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asyml / ForteHealth

The project is in the incubation stage and still under development. ForteHealth is a flexible and powerful ML workflow builder for biomedical and clinical scenarios. This is part of the CASL project: http://casl-project.ai/

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Some bugs in Quick Start Guide in README.md

Leolty opened this issue · comments

commented

Describe the bug
I followed the instructions of Python code in the Quick Start Guide, and I found some bugs that needed to be fixed:
In the following codes:

pl.add(SpacyProcessor(), config={
    processors: ["sentence", "tokenize", "pos", "ner", "umls_link"],
    medical_onto_type: "ftx.medical.clinical_ontology.MedicalEntityMention"
    umls_onto_type: "ftx.medical.clinical_ontology.UMLSConceptLink"
    lang: "en_ner_bc5cdr_md"
    })

processors, medical_onto_type, umls_onto_type, lang need double quatation marks;
and some commas are also needed.

I will pull a request to give the codes I successfully debug.

To Reproduce
Steps to reproduce the behavior:

  1. follow all the instructions in README.md (copy)
  2. run

Desktop (please complete the following information):

  • OS: Windows
  • Version: 10
  • Compiler: Spyder
commented

@Leolty Sounds good. It would be great if you could create a PR for these changes as soon as possible; you can add me as a reviewer. Just want to make sure we push these Readme changes immediately, so no one else faces the same issue while setting up ForteHealth.

commented

Pushing the changes for this since I feel its time sensitive to have a working readme. Feel free to propose any more changes based on your experience with the sample code.