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COB Transition Demo 1 #1812

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wants to merge 41 commits into from
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COB Transition Demo 1 #1812

wants to merge 41 commits into from

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sebastianduesing
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@sebastianduesing sebastianduesing commented Aug 12, 2024 •
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COB transition work to be discussed on 2024-08-12 OBI dev call.

sebastianduesing and others added 27 commits August 5, 2024 10:47
@sebastianduesing
Switch non-versioned OMO import to the current version of OMO.
8a1044c
@sebastianduesing
Replace RO-core import with OntoFox RO import.
0ed714a
@sebastianduesing
Prepare IAO import module.
43990a3
@sebastianduesing
Remove BFO import.
19d4e32
@sebastianduesing
Add COB import
bce2c6b
@sebastianduesing
Rename 'alternative term' column to 'alternative label' in all templates
9fe2471
@sebastianduesing
Replace 'inheres in' and 'bearer of' with 'characteristic of' and 'ha…
9ea9345 
…s characteristic' in all templates
@sebastianduesing
Redirect references to CHEBI:atom to COB:atom
b3b54ad
@sebastianduesing
Redirect references to CHEBI:molecular entity to COB:molecular entity
05e16bd
@sebastianduesing
Update device module
5eca0d1
@sebastianduesing
Obsolete OBI:device
b650131
@sebastianduesing
Fix typo in RO import
0ced5d7
@sebastianduesing
Remove mentions of CHEBI:molecular entity from assays.owl
d02c932
@sebastianduesing
Remove BFO:0000028
fa7ddda
@sebastianduesing
Redirect references to IAO:measurement datum to COB:measurement datum
2a894e5
@sebastianduesing
Remove references to BFO:entity
721f22a
@sebastianduesing
Remove reference to BFO:continuant
71cf811
@sebastianduesing
Remove references to BFO:quality
b2a2369
@sebastianduesing
Move IAO import of ICE out from under GDC
d4897e7
@sebastianduesing
Remove unused information carrier term
be301b2
@sebastianduesing
Run make modules
64f9314
@sebastianduesing
Remove references to BFO:0000055 (realizes)
af55725
@sebastianduesing
Remove references to RO:0000059 (concretizes)
d2a24a0
@jamesaoverton
Merge branch 'master' into cob_transition_1
b93ac97
@jamesaoverton
Drop external-byhand.owl
96ba715 
This file contain axioms about non-OBI terms:
10 object properties and 2 classes.
The annotations about the 2 CLO classes
are no longer needed.
The 10 object properties should be imported from RO.

I did not delete the external-byhand.owl file
in case it's still used by something somewhere.
@sebastianduesing
Fix almost all unsatisfiability issues
ec60b63
@sebastianduesing
Remove unused unsatisfiable class
09166e7
@jamesaoverton
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We never, ever remove a term that we've published. Please add OBI:0001720 to the obsolete template.

@jamesaoverton jamesaoverton mentioned this pull request Aug 30, 2024
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@sebastianduesing
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Sorry, that was a sloppy mistake on my part. I'm not sure how I missed that step. Fixed.

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jamesaoverton commented Sep 5, 2024 •
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Everything seems to be working except:

  1. COB_based_on which violates src/sparql/iri-violation.rq, see COB_based_on annotation property without proper OBO ID OBOFoundry/COB#280
  2. obi.obo conversion, because of a problem in COB:
OBO STRUCTURE ERROR Ontology does not conform to OBO structure rules:
multiple comment tags not allowed. in frame:Frame(CHEBI:33252 id( CHEBI:33252)name( atomic nucleus)comment( This is equivalent to CHEBI:33252)comment( Some people may be uncomfortable calling every proton an atomic nucleus)is_a( CHEBI:36342))

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@sebastianduesing will have an updated version of this PR soon, so closing this one.

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@sebastianduesing @jamesaoverton