search

obophenotype / provisional_cell_ontology

Draft cell type definitions from data - candidates for inclusion in CL
Creative Commons Attribution 4.0 International
11 stars 1 forks source link

Base file imports #21

Closed shawntanzk closed 2 years ago

shawntanzk commented 2 years ago

Switch to base file imports

shawntanzk commented 2 years ago

Current issue seems to be Cause: /work/src/ontology/imports/merged_import.owl (No such file or directory) This error occurs when i try to run sh run.sh make imports/merged_import.owl or sh run.sh make no-mirror-refresh-imports not too sure how to fix given that it almost seems cyclical

shawntanzk commented 2 years ago

Issue seems to be merge is trying to bring in edit file and edit file is trying to bring in merge - removed merge import from edit file and ran sh run.sh make imports/merged_import.owl and worked - now running sh run.sh make no-mirror-refresh-imports and will check that everything is in place

shawntanzk commented 2 years ago

Currently HEAPS of CHEBI and CARO dangling classes - I think this is the downside to base file imports. We can fix it by importing them in, or deleting the axioms. Downside to importing: they will probably bring in even more dangling classes Downside to deleting: if we programmatically do it, it might result in future users not being able to use that import if they don't know we did that Happy to do either.

shawntanzk commented 2 years ago

Of note: other ontologies remove it

matentzn commented 2 years ago

Best import Chebi. You can potentially delete CARO, but try to import it.. just to see wether you run into consistency issues..

shawntanzk commented 2 years ago

Note to self: there are a couple of NBO terms to deal with too. Will try to fix them in this PR too: https://github.com/obophenotype/provisional_cell_ontology/pull/24

shawntanzk commented 2 years ago

dangling classes still present

shawntanzk commented 2 years ago

after refreshing chebi mirror (in case it was an error from before) and rerunning sh run.sh make no-mirror-refresh-imports dangling classes still present. Not sure if I need to make a release to fix it? will try.

matentzn commented 2 years ago

Ask me in slack.. You dont need a release.

shawntanzk commented 2 years ago

2 things left to fix:

shawntanzk commented 2 years ago

after alot of stupid mistakes my me, and heaps of help from @matentzn, branch is finally clean. Just before I merge just wanted to make sure @dosumis is alright with the stuff I exclude:

  exclude_iri_patterns:
    - <http://www.informatics.jax.org/marker/MGI:*>
    - <http://purl.obolibrary.org/obo/OBA_*>
    - <http://purl.obolibrary.org/obo/ENVO_*>
    - <http://purl.obolibrary.org/obo/OBI_*>
    - <http://purl.obolibrary.org/obo/GOCHE_*>
    - <http://purl.obolibrary.org/obo/CARO_*>
    - <http://purl.obolibrary.org/obo/NCBITaxon_Union_*>
    - <http://www.genenames.org/cgi-bin/gene_symbol_report*>

If so, could you help give a thumbs up please?