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oborel / obo-relations

RO is an ontology of relations for use with biological ontologies
http://oborel.github.io/
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Add additional PTMs #589

Closed cthoyt closed 2 years ago

cthoyt commented 2 years ago

As a follow-up to #581, #583, and #586, this PR adds several more PTM relationships. It also adds a slot for defining opposites.

Alternatively, this structure might be better for collapsing some stuff in the ObjectPropertyDefinedByInteractionProcess which needs two separate entries for addition and removal right now: 

- conforms_to: ObjectPropertyDefinedByInteractionProcess
  uses_rolified_property:
    id: RO:0018001
    label: is myristoyltransferase activity
    rolification_of: GO:0019107
  definition: >-
    A molecularly-interacts-with relationship between two entities,
    where the subject catalyzes a myristoylation activity that takes the object as input
  contributor: orcid:0000-0003-4423-4370
  subproperty_of: RO:0002436  ## molecularly interacts with
  addition:
    id: RO:0018002
    label: myristoylates
    inverse_of:
      id: RO:0018003
      label: myristoylated by
      definition: inverse of demyristoylates
  removal:
    id: RO:0018004
    label: demyristoylates
    inverse_of:
      id: RO:0018005
      label: demyristoylated by
      definition: inverse of demyristoylates
  subject_to_process_property: RO:0002215  ## capable of
  process_to_object_property: RO:0002400   ## has direct input
cthoyt commented 2 years ago

Seemed to not be an issue but I got the following warning from funowl @hsolbrig

/Users/cthoyt/.virtualenvs/obo/lib/python3.10/site-packages/funowl/literals.py:180: UserWarning: Code: f is not defined in namespace XSD
  l = g.value(XSD.f, RDF.type)