ontology_workflow - kaiiam/phd GitHub Wiki
Table of contents:
Daily work flow
Update PR
ENVO
PMO
CHEBI
UO
SRPDIO
PATO
Editors
ENVO editors daily work flow
To make changes to github repository via pull requests protocol based on GO Daily workflow
- Make sure you're up to date
git pull
- Start or address an issue on envo github
e.g. issue 666
- checkout a branch corresponding to that issue.
git checkout -b issue-666
-
Make changes
-
Add/commit changes (-a for all files staged to commit) with a message
git commit -am 'Add utility to convert file format fixes #666'
- Push branch to origin to create a pull request
git push origin issue-666
-
On envo pull requests page click on
Compare and Create Pull Request -
On envo pull requests page editors can view the pull request and check if the build passes.
-
Request reviews of pull request and or make changes as necessary
Leave this step for the lead ENVO editors click Merge Pull Request
- Switch from branch back to master
git checkout master
- Delete the branch after the changes are merged
git pull (to get the new origin with the merged branch.
git branch -d issue-666
Update PR
git checkout issue-666
- Make changes
commit
git push --set-upstream origin issue-666
ENVO
Entity IRI:
Start with: (choose) Specified IRI: http://purl.obolibrary.org/obo
Followed by: (choose) /
End with: (choose) Auto-generated ID
Entity Label (for use with Auto-generated ID) (choose) Same as label renderer
Auto-generated ID: (choose) Numeric (iterative)
prefix: ENVO_
Digit count 8
Start: 3,000,146
End: 3,100,000
Check the Remember last ID between Protege sessions box
Next ID: ENVO:03000148 updated: June 9th 2021
PMO
Entity IRI:
Start with: (choose) Specified IRI: http://purl.obolibrary.org/obo
Followed by: (choose) /
End with: (choose) Auto-generated ID
Entity Label (for use with Auto-generated ID) (choose) Same as label renderer
Auto-generated ID: (choose) Numeric (iterative)
prefix: PMO_
Digit count 8
Start: 193 might be 198 check.
End: 999,999
Check the Remember last ID between Protege sessions box
Plan of action for PMO releases when I make a new PMO release I run will ./run.sh make all_imports_owl then comment out the lines from the make file,
#imports/%_import.owl: mirror/%.owl imports/%_terms_combined.txt
# $(ROBOT) extract -i $< -T imports/$*_terms_combined.txt --method BOT \
annotate --ontology-iri $(ONTBASE)/$@ --version-iri $(ONTBASE)/releases/$(TODAY)/$@ --output $@
#.PRECIOUS: imports/%_import.owl
Then manually delete the problematic axioms: the bad equivalence axiom in OBI:comment on investigation and subclass of disposition in PATO:fluorescence), then run ./run.sh make prepare_release. Finally un-comment or don't save the changes to the makefile.
CHEBI
CHEBI submission tool: You can request access to this via https://www.ebi.ac.uk/chebi/submission/login. The submission tool will allow you to draw in the chemical structure, add in the synonyms, add any ontology terms and appropriate citations. The information becomes visible on the ChEBI website within 24 hrs. They then check and annotate the entries.
Request new terms is via CHEBI Github. Please only use this channel if the number of terms you are requesting are less than 5. If you continuously want to submit new terms to ChEBI, then using the submission tool is the best option.
UO
SRPDIO
Entity IRI:
Start with: (choose) Specified IRI: http://purl.obolibrary.org/obo
Followed by: (choose) /
End with: (choose) Auto-generated ID
Entity Label (for use with Auto-generated ID) (choose) Same as label renderer
Auto-generated ID: (choose) Numeric (iterative)
prefix: SRPDIO_
Digit count 7
Start: 1
End: 999999
PATO
Editing via my fork see more details here
Entity IRI:
Start with: (choose) Specified IRI: http://purl.obolibrary.org/obo
Followed by: (choose) /
End with: (choose) Auto-generated ID
Entity Label (for use with Auto-generated ID) (choose) Same as label renderer
Auto-generated ID: (choose) Numeric (iterative)
prefix: PATO_
Digit count 7
Start: 85001
End: 90000
Next ID: PATO:0085002 updated: Feb 10 2021
Editors:
Kai Blumberg http://orcid.org/0000-0002-3410-4655
Pier Buttigieg http://orcid.org/0000-0002-4366-3088
Chris Mungall https://orcid.org/0000-0002-6601-2165
Anne Thessen https://orcid.org/0000-0002-2908-3327
Simon Cox: https://orcid.org/0000-0002-3884-3420
Ramona L. Walls https://orcid.org/0000-0001-8815-0078
Steven Chong https://orcid.org/0000-0003-1264-1166