# Prodigy with scispacy models

**URL:** <https://support.prodi.gy/t/prodigy-with-scispacy-models/3920>\
**Category:** Uncategorized\
**Tags:** usage, ner, spacy, solved\
**Created:** [February 22, 2021, 1:13pm UTC](https://support.prodi.gy/t/prodigy-with-scispacy-models/3920 "2021-02-22T13:13:06Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![fsa](https://avatars.discourse-cdn.com/v4/letter/f/e9a140/32.png) [@fsa](https://support.prodi.gy/u/fsa)\
**Post date:** [February 22, 2021, 1:13pm UTC](https://support.prodi.gy/t/prodigy-with-scispacy-models/3920/1 "2021-02-22T13:13:07Z")

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I am totally new to Prodigy

My environment:  
Python: 3.7.0  
Spacy: 2.3.5  
Scispacy: 0.2.5  
Prodigy: 1.10.6

I used the spacy model "en\_core\_web\_sm" to annotate a given text with no issue:  
prodigy ner.teach ner\_news en\_core\_web\_sm ./news\_headlines.jsonl --label PERSON,EVENT

However, I have a different type of text "biomedical" and I would like to use one of the scispacy model for annotation e.g., "en-ner-bc5cdr-md" for disease and chemical. I though scispacy models will be treated as spacy models in Prodigy?

I installed the "en-ner-bc5cdr-md-0.2.0" and I used:  
prodigy ner.teach ner\_disease en-ner-bc5cdr-md ./dis\_source\_text.jsonl --label DISEASE,CHEMICAL

I got this error: "Can't find model 'en-ner-bc5cdr-md'. It doesn't seem to be a shortcut link, a Python package or a valid path to a data directory". However, the models works fine when I load it in the same environment in a python code.  
nlp = spacy.load("en\_ner\_bc5cdr\_md")

with pip list, the model is there as it is the case with "en\_core\_web\_sm"

any ideas in how to solve the issue?

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**Author:** ![SofieVL](https://sea2.discourse-cdn.com/flex020/user_avatar/support.prodi.gy/sofievl/32/915_2.png) [@SofieVL](https://support.prodi.gy/u/SofieVL)\
**Post date:** [February 22, 2021, 8:24pm UTC](https://support.prodi.gy/t/prodigy-with-scispacy-models/3920/2 "2021-02-22T20:24:51Z")

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Hi!

> [@fsa](#):
>
> I installed the "en-ner-bc5cdr-md-0.2.0" and I used:  
> prodigy ner.teach ner\_disease en-ner-bc5cdr-md ./dis\_source\_text.jsonl --label DISEASE,CHEMICAL

I think you need to specify the model with underscores instead - i.e. `en_ner_bc5cdr_md` - could you give that a try?

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**Author:** ![fsa](https://avatars.discourse-cdn.com/v4/letter/f/e9a140/32.png) [@fsa](https://support.prodi.gy/u/fsa)\
**Post date:** [February 23, 2021, 8:45am UTC](https://support.prodi.gy/t/prodigy-with-scispacy-models/3920/3 "2021-02-23T08:45:21Z")

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Hi  
Thanks a lot ! this was the mistake.

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**Author:** ![SofieVL](https://sea2.discourse-cdn.com/flex020/user_avatar/support.prodi.gy/sofievl/32/915_2.png) [@SofieVL](https://support.prodi.gy/u/SofieVL)\
**Post date:** [February 23, 2021, 8:51am UTC](https://support.prodi.gy/t/prodigy-with-scispacy-models/3920/4 "2021-02-23T08:51:37Z")

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Sure, no worries! Happy to hear it works now.