OMOP2OBO

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Generate OMOP2OBO Mappings to OHDSI Cohort Definitions

3

### TASK Create a Jupyter Notebook (or other tool) that takes in an OHDSI Cohort Definition (from [here](https://data.ohdsi.org/PhenotypeLibrary/)) and returns the `OMOP2OBO` mappings. @jmbanda - What do you think about...

callahantiff

Add vanity CLI

4

If the `main.py` were included in the source code hierarchy, the python entrypoints in setuptools could be used ot make a vanity cli called `omop2obo` along with installation of the...

cthoyt

TODO: Mapping Release Formatting

1

Due to some of the OMOP clinical vocabularies having licensing restrictions, we need to decide how and in what format the mappings will be publicly released. Regardless of the above...

callahantiff

Move main.py into package and add vanity CLI

4

Closes #56 This PR does the following: 1. Moves `main.py` into the main package hierarchy. My personal preference is to name the file `cli.py`, but I'll leave this as an...

cthoyt

Mapping rdfization

1

Adding new functionality to convert clinical mappings into semantic definitions. This primarily addresses issue #34

callahantiff

Coding: Add RDF-ization code to convert mappings to RDF

23

**Needed Scripts:** Write a script that converts mappings into RDF @nicolevasilevsky -- thank you for meeting with me a few weeks ago and confirming our approach looks reasonable. I am...

callahantiff

**Task:** Create a simple YouTube video to accommodate the repo that provides: - A brief overview of the project - Requirements/dependencies - How to run the code in the `main`...

callahantiff

Improve string delimiter detection in mapping pipline

1

### Describe the Bug An assumption is made that all concept synonyms and ancestor information will be input in an aggregated format with each aggregated concept separated by a `...

callahantiff

Currently, the mapping code for DbXRefs is designed to map OMOP source codes to UMLS SABs. There is potential to easily extend this to take advantage of existing UMLS mappings...

callahantiff

**Script:** **[`string_similarity.py`](https://github.com/callahantiff/OMOP2OBO/blob/master/omop2obo/string_similarity.py)** **Needed Changes:** - [ ] Parallelize the `scores_tfidf()` method to run each input ontology `ontology_type` in parallel. - [ ] Aggregate/merge mapping results for each ontology

callahantiff