Create Global Codebook Ontology - Githubissues

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Create Global Codebook Ontology #48

Open marcosmro opened 7 months ago

marcosmro commented 7 months ago

@matthewhorridge: please add a short description here, and feel free to edit the task title and the use cases below.

Main RADx use cases for this ontology:

Semantic search, including faceted search of data elements.
Search by diseases, symptoms etc.
Add synonyms (from referenced/imported ontologies) to data elements
Map data dictionaries to data elements in the Global Code Book (GCB) during the harmonization process.
Automated GCB validation.
Automated GCB generation.

Part of https://github.com/bmir-radx/radx-project/issues/47

ckindermann commented 4 months ago

@matthewhorridge can you give me access to the ontology you've been working on so far?

matthewhorridge commented 4 months ago

Here is the experimental RADx Global Code Book data dictionary ontology ont.owl.zip

matthewhorridge commented 4 months ago

Here is a version of the experimental Data Hub Ontology. You need to (create an account and) sign in for this.

ckindermann commented 4 months ago

Great, thank you!

matthewhorridge commented 4 months ago

Basic flow:

1) Annotate data elements with ontology terms (manual process) 2) Extract modules for these terms (I suspect this amounts to a bottom SL module) along with synonyms 3) Generate classes for data elements and possible values 4) Associate data element classes with ontology terms in the ontology 5) Write definitions to classify the data elements

ckindermann commented 4 months ago

That sounds reasonable. Seems like steps 2-5 can be automated. Do you have code for that? Should I build on the annotations you've already created in step 1?

matthewhorridge commented 4 months ago

Some very rough code here: https://github.com/bmir-radx/radx-dict2ont. This isn't a proper app or tool but you should be able to figure it out.

matthewhorridge commented 4 months ago

Input URL.... https://docs.google.com/spreadsheets/d/1wYgRCO7gj-wDi1MJ-TvOf9BsTVYOYJxVoMlBOVdn1vM/gviz/tq?tqx=out:csv&sheet=Sheet1, which is the RADx Global Code Book Data Dictionary.

ckindermann commented 1 month ago

See the first version of GCBO here. Changes and updates can now be requested via GitHub issues.