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sivarajankumar / phenotype-ontologies

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Strange anatomy hierarchy in vertebrate.owl #54

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
Hi,

Loaded vertebrate.owl. Run Elk. Search for "Short upper lip". Click on the 
anatomical class used in logical definition ('upper lip'). See attached 
screenshot.

- The definition this hp-class now refers to the ZFA-upper lip not to 
UBERON-upper lip as it is defined in hp-edit.owl. Why?
- The subclass-hierarchy around upper lip looks weird. ... see attached 
screenshot. Is everything as expected here?

Sebastian

Original issue reported on code.google.com by dr.sebas...@gmail.com on 18 Aug 2014 at 11:34

Attachments:

GoogleCodeExporter commented 8 years ago 
Protege bug. Protege gets confused if two classes render to the same two 
strings. This is why we must prepend "obsolete " to all obsolete classes. 
Annoying but necessary.

Even without the bug, the fact that ZFA and Uberon use the same labels will 
confound you unless you configure Protege to show OBO foundry unique label if 
available.

See my config (attached). This should make your lips look like mine (see 
attached). My lips don't look like fish lips.

Added docs here:
https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontolo
gies

Original comment by cmung...@gmail.com on 22 Aug 2014 at 9:07

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