Improvements to protein synonyms/NER

clulab / bioresources

Data resources from the biomedical domain

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Improvements to protein synonyms/NER #51

Closed bgyori closed 3 years ago

bgyori commented 3 years ago

This PR makes the following changes:

Add a note about NER and organisms to the README (see #50)
Update the list of synonyms from UniProt
Remove single-letter protein synonyms from uniprot-proteins and the corresponding NER file (Note that most NER files other than Gene_or_gene_product.tsv.gz are effectively unchanged, though they show up in the diff)

MihaiSurdeanu commented 3 years ago

Thanks @bgyori! Can you please add a summary of this PR to the CHANGES file?

MihaiSurdeanu commented 3 years ago

@kwalcock: this is a significant PR. Can you please release it, and update Reach (assuming tests pass)?

bgyori commented 3 years ago

@MihaiSurdeanu thanks, I added a line to CHANGES in #52. I agree that releasing this would be good, though there aren't huge changes to the default resource files, my 2 PRs today are mostly to support local custom builds.

MihaiSurdeanu commented 3 years ago

Thanks! Merged.

kwalcock commented 3 years ago

Yes. Hopefully the other recent reach and possibly processor changes can be coordinated with this. There's a reach PR now. It looks like @bgyori updated the files in the ner directory before the first merge into master. Can I assume that the second merge into master does not require an update to those files?

MihaiSurdeanu commented 3 years ago

I think that's correct.

kwalcock commented 3 years ago

The tests passed with reach, both the master branch of reach and the one with forthcoming fixes. I'll try to get this published then.

MihaiSurdeanu commented 3 years ago

Thank you!

On Thu, Jan 7, 2021 at 11:26 AM Keith Alcock notifications@github.com wrote:

The tests passed with reach, both the master branch of reach and the one with forthcoming fixes. I'll try to get this published then.

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