scispacy
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allenai
A full spaCy pipeline and models for scientific/biomedical documents.
any other model fro drug name entity recognition. I found that both BC5CDR model ande med7 model are not that accurate for drug name recognition.
when I run follow line: nlp.add_pipe("scispacy_linker", config={"resolve_abbreviations": True, "linker_name": "umls"}) There was an error, “zipfile.BadZipFile: File is not a zip file”
Let me start by thanking you for developing and putting out this tremendously helpful framework for biomedical text processing. I (and am sure many others) are deeply grateful for all...
Hi, I'm trying to install Scispacy on mac m1, python version 3.8.13, pip version 22.1.2, conda 4.11.0. Error log: (base) ➜ ~ conda activate bio (bio) ➜ ~ pip install...
I'm attempting to use your "en_core_sci_lg" pipeline to extract chemical entities from documents, and then using those entities as a basis to train Spacy's Entity Linker (as shown in this...
It seems the config isn't quite right to include token probabilities. I'm not 100% sure of the solution, but this issue should help (https://github.com/explosion/spaCy/discussions/6388#discussioncomment-330606). The vocab files include the probabilities,...
Hi, First and foremost, thank you so much for all of your efforts on scispacy! 👍 When "linker_name": "rxnorm" is selected for NER, can we get the RxCUI of an...
Hi, was wondering if there is a timeline for supporting Spacy >=3.3.0? What pitfalls should i expect if i tried to manually modify the requirements to allow it? thank you.
Hi, First of all, thankyou very much for all the hard work you've put in to make SciSpacy for us. I need some help with NEL; it's my first time...
I was wondering if you all had any thoughts on developments in the python ecosystem for entity linking since the original 2019 ScispaCy paper. I see a number of comparisons...
