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obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
https://obophenotype.github.io/upheno/
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Use of RO:0001025 in conjunction with SO terms #556

Open matentzn opened 5 years ago

matentzn commented 5 years ago

FYPO uses some EQs using RO:0001025, located in, in conjunction with SO terms such as

These are the classes:

@dosumis can you figure out, together with @mah11, whether the relation is used approporiately, and if so, whether you can derive a general pattern here? Thanks!

dosumis commented 4 years ago

This is an edge case for located_in.

  1. SO terms officially refer to generically dependent continuants (abstract sequence), not to the physical entities in which these inhere. However, many ontologies, including GO, use SO terms as if they refer to physical entities.
  2. If the SO terms are taken to refer to physical entities then located_in may still not be strictly valid as these are phenotypes of structures in chromatin regions that correspond to particular sequence regions defined by SO terms. We have some relations defined for GO (which I think are in RO), designed to bridge this. Will dig out details.
dosumis commented 4 years ago

Actually - I think there's a simpler solution: substitute SO terms for GO chromatin region terms (& leave the job of bridging to SO to GO developers)

matentzn commented 4 years ago

@mah11 Do you think this would be an option for you?

mah11 commented 4 years ago

Probably. FYPO already uses a lot of the GO chromatin region terms. Of the four logical defs using located_in, two can change to existing GO CC terms. I can request terms to replace the other two, and use them if GO adds them. Watch this space in case they reject one or both.

Note to self: FYPO:0005923 -> GO:1990421 FYPO:0004846 -> GO:0000781 FYPO:0004820 -> GO:new FYPO:0005924 -> GO:new

mah11 commented 4 years ago

ticket opened; we'll see what they make of it

mah11 commented 4 years ago

Also see https://github.com/geneontology/go-ontology/issues/19178 - GO may second-guess the newest of these terms. In the meantime, FYPO logical defs haven't changed.