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OAK contains a "secret" application, the Ontology Mapping Kit
Code:
https://github.com/INCATools/ontology-access-kit/tree/main/src/oaklib/omk
Currently there is one core method, for performin…
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There are a number of different tools that perform NER on text, from bioportal/zooma through to scispacy, @cthoyt's Gilda ( gilda https://www.biorxiv.org/content/10.1101/2021.09.10.459803v1.full )
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## Summary
I have a list of terms and I'm trying to get their labels using, but I got errors in some cases, and no label in others.
## 1-3: Using `SqlImplementation`
### 1. No `get_label_by_uri()…
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We have a bioportal implementation here:
https://github.com/INCATools/ontology-access-kit/tree/main/src/oaklib/implementations/bioportal
(despite the name this is actually a more general ontopor…
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Currently we reuse a named click option for `-O`
This means every command shows the same thing:
E.g. https://incatools.github.io/ontology-access-kit/cli.html#runoak-obsoletes
This is subo…
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BCIO features heavily in the national academies report:
https://nap.nationalacademies.org/catalog/26464/ontologies-in-the-behavioral-sciences-accelerating-research-and-the-spread
https://www.ebi…
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Talking about: https://github.com/INCATools/ontology-access-kit/blob/main/src/oaklib/datamodels/similarity.yaml
This looks like for every similarity algorithm we want to implement, we will define a…
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This panic happens when a user specifies only a predicate that doesn't exist in ontology (I'm using the `try_rwlock_instead_of_mutex` branch, since it looks like this will be merged soon-ish). This is…
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From https://github.com/monarch-initiative/mondo-ingest/blob/main/src/ontology/lexmatch/unmapped_ncit_lex.tsv
subject_id | subject_label | predicate_id | object_id | object_label | mapping_justific…