https://github.com/dhimmel/mesh

User-friendly extensions to MeSH
https://github.com/dhimmel/mesh

hetionet medical-subject-headings mesh ontology rephetio

Last synced: 3 months ago
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User-friendly extensions to MeSH

• Host: GitHub
• URL: https://github.com/dhimmel/mesh
• Owner: dhimmel
• Created: 2015-05-09T23:49:23.000Z (over 9 years ago)
• Default Branch: gh-pages
• Last Pushed: 2016-02-04T21:40:02.000Z (almost 9 years ago)
• Last Synced: 2024-05-02T06:00:20.965Z (8 months ago)
• Topics: hetionet, medical-subject-headings, mesh, ontology, rephetio
• Language: Jupyter Notebook
• Homepage:
• Size: 80.7 MB
• Stars: 9
• Watchers: 2
• Forks: 4
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# User-friendly extensions to MeSH

[![DOI: 10.5281/zenodo.45586](https://zenodo.org/badge/doi/10.5281/zenodo.45586.svg)](https://doi.org/10.5281/zenodo.45586 "Zenodo deposition of v1.0")

The [Medical Subject Headings](https://www.nlm.nih.gov/mesh/) (MeSH) is a controled vocabulary produced by the NLM for cataloging biomedical information. The resource is structured as an ontology and is used for PubMed/MEDLINE annotation. Here we provide user-friendly datasets derived from MeSH. Currently, two [record types](https://www.nlm.nih.gov/mesh/intro_record_types.html "MeSH Record Types") are processed: Descriptors and Supplementary Concept Records.

## Notebooks

+ [`descriptors.ipynb`](descriptors.ipynb) — processes Descriptors (also known as Main Headings)

+ [`supplementary-concept-records.ipynb`](supplementary-concept-records.ipynb) — processes Supplementary Concept Records (SCRs)

## Datasets

The `data` directory contains the created datasets:

+ [`terms.tsv`](data/terms.tsv) — table of Descriptor terms.

+ [`descriptor-terms.tsv`](data/descriptor-terms.tsv) — table of Descriptor names.

+ [`mesh.json`](data/mesh.json) — a JSON-formatted representation of the Descriptor ontology. Includes term identifiers, names, semantic types, parents, and tree numbers.

+ [`ontology.gexf.gz`](data/ontology.gexf.gz) — a [GEXF](https://gephi.org/gexf/format/) representation of the descriptor ontology that is compatable with [`newtorkx`](https://networkx.github.io/).

+ [`symptoms.tsv`](data/symptoms.tsv) — symptom Descriptors (the 438 descendants of [`D012816`](http://www.ncbi.nlm.nih.gov/mesh/D012816 "MeSH Descriptor: Signs and Symptoms")

+ [`tree-numbers.tsv`](data/tree-numbers.tsv) — table of tree numbers for each Descriptor. A tree number represents a path to the the root. This file is handy for mapping to external resources which occasionally identify MeSH Descriptors by their tree numbers (a bad but prevalent practice).

+ [`supplemental-records.tsv`](data/supplemental-records.tsv) — table of SCR terms.

+ [`supplemental-terms.tsv`](data/supplemental-terms.tsv) — table of SCR names.

## License

This repository is released as [CC0](https://creativecommons.org/publicdomain/zero/1.0/ "Creative Commoms · CC0 1.0 Universal · Public Domain Dedication")