Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

COB Transition #1853

Open
wants to merge 24 commits into
base: master
Choose a base branch
from
Open

COB Transition #1853

wants to merge 24 commits into from

Conversation

sebastianduesing
Copy link
Contributor

This PR transitions OBI to using COB as its upper-level ontology. Key changes include the following:

  • Replaced BFO import with COB import.
  • Replaced RO-core import with a limited import of some RO terms using OntoFox to reduce the number of BFO terms brought in by RO.
  • Redirect usages of certain non-COB terms to their COB equivalents, e.g., CHEBI:atom to COB:atom.
  • Obsolete some OBI terms that were "donated" to COB, e.g., OBI:planned process, and redirect usages of those terms to their COB equivalents.
  • Remove or substitute references to BFO terms that are no longer being imported.

@sebastianduesing
Remove BFO import
75d5928
@sebastianduesing
Import COB v2025-01-23
bfb10fd
@sebastianduesing
Replace RO-core import with OntoFox RO import
f60764b
@sebastianduesing
Merge branch 'clean_up_imports' into cob_transition_final
c89877a
@sebastianduesing
Redirect usages of CHEBI:atom to COB:atom
eafc1df
@sebastianduesing
Redirect usages of CHEBI:molecular entity to COB:molecule
76cf984
@sebastianduesing
Obsolete OBI:device and redirect references to COB:device
8c7784c
@sebastianduesing
Obsolete OBI:organism and redirect references to COB:organism
c9cbba5
@sebastianduesing
Obsolete OBI:planned process and redirect references to it to COB:CEPP
8bfb496
@sebastianduesing
Obsolete OBI:material processing and redirect to COB:material processing
915f283
@sebastianduesing
Line update by Protege
c01fcf7
@sebastianduesing
Replace dropped axiom asserting material acquisition disjoint with ma…
9c15c88 
…terial processing
@sebastianduesing
Remove references to BFO:0000019
7f4be80
@sebastianduesing
Remove references to BFO:0000020
ff5ace8
@sebastianduesing
Remove references to BFO:0000028
adeabf4
@sebastianduesing
Remove references to BFO:0000031
594609b
@sebastianduesing
Remove unused BFO:0000066
5bd0306
@sebastianduesing
Obsolete OBI:processed material and redirect references to it to COB:…
b47e82f 
…processed material entity
@sebastianduesing
Change alternative term to alternative label in specimens.tsv
2aeae6c
@sebastianduesing
Run make modules
5d6bb83
@sebastianduesing
Line order update by Protege
c2fda00
@sebastianduesing
Align some definitions with COB and fix language tags
7e21b19
@sebastianduesing
Remove conflicting domains/ranges
a25c6ec
@sebastianduesing
Merge branch 'master' into cob_transition_final
4f01d13
@sebastianduesing sebastianduesing marked this pull request as ready for review February 27, 2025 22:22
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jamesaoverton jamesaoverton Awaiting requested review from jamesaoverton

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@sebastianduesing