NCBI Gene

| Documentation |

The NCBI Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

Data Sources

• NCBI bulk downloads

Gene Information

Genes for all NCBI species (Dog, Cow, Pig, Chicken, et alia) are loaded using the ingest file (filtered to only NCBI taxon ID).

Biolink Captured

• biolink:Gene
  • id
  • symbol
  • description
  • in_taxon
  • provided_by (["infores:ncbi-gene"])

Citation

National Center for Biotechnology Information (NCBI)[Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; [1988] – [cited 2024 Dec]. Available from: https://www.ncbi.nlm.nih.gov/

Requirements

• Python >= 3.10
• Poetry

Installation

cd NCBI Gene
make install
# or
poetry install

Note that the make install command is just a convenience wrapper around poetry install.

Once installed, you can check that everything is working as expected:

# Run the pytest suite
make test
# Download the data and run the Koza transform
make download
make run

Usage

This project is set up with a Makefile for common tasks.
To see available options:

make help

Download and Transform

Download the data for the ncbi_gene transform:

poetry run ncbi_gene download

To run the Koza transform for NCBI Gene:

poetry run ncbi_gene transform

To see available options:

poetry run ncbi_gene download --help
# or
poetry run ncbi_gene transform --help

Testing

To run the test suite:

make test

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This project was generated using monarch-initiative/cookiecutter-monarch-ingest.
Keep this project up to date using cruft by occasionally running in the project directory:

cruft update

For more information, see the cruft documentation