Ontology workshop Jan 2013

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Dates: Sun Jan 27 - Tue Jan 29 of 2013 (*FINAL*)

Location: CA

Attendees:

  • Chris (Local - LBL)
  • Heiko (Local - LBL)
  • Suzi (Local - LBL)
  • Tanya (Local - Carnegie - guest pass & parking permit organized)
  • David (staying local)
  • Paola
  • Jane
  • Judy
  • Nicole V (OHSU)

Agenda

Sunday Jan 26

AM

  • 9-9.30 breakfast and coffee
  • 9.30-10 intro remarks
  • 10-10.30 temp switch of editors ontology to owl?
  • 10.30-10.45 break
  • 10.45-11.30 Hinxton refresher. existing workflow. catalogs. DL queries.
  • 11.30-12.30 installing and using new plugins Ontology_editor_plugins

Lunch: Pizza

 AI: Request ChEBI to have a regular owl release?  Jane will request this from Janna.


 AI: Heiko will update the inferred links after ChEBI monthly releases and send around 
report/message with link to report for GO Eds to review. 

New workflow:

 AI: TermGenie editor: Right now, links are inferred as part of Jenkins release 
pipeline and added to the public version.  Suggested change: editors do the inference, add the inferred links 
to the gene_ontology_write.obo version and these links are then propagated to the public version.  This 
provides a layer of review for the inferred links and will allow us to see the 'zombie' links.  The TG editor 
will take on this task at the end of the week. 


 AI: Heiko to remove the inference step of the Jenkins release pipeline for the public version. 

Note: SPARQL querying might be useful in the future for things that cannot be addressed by OE querying. We will likely used canned queries that can be modified so there is no need for the editors to learn the SPARQL syntax.

PM

  • 1.30-2.30 disjointness axioms (x-disjoints.owl)

Can add metadata to x-disjoint.owl (or other owl files) through adding comments to the ontology header. Properties that are good to use for this purpose: "comment", "seeAlso" (to link to outside page, change type to anyURI)

Making classes disjoint from each other: Start with one class: [+]Disjoint with:, go to Class Hierarchy in window that pops up, navigate to and select the set of terms that you want to include, highlight them and click ok. The set will be added as a list to the Disjoint with group.

General Class Axioms: Active ontology View, General axioms tab: example: (part_of some 'G1 phase') DisjointWith (part_of some 'G2 phase) Why this? To state that the two phases do not share parts. This is a symmetrical statement. Stronger than making the statement for one of the terms that one is not a subclass of the others. This is lost in the translation to OBO because it is a class axiom.

 AI: Add new disjoints in the process of normal editing. 

Monday Jan 27

AM

  • 9-10.30 cell cycle logical definitions
  • 10.30-10.45 break
  • 10.45-12.30 ontology editing in protege. x-signaling.owl ?

opened JIRA issue [GO-128] to tackle addition of complex cross-products to the xp file

Lunch / Outing?

PM

  • 2.30-3.30 papers
  • 3.30-4 break
  • 4-5.30 documentation and website

Tuesday Jan 28

AM

  • 9-9.30 review so far, Nicole V intro
  • 9.30-10 exploring cl-edit.owl
  • 10-12.30 enhancing x-cell.owl and cl-edit. split into two groups, one editing

Lunch: cafeteria

PM

  • 1.30-3 continue exercise
  • 3-3.30 break
  • 3.30-5 review, draw up timelines for templates etc


Agenda Item Scratchpad:

Transition to OWL

See Transition to OWL

  • Review/refresher on Hinxton_OBO-Edit/Protege_4_workshop_Jan_2012
    • How to update GO external disjointness axioms
    • Debugging tips - understanding Jenkins pipeline, etc
    • How to update GO extensions (x-signaling, x-plant-anatomy, ...)
  • Some updates on obo/owl tools
    • Oort updates
    • New relevant protege plugins since Hinxton. Find the full list here Ontology_editor_plugins
      • Jim Balhoff's obo-lint P4 plugin
      • Jim Balhoff's obsoletion-util p4 plugin
      • Jim Balhoff's depictions plugin
      • Heiko's OE GV plugin for p4
      • Any more? What would people like?
  • Exercises
    • Try day to day editing tasks in P4, convert to obo, commit
    • Editing CL in OWL?
  • Create Wishlist/feature/tool requests

Cell types and GO

  • work on x-cell.owl
  • procedure for working on cl-edit

Content

  • Signaling?
  • F-P links
  • incorporation of column16 relationships into ontology terms
  • add disjoint axioms
  • identify new templates
  • response to toxin terms keep coming back after the reasoner runs (how can we keep that from happening?)

Additional material

List any new material, papers etc of interest published since Hinxton

Papers to write

  • Target JBMS issue? Primarily for 'ontologist-centric' papers.
    • SAO/CC integration? General update on CC ontology?
  • Content-specific papers - target bio journals - integrate with annotation
    • Kidney
    • Signaling?
  • Tools
    • Oort
    • TermGenie

LOGISTICS

Meeting room

Getting to building 74:

From guest house: you can walk there in about 10 mins. Shuttles run regularly on weekdays

From berkeley, driving: you have to take the blackberry gate on sunday. The strawberry gate is more convenient for monday and tuesday

From berkeley, no car: shuttles run regularly monday and tuesday. Free cabs at the weekend. You can walk it but it would take a while

Accommodation

Travel

Paola:

arriving SFO on Sat. Jan. 26th at 7:15pm (UA8883);

departing SFO on Tue. Jan. 29th at 9:10pm (UA8882).


Jane:

arriving SFO on Sat. Jan. 26th at 5.25pm (AA6190);

departing SFO on Tue. Jan. 29th at 7.45pm (AA6189).

Judy:

arriving Fri Jan 25

departing Tue Jan 29