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Create an example for building bio NER pipeline #63

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Leolty opened this issue Oct 6, 2022 · 0 comments
Open

Create an example for building bio NER pipeline #63

Leolty opened this issue Oct 6, 2022 · 0 comments

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@Leolty
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Leolty commented Oct 6, 2022

Describe the solution you'd like

In ForteHealth, we incorporate ScispaCy for bio ner annotation, I think, as the very first example, we can simply create a pipeline for bio NER annotation. The demo from scispacy is here

In scispacy, with model en_ner_bc5cdr_md, we can annotate Disease and Chemical, with model en_ner_bionlp13cg_md, we can annotate Cancer, Organ, etc. We can also show this by using different configuration to build the pipeline.

Possible included componets:

  1. Sentence Segementor
  2. Tokenizer
  3. Bio NER Tagger
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