Ontology meeting 2014-05-01: Difference between revisions

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=== Follow up: editing in Protege ===
=== Follow up: editing in Protege ===
The current version of the plugin is available here: [https://github.com/hdietze/protege-obo-plugins/blob/master/org.protege.oboeditor.jar?raw=true org.protege.oboeditor.jar]
Please install and test the plugin. The installation should be simple.
#  Download the jar and copy it in the Protege plugin folder.
#  Start Protege, there will be a new view available<br />    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 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
See here for wish list: http://wiki.geneontology.org/index.php/Protege_Feature_Requirements

Revision as of 12:47, 30 April 2014

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