2012 GOC Meeting Caltech
2012 Caltech GOC Meeting Logistics
Follow Link to meeting minutes as a Google Doc
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)
- PAINT annotation progress
Annotation Production - Judy Tuesday morning
- Annotation Production Progress/Tracking (Paul S)
- volume of annotations
- backlog of papers selected
- New reporting page
- Observations/Comments
- Term requests (Judy/Jane)
- Current rate of additions & rate of clearance
- Standard processing of uploaded annotations
- Automated annotation QC (Chris/Heiko ~5 slides + demo) File:GOC-Meeting-2012-Oct-Automated QC for annotations.pdf
- Annotation "Quality", Reproducibility, measures (Mike)
- Filtering of taxid that are not supported. (Mike)
- Have removed JCVI, Gramene, GeneDB P. falciparum, GeneDB tsetse, Pseudocap
- Propose to remove CGD, AspDB, GeneDB L. major, GeneDB T. brucei, and 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?
- Redundant/non-redundant annotations (Rama will summarize what was discussed during Annotation Calls)
- Provenance of evidence (Rama)
- Current ontology development and annotation topics on the table (one slide each, Judy to present)
- cardio conduction (Ruth)
- apoptosis (Paola)
- cell cycle (Val or Judy)
- tRNA Modification (Harold)
- review of approach, staging (Judy)
- Ontology development workflow and coordination (Paul and Judy)
- BioCreative Challenge IV - GO Triage and Annotation (Kimberly, James, Donghui, Judy)
- Submissions and outreach to outside groups
- Web page with instructions (Rama)
- Pulling in external annotations
- Future work - who has been in contact? any active outreach?
Set objectives for next period (Paul S) Tuesday 1140
- Strategy for prioritization of ontology development topics (Paul S and Paul)
- Emily summation of needed areas aka textbook
- Information content approach