INCATools / INCATools/ontology-access-kit

set_label_for_curie not implemented for owl files?

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bug
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Python
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Merged PRs (30d)
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Description

The use case here is adding rdf labels to existing owl files using lexmatch from OAK. When you do this there is an error that the set_label_for_curie method is not implemented. Per @cmungall lexmatch rdflabel generation should work with the PRONTO implementation currently.

runoak -i ../../DLO/deep-learning-ontology/deep-learning-ontology-full.owl -a ../../DLO/deep-learning-ontology/external/ml-ontology-202010021305.owl lexmatch --add-labels
WARNING:root:Using rdflib rdf/xml parser; this behavior may change in future
WARNING:root:Using rdflib rdf/xml parser; this behavior may change in future
WARNING:root:Not a curie: deep-learning-ontology/deep-learning-ontology-full.owl
WARNING:root:Not a curie: deep-learning-ontology/deep-learning-ontology-full.owl
Traceback (most recent call last):
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/bin/runoak", line 8, in
sys.exit(main())
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/oaklib/cli.py", line 1150, in lexmatch
add_labels_from_uris(impl)
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/oaklib/utilities/lexical/lexical_indexer.py", line 46, in add_labels_from_uris
oi.set_label_for_curie(curie, label)
File "/Users/marcin/Documents/VIMSS/ontology/OAK/ontology-access-kit/venv/lib/python3.9/site-packages/oaklib/interfaces/basic_ontology_interface.py", line 203, in set_label_for_curie
raise NotImplementedError
NotImplementedError

Contributor guide

Open the contributing guide

Research direction

Start with the lexmatch entry point in oaklib/cli.py and trace add_labels_from_uris in oaklib/utilities/lexical/lexical_indexer.py to the NotImplementedError in oaklib/interfaces/basic_ontology_interface.py. Reproduce the command from the issue against the OWL files and determine the required implementation for the PRONTO path. Done means lexmatch --add-labels completes without this error and adds the expected RDF labels.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend, cli
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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