2017 Berkeley GO Editors Workshop II
Party! (or at least dinner together)
- Where: 2 Biehs Court, Oakland, CA 94618
- When: Wednesday, August 16 (whenever the meeting closes down and you get over there)
- Ideas for what you'd like to eat? And drink?
Agenda (Draft)
Tuesday 15th
Note: Jim may have a hard time calling in on wed afternoon, tue better, so we may rearrange to accomodate
Tue Morning
- Intro, goals (Chris)
- Advanced OWL Tutorial (Chris, DOS)
- Work through exercises: https://github.com/geneontology/protege-tutorial
- Improving the tutorial for others
- Advanced concepts
- GCIs
- Hidden GCIs
- How to write good logical definitions
Tue Afternoon
sparkly swirly things
- SPARQL (Eric, Chris)
- SWRL (DavidOS)
How to do cool stuff on the command line
- ROBOT tutorial
- Setup (Eric)
- Commands (Chris)
- You'll love Makefiles. No, really you will
- Makefile concepts
- Overview of the GO makefile
Pipes and stuff
- Pipelines and Continuous Integration (Chris, Seth, Eric)
- Travis deep dive
- How to figure out WTF went wrong with your pull request
- Jenkins Release pipeline (Seth)
Wednesday 16th
Wed Morning
DOSDPs, yaml, INCA is the new TermGenie
- TermGenie Replacement
- Plan Overview (Chris)
- yaml design pattern overview (Nicole V, David OS)
- INCAForm demo (Nicole V)
- Exercises
- Add a new term in INCAForm
- Make a new design pattern
- Discussion
- Reusing templates in Noctua
- Getting stricter about accepting compositional terms
Planning for the future
- Protege and WebProtege (Tentative) (Matt H)
- Discussion: What would an ideal ontology development environment be like?
Wed Afternoon
- RO
- Overview (DavidOS, Chris)
- Gene product to class relations (KVA)
- Exercise: making an RO pull request
- GORel (for extensions) (DavidOS)
- Discussion
- retiring GORel
- Documentathon: documenting RO for curators
- ABox Ontologies (DavidOS)
- Overview (DavidOS, Chris)
- Noctua
- Ontology-based QC of Noctua (Chris)
- The Arachne reasoner (Chris, or Jim if he can call in)
- Debugging using the explanation panel
- Table Mode demo (Dan) 4pm
Thursday 17th
Morning
Ontology Content
- Problematic GitHub tickets/mini Projects, backlog
- Update on status of Molecular Function re-factor
- Review the accumulated use cases for GO from ontology ticket #13606. Discuss how we can continue to best meet the needs of our various communities.
- Review all documentation of SOPs for ontology editors.
Afternoon
- Improving editors documentation
- Goals for signaling workshop
Topics
Fundamentals
- Understanding OWL reasoning. A practical sessions with problem solving exercises, covering:
- Equivalent Class, SubClass; Relations: Characteristics, disjoints, hierarchy, chains, domain and range; GCIs; advanced querying; explanations.
- Understanding the current GO relation set. (A practical session with problem solving exercises + aim to develop better doc)
- The art of designing robust equivalence axioms & design patterns ( editors would like more guidelines on how to construct these.)
Infrastructure
- Design pattern infrastructure
- Pipelines and how they run, both imports and file output. Starting jobs with ROBOT.
- Build failures
- Document the various fail messages and how to correct the issues.
- Ontology work for GO-CAM
- QC-checking property chains and relations that will be used for GPAD generation
- Removing the part_of o regulates chains--- Do we want to instantiate all of the current inferences before removal?
- How will design patterns be implemented in Noctua?
- What design patterns should have priority for Noctua?
Logistics
Accommodations
Getting there:
Taxis also available from either MacArthur or Ashby
Parking
Visitor parking is available, see:
Meeting Location
Berkeley Lab, Aquatic Park Offices
Lawrence Berkeley National Laboratory (LBNL), Aquatic Park office of Biosciences Operations at Berkeley Physical address: 717 Potter Street, Berkeley, CA 94710
Meeting room: room 181
Travel between hotel and meeting
- Walk, 1.3 miles
- Free Hollis Shuttle
- Taxi/Lyft/Uber
Aim to be at the lab for 9am
Participants
Name | Organization | Comments | |
---|---|---|---|
David Hill | Jackson Laboratory | ||
Harold Drabkin | Jackson Laboratory | ||
Kimberly Van Auken | Caltech | Arriving SFO Monday, 8/14, 5:03PM | |
Pascale Gaudet | SIB Swiss Institute of Bioinformatics | ||
David Osumi-Sutherland | EBI | ||
Karen Christie | Jackson Laboratory | ||
Tanya Berardini | TAIR/Phoenix | ||
Huaiyu Mi | USC | ||
Nicole Vasilevsky | OHSU | ||
Matt Horridge | Stanford | possible |
LBL:
- Chris Mungall
- Eric Douglass
- Monica Munoz-Torres
- Seth Carbon
- Suzi Lewis