Create an example for building bio NER pipeline
- 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
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