (Jane) | ||
** BFO 2.0 - (Chris) | ** BFO 2.0 - (Chris) | ||
*** do we comply with BFO and split part_of into 2 relations? Need 'official' signoff of GO's stance | *** 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 | * Extensions to the GO annotation model | ||
** LEGO data model, an 'annoton' (Chris and Paul) | ** LEGO data model, an 'annoton' (Chris and Paul) [http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/meeting/consortium/Pasadena2012/GO-lego-20121007.pptx pptx] | ||
*** For prototyping: Protege plug-in for annotation (Heiko) | *** For prototyping: Protege plug-in for annotation (Heiko) | ||
*** Current examples (Kimberly and David) | *** Current examples (Kimberly and David) | ||
Line 47: | Line 55: | ||
*** relationship to LEGO | *** relationship to LEGO | ||
= Project infrastructure - Suzi - Monday | = Project infrastructure - Suzi - Monday afternoon = | ||
* CAT | * CAT | ||
** Architecture, services (Suzi) | ** Architecture, services (Suzi) [[File: CAT-webservices.pdf]] | ||
** protein2go introduction (Rachael) | ** protein2go introduction (Rachael) | ||
** WormBase experience with protein2go (Kimberly) | ** WormBase experience with protein2go (Kimberly) | ||
** Wormbase CC tool (Kimberly) | ** Wormbase CC tool (Kimberly) | ||
** Migration plans (Suzi) | ** Migration plans (Suzi) [[File: p2go transition.pdf]] | ||
*** Short term: towards protein2go | *** Short term: towards protein2go | ||
*** Longer term: capabilities to support LEGO | *** Longer term: capabilities to support LEGO | ||
* Enrichment (and other) tool improvement plans (Chris) | * Enrichment (and other) tool improvement plans (Chris) | ||
** Standardize interface to tools & allow plug in play eg via [[Galaxy]] | ** 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 | ||
* PAINT (Paul T) | |||
** SwissProt strategy for protein family annotation (Alan) | |||
** PAINT user guide (Huaiyu) at http://wiki.geneontology.org/index.php/PAINT_User_Guide | |||
** PAINT annotation progress | |||
= Annotation Production - Judy Tuesday | = Annotation Production - Judy Tuesday morning= | ||
* Annotation | ==Annotation== | ||
** | * Annotation Measurement of Success(Mike) | ||
** | ** [[File:GO-annotations.201201008-2.pdf | Measures 2012]] | ||
** | ** "Quality" aka Reproducibility | ||
** | * 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 | * Standard processing of uploaded annotations | ||
** [http://www.geneontology.org/GO.annotation_qc.shtml Automated annotation QC] (Chris/Heiko) | ** [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]] | ||
* | * Redundant/non-redundant annotations (Rama) [[File:RedundantCaltech2012.pdf]] | ||
* Provenance of evidence (Rama) | |||
* | |||
* Submissions and outreach to outside groups | * Submissions and outreach to outside groups | ||
** Web page with instructions (Rama) | ** Web page with instructions (Rama) | ||
** Pulling in external annotations | ** 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 | |||
[[File:GOC Caltech-1..JPG|200px|thumb|left|Photo 1]] [[File:GOC-Caltech-2.JPG|200px|thumb|center|Photo 2]] |
Latest revision as of 12:25, 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]
- GO as a biological reference (critique?) File:GOC12-slidesPaulSternberg.pdf
- Biological utility survey (Rama, Ranjana) File:GOCwebsiteCaltech12.pdf
- Objectives for this meeting
- set quarterly objectives process
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) (GoMine)
- Switch to Drupal (Seth) File:Drupal-community.pdf
- dynamic monitoring of discussions (biostars, Tweets, etc.)
- demo site
- New logo (contest is happening : 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
- Jira tracking system (Jane)
- Automated ontology checks Jenkins (Chris) pptx
- 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)
- 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
- LEGO data model, an 'annoton' (Chris and Paul) pptx
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)
- SwissProt strategy for protein family annotation (Alan)
- PAINT user guide (Huaiyu) at http://wiki.geneontology.org/index.php/PAINT_User_Guide
- PAINT annotation progress
Annotation Production - Judy Tuesday morning
Annotation
- Annotation Measurement of Success(Mike)
- File:GO-annotations.201201008-2.pdf
- "Quality" aka Reproducibility
- 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
- Automated annotation QC (Chris/Heiko ~5 slides + demo) File:GOC-Meeting-2012-Oct-Automated QC for annotations.pdf
- 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
- ONE: Term requests (Jane)
- Priority of Ontology development workflow and coordination
- Strategy for prioritization of ontology development topics
- Emily summation of needed areas aka textbook
- Information content approac
- Strategy for prioritization of ontology development topics
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