Ontology meeting 2014-05-01
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.
- Download the jar and copy it in the Protege plugin folder.
- 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