Harry Caufield

I experienced the same issue. Running "menextract2pdf__overwrite.sh" or the "menextract2pdf.py" with --overwrite both produced files with only annotations and none of the original document content. Without any attempt to overwrite...

It looks like it should work, though there is some kind of name collision between Embiggen's `transformers` and the `transformers` providing the tokenizer: ``` >>> get_okapi_tfidf_weighted_textual_embedding(path) Traceback (most recent call...

I think that should work fine - at least I can't see a package on Pypi with that name so it shouldn't create the same kind of collision

Great - for now, being able to save a perceptron during the course of link prediction would be helpful.

With kgx 1.5.9, if I run essentially the same thing as above from the CLI: ``` $ curl https://raw.githubusercontent.com/vaccineontology/VO/master/src/VO_merged.owl > VO_merged.owl $ kgx transform -i owl -f json -o VO_merged.json...

@sierra-moxon would you mind if I pick up this PR from here? Or we can talk about where you left off.

Between the Ontoportal client (https://github.com/INCATools/ontology-access-kit/issues/168) and mapping functions, we can use OAK functions for much of this - and can even take some of the existing Biolink cat assignment and...

I'm in favor of including the associated entity relationships in the same file, for the sake of easier KG ingests and hopefully more informative models (e.g., phenotype entities should have...

Thanks @cthoyt ! Let me know if/when the ingests hit any snags so I can fix the table

For these sources, here's the relationships for mapping availability: | Source/target | CHEBI | CHEMBL | DrugBank | DrugCentral | PharmGKB.drug | ttd.drug | |----------------------|-------|-----------------|----------|-------------|---------------|----------| | CHEBI to | |...