Cogstack docker download issues about cogstack-pipeline HOT 6 CLOSED

We are in the process of migrating all the containers to cogstacksystems/cogstack.

For BioYodie I think there may be some licencing issue (I'm just checking).

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@polyglot-v original bioyodie pipeline was not opensourced at the original time, it has since been released https://github.com/GateNLP/Bio-YODIE.

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cc/ @angusroberts are there remaining issues releasing the working BIOYODIE pipeline
cc/ @Honghan pls comment on MetaMap alternative

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The issue here is around releasing the UMLS resources which are under licence, the BioYODIE application is under AGPL. We therefore can't release a docker container image with it.

UMLS licence required for ontology resource files

• for research purposes: https://uts.nlm.nih.gov/license.html.

BioYODIE

• https://gate.ac.uk/applications/bio-yodie.html (docs)
• https://github.com/GateNLP/Bio-YODIE (repo)

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I think maybe the PR #44 should provide a workaround to this this as well since its built during docker-compose up

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Regarding obtaining and running the BioYodie, we unfortunately cannot provide the BioYodie image bundled with the UMLS resources.
FYI, we are also slowly moving away from using NLP applications inside CogStack Pipeline where the newest approach, running a multi-step processing pipeline, has been covered in the official documentation with the available source code under: https://github.com/CogStack/CogStack-Recipes
Alternatively, one can run BioYodie as a part of SemEHR.

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