https://github.com/dhimmel/entrez-gene

Processing the human Entrez Gene subset
https://github.com/dhimmel/entrez-gene

entrez-gene genes hetionet human rephetio terminology

Last synced: 29 days ago
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Processing the human Entrez Gene subset

• Host: GitHub
• URL: https://github.com/dhimmel/entrez-gene
• Owner: dhimmel
• License: cc0-1.0
• Created: 2015-04-20T17:36:15.000Z (over 9 years ago)
• Default Branch: gh-pages
• Last Pushed: 2016-02-20T02:48:14.000Z (over 8 years ago)
• Last Synced: 2024-05-02T06:00:20.478Z (6 months ago)
• Topics: entrez-gene, genes, hetionet, human, rephetio, terminology
• Language: Jupyter Notebook
• Homepage: https://doi.org/10.15363/thinklab.d34
• Size: 10.1 MB
• Stars: 3
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

        
# Creating user-friendly Entrez Gene datasets for humans

[![DOI: 10.5281/zenodo.45524](https://zenodo.org/badge/doi/10.5281/zenodo.45524.svg)](http://dx.doi.org/10.5281/zenodo.45524 "Zenodo deposition of this repository")

Entrez Gene is the NCBI database of gene-specific information. It provides "tracked, unique identifiers for genes" and reports "information associated with those identifiers for unrestricted public use [[source](https://doi.org/10.1093/nar/gki031 "Entrez Gene Publication: gene-centered information at NCBI")]." We [use Entrez Gene](https://doi.org/10.15363/thinklab.d34 "Thinklab discussion: Using Entrez Gene as our gene vocabulary") as the primary gene vocabulary for our drug repuposing research.

This repository creates user-friendly datasets from Entrez Gene. We currently focus on human genes only.

The python notebook [`process.ipynb`](process.ipynb) executes the analysis. Files downloaded from external locations are stored in [`download`](download). The following created datasets reside in [`data`](data):

+ [`genes-human.tsv`](data/genes-human.tsv): human genes with a select set of fields storing additional attributes

+ [`symbols-human.tsv`](data/symbols-human.tsv): a table of GeneID, symbol, and symbol type (synonym or primary)

+ [`symbols-human.json`](data/symbols-human.json): a Symbol–GeneID mapping of primary symbols only

+ [`synonyms-human.json`](data/synonyms-human.json): a Symbol–GeneIDs mapping for synonyms

+ [`symbol-map.json`](data/symbol-map.json): a Symbol–GeneID mapping with approved symbols and unambiguous synonyms

+ [`xrefs-human.tsv`](data/xrefs-human.tsv): mappings to external resources