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phenoscape / Phenex

Phenex is an application for annotating character matrix files with ontology terms using the Entity-Quality syntax for describing phenotypes.
http://phenex.phenoscape.org/
MIT License
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'null' in post-comp #21

Closed wdahdul closed 10 years ago

wdahdul commented 12 years ago

Using Phenex 1.5 with the data migration features, noticed that a post-composed entity appears as: dorsal mesentary^null(swim bladder).( Fink and Fink 1981 character 57)

'null' should probably be 'part_of'

balhoff commented 12 years ago

This is a "dangler" issue. There is some property that's not loaded. I need to make post-comps show identifiers instead of null when they contain a dangler. Double-click to edit and you will see the ID, I think.

wdahdul commented 12 years ago

Should these properties be added to Phenex, or the relations ontology? Not sure what we should do here. I think most of the files have nulls (e.g., adjacent_to is an example) and we would want to use these properties.

wdahdul commented 11 years ago

Related to the this issue, 'adjacent_to' is not showing up in the post=comp field. It's in the relations ontology: [Typedef] id: RO:0002220 name: adjacent to def: "x adjacent to y if and only if x and y share a boundary" [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "belongs in BFO?" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_a: RO:0002163 ! spatially disjoint from

balhoff commented 10 years ago

This issue was fixed in the data files.