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COB Transition Demo 2 #1819

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COB Transition Demo 2 #1819

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sebastianduesing
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Still not final, but updated and cleaner than the first version.

@sebastianduesing
Replace OMO import with versioned OMO import
971d697
@sebastianduesing
Add OntoFox import for RO
eda610e
@sebastianduesing
Update IAO import module & switch to computed intermediates
1e2bf6b
@sebastianduesing
Replace BFO import with COB import
38c0a7d
@sebastianduesing
Rename alternative term to alternative label column in templates
3f07f56
@sebastianduesing
Replace 'inheres in' with 'characteristic of' and 'bearer of' with 'h…
0fae4d9 
…as characteristic'
@sebastianduesing
Redirect usages of CHEBI:atom to COB:atom
1e51788
@sebastianduesing
Redirect usages of CHEBI:molecular entity to COB:molecular entity
7191f60
@sebastianduesing
Redirect usages of OBI:device to COB:device and obsolete OBI:device
6e543b3
@sebastianduesing
Redirect usages of IAO:measurement datum to COB:measurement datum
8d657ba
@sebastianduesing
Redirect usages of BFO:realizes to COB:realizes
4b8964f
@sebastianduesing
Redirect usages of RO:concretizes to COB:concretizes
4f49dfb
@sebastianduesing
Remove unused duplicate 'action specification' IAO term
f8a2a0b
@sebastianduesing
Remove unused 'information carrier' IAO term
dbf696b
@sebastianduesing
Remove unused BFO_0000028
8a1d9ff
@sebastianduesing
Line order update to obi-edit.owl by Protege
31d3ee4
@sebastianduesing
Remove BFO:0000001 and its usages
fc43326
@sebastianduesing
Remove BFO:0000002 and resolve its usages
7a81081
@sebastianduesing
Drop external-byhand
5ced43c
@sebastianduesing
Remove BFO:0000003 and resolve its usages
5166707
@sebastianduesing
Remove BFO:0000004 and resolve its usages
020f395
@sebastianduesing
Remove BFO:0000019 and resolve its usages
4362c18
@sebastianduesing
Remove all non-OMO usages of BFO_0000031
12e9c23
@sebastianduesing
Remove BFO:0000035 and resolve its usages
589bc0c
@sebastianduesing
Run make modules
382d5d9
@sebastianduesing
Fix unsatisfiable classes
3a6a982
@sebastianduesing
Fix multiple-textual-definitions-violation
38a6222
@sebastianduesing
Relabel is_specified_input_of to is specified input of
b85ac8d
@sebastianduesing
Relabel is_specified_output_of to is specified output of
bdd796f
@sebastianduesing
Relabel has_specified_input to has specified input
f02b1b1
@sebastianduesing sebastianduesing marked this pull request as ready for review September 16, 2024 16:26
@jamesaoverton
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Hey OBI developers! Please consider using the obi.owl file linked below to test this OBI-to-COB work. The main known-issue remaining is a dangling "BFO:0000031" class at the top level, due to our OMO import.

https://github.com/obi-ontology/obi/raw/d5ca6099acdfc548931fb461b42aa32e1ea1a064/obi.owl

If you're using ODK, testing this should be a matter of adding a mirror_from setting to the import configuration in your src/ontology/foobar-odk.yaml -- something like:

import_group:
  products:
  - id: obi
    mirror_from: https://github.com/obi-ontology/obi/raw/d5ca6099acdfc548931fb461b42aa32e1ea1a064/obi.owl

Let us know how it goes!

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2 participants
@sebastianduesing @jamesaoverton