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monarch-initiative / omim

Data ingest pipeline for OMIM.
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biomedical-informatics ontology-engineering

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OMIM Data Pipeline Tools

About OMIM & this repository

OMIM stands for "Online Mendelian Inheritance in Man", and is an online catalog of human genes and genetic disorders. The official site is: https://omim.org/

This purpose of this repository is for data transformations for ingest into Mondo. Mainly, it is for generating an omim.ttl and other release artefacts.

Disclaimer: This repository and its created data artefacts are unnofficial. For official, up-to-date OMIM data, please visit omim.org.

Setup

1. API Key and .env

  1. Run: cp .env.example .env
  2. Change the value of API_KEY to your own. If you don't have one, you can request one at https://omim.org/downloads. This will probably be sufficient for the purposes of downloading the necessary text files, but if not, you can also require access to the REST API as well: https://omim.org/api.

2. Python dependencies

2.1 Python installation

2.2 Setup virtual environment & installing packages

  1. Run: make install
  2. There is a known possible issue with dependency psutil on some systems. If you get an error related to this when installing, ignore it, as it is does not seem to be needed to run any of the tools. If however you do get a psutil error when running anything, please let us know by creating an issue.

Running & creating release

Run: sh run.sh make all

Running this will create new release artefacts in the root directory.

You can also run make build or python -m omim2obo. These are all the same command. This will download files from omim.org and run the build.

Offline/cache option: python -m omim2obo --use-cache If there's an issue downloading the files, or you are offline, or you just want to use the cache anyway, you can pass the --use-cache flag.

Additional tools

Details

### Get PMIDs used for OMIM codes from `omim.ttl` Command: `sh run.sh make get-pmids` ### OMIM Code Web Scraper Currently, the only feature is `get_codes_by_yyyy_mm`, which returns a list of OMIM codes and their prefixes from https://omim.org/statistics/update. #### Usage: Command Line Interface ##### Syntax 1. `make scrape y= m=` 2. `make scrape y= m= > ` ##### Usage 1. Get codes for May 2021, printed to terminal: `make scrape y=2021 m=5` 2. Get codes for May 2021 and output to a file "myfile.txt": `make scrape y=2021 m=5 > myfile.txt` ##### Examples Command: `make scrape y=2021 m=5` Response: ```py [('#', '619340'), ('#', '619355'), ('*', '619357'), ('*', '619358'), ('*', '619359'), ('#', '619325'), ('#', '619328'), ('*', '100850'), ... ('#', '613102')] ``` ### Usage: Python API Using `get_codes_by_yyyy_mm()` will return a list of tuples. ```py from omim2obo.omim_code_scraper import get_codes_by_yyyy_mm code_tuples = get_codes_by_yyyy_mm('2021/05') ```