pythonnlpbioinformaticsnamed-entity-recognition

Scispacy for biomedical named entitiy recognition(NER)


How to label entities using scispacy?

When I tried to perform NER using scispacy, it identified the biomedical entities by labeling them as Entity but failed to label them as gene/protein, etc.. So how do I do that using scispacy? Or is scispacy not capable of labeling data? The image is attached for reference: jupyter notebook snippet


Solution

  • The models en_core_sci_sm, en_core_sci_md and en_core_sci_lg do not name their entities. If you want labeled entities use the models

    each of which has its own type of entities see:-

    https://allenai.github.io/scispacy/

    for more information