Ontology meeting 2014-05-01

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Attendees:

Minutes:

Follow-up: 'colocalizes with' nuclear chromatin

Carried over, see http://wiki.geneontology.org/index.php?title=Ontology_meeting_2014-03-13

Where are we with the planned action items? David OS made a start on this. Transitive?

The latest AI was for David OS to put together a proposal for this, and run it by Tony.

Progress: Added to RO with URI http://purl.obolibrary.org/obo/RO_0002008

Definition: "A relation that holds between two linear structures, X and Y where X is approximately parallel to Y for its entire length. This relation is agnostic about any parthood relationship between X and Y. This relation is transitive."

Comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.

is_transitive: true

subPropertyOf: mereotoplogically related to

domain: continuant that 'bearer of' some linear*

range: continuant that 'bearer of' some linear* <--- Might be problematic for SO terms as range?

  • PATO_0001199 - Need to update imports.

TODO: Make RO release

Will annotation extension support the relevant targets? From talking to Aleks - SO terms and Ensembl IDs can already be used.

Follow up: editing in Protege

The current version of the plugin is available here: org.protege.oboeditor.jar

Please install and test the plugin. The installation should be simple.

  1. Download the jar and copy it in the Protege plugin folder.
  2. Start Protege, there will be a new view available
    Window > Views > OBO views > OBO annotation

See here for background: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-04-24#Follow-up_on_Protege

See here for wish list: http://wiki.geneontology.org/index.php/Protege_Feature_Requirements

Assert Inferences

A simplified version of the assert-inferences job is now running again. This job will only add new inferred axioms.
We had quite the back log of axioms, see here for all added axioms after the first run.

The previous configuration is still available as a report.