Ontology workshop Jan 2013

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

Location: CA


  • 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)



Sunday Jan 26


  • 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:Flowchart.JPG

 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.


  • 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


  • 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

ontology diff tool: [Bubastis] currently throwing error, may adapt this run to locally and to be more GO specific

TO DO: mark all links that can be inferred as {is_inferred=true}, will be done en masse [GO-130]

infer links - review - if the source can be fixed, do this right away, if not, remove the egregious inferred link and remember to open a SF item or notify the outside group asap

Manual: (should not have to do this as it will be automated) - remove --dryRun if for real

 $ /Applications/OBOReleaseManager/scripts/obo-assert-inferences editors/gene_ontology_write.obo 
editors/gene_ontology_xp_write.obo extensions/bio-chebi.owl --dryRun --markIsInferred --reportFile 

DONE: added new xps for the transport terms, also asserted the implied links

Lunch / Outing?


  • 2.30-3.30 papers

finished TG abstract for Biocurator meeting

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

ontology downloads needs to be sorted out - new proposal below

Ontology files to download.jpg

Need to review the documentation and split out the files for the public to put on the website (public) vs. the editors (on the wiki). Created new JIRA issues [GO-132] and subtasks.

Tuesday Jan 28


  • 8-8.30 review so far, Nicole V intro
  • 9-10 exploring cl-edit.owl
    • http://cell-ontology.googlecode.com/
    • added Jane, David, Tanya, Nicole as editors (Paola and Chris already)
    • made CL:cell equivalent to GO:cell
    • CL used for col 16 data and for logical definitions for GO terms
    • editing in owl - obsoletion tested, adding comment tested, term addition tested
    • setting your id range: (Look at your range here: /cell-ontology/src/ontology/cl-idranges.owl)
"Remember, never fully trust this." -cjm

Protege ID setup.png

    • adding a new term - should have the id that you need automatically generated
    • don't forget to add an Annotation on the definition for the editor, use @ symbol on the definition, database_cross_reference
    • build-cl in Jenkins
    • Jenkins in the OBO Foundry
  • 10-11.30 enhancing x-cell.owl and cl-edit. split into two groups, one editing

Lunch: cafeteria


  • 1 - 1.30 discussion about GO supplement grant to fund CL work
    • created outline - to be fleshed out and reviewed
    • plugin for better annotation editing (metadata)
  • 1.30-3 continue exercise
    • good tip, COMMAND-U while hovering over term name to get to ID, which you can copy and paste
    • general strategy for adding new logical definitions:
      • if CL term exists, add new xp, if there is variation in CL name and GO name, take the CL name as the primary name and add appropriate synonyms to the GO term
      • if no CL term exists, add a new CL term if the proposed new CL term is straightforward
      • if no CL term exists and addition is controversial (e.g. immunology cells), tag the GO term with a *new* subset, save them

up for later review and resolution

    • core logical def: 'cell differentiation' and results_in_acquisition_of_features_of some cell
    • there is still an existing retinal cell type ontology that needs reviewing and incorporation into CL - Alex has this somewhere and will stick it into a version control system
    • added in a bunch of xps into x-cell.owl. Did some editing of gene_ontology_write.obo to synchronize CL and GO terminology.
  • 3-3.30 break
  • 3.30-4 review, draw up timelines for templates etc
  • don't forget Ontology extensions and c16
    • go_annotation_extension_relations.obo = some BFO1.2 + some RO.owl + some extra (have xref:GOREL:xxx) --> migrate to owl? would be nice
    • go_xp_write (obo format) copies in some BFO1.2 and some RO.owl
    • owl files (example, x-cell.owl) can import RO.owl directly because the formats are compatible
    • if xref for one of the rels in go_annotation_extension_relations.obo is to BFO or RO (an external ontology) do not overwrite their def/domain/range with own definition and domain with our own. Retain this information somewhere else, as a comment, perhaps.

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


  • 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


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




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

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


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

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


arriving Fri Jan 25

departing Tue Jan 29