asyml / asyml/ForteHealth

Create an example for building bio NER pipeline

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Dominant language
Python
Stars
14
Forks
5
PR merge metrics
No merged PRs in 30d

Description

**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](https://scispacy.apps.allenai.org/)

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

Contributor guide

Open the contributing guide

Research direction

Start with the linked SciSpaCy demo and review the specified en_ner_bc5cdr_md_ and en_ner_bionlp13cg_md_ models, along with the proposed sentence segmentor, tokenizer, and Bio NER tagger components. Done means a ForteHealth example that builds a biomedical NER pipeline and demonstrates configurable annotations for the supported entity types.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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