README.md

Computing term cooccurrence in MEDLINE

This repository quantifies term cooccurrence in MEDLINE. It's designed for computing the cooccurence of all pairs between two MeSH termsets. The repository computes MEDLINE cooccurences for the Rephetio hetnet. See the corresponding Thinklab discussion for more information.

Modules

• eutility.py defines an esearch_query function for retreiving PubMed IDs matching a user-defined query.
• cooccurrence.py computes the cooccurences bewteen two termsets, whose associated PubMed IDs have been retrieved.

Notebooks

The following notebooks were used to compute relationships for Hetionet v1.0 by Project Rephetio:

• diseases.ipynb computes disease-disease cooccurrence
• symptoms.ipynb computes symptom-disease cooccurrence
• tissues.ipynb computes anatomy-disease cooccurrence. This notebook depends on data/disease-pmids.tsv.gz, a dataset created by symptoms.ipynb.

The following notebooks are for a more general analysis to support custom user queries:

• download-topics.ipynb downloads the PubMed IDs for all MeSH descriptors and supplementary disease concepts and saves this to data/mesh-term-topics-noexp.jsonl.gz.
• cooccur-topics.ipynb reads mesh-term-topics-noexp.jsonl.gz to compute cooccurrence between a user-selected term with all other MeSH terms.

Environment

# create environment
conda env create --file=environment.yml

# update environment
conda env update --file=environment.yml

# activate environment
conda activate medline

# run jupyter lab for notebook development
jupyter lab

History

On 2021-04-09, ownership of this repository on GitHub was changed from dhimmel/medline to hetio/medline. The hetio organization has GitHub LFS quota, providing a more convenient way to store large compressed files.

At the time of the transfer, the only default (and only) branch was gh-pages. The gh-pages branch was renamed to pre-lfs-archive. A new default branch main was created, whose history has been migrated to use Git LFS. For the version of this repository used by Project Rephetio to create Hetionet v1.0, refer to the v1.0 release.

Comparison to MRCOC

MEDLINE produces co-occurrence files under the codename MRCOC. More information is available in the 2016 report Building an Updated MEDLINE Co-Occurrences (MRCOC) File. These files might be a viable alternative to the analyses in this repository for certain applications. However, they don't appear to contain topics for supplemental concept records (for example MeSH term C000591739). Feel free to open an issue with additional insights on or comparisons to MRCOC.

License

This repository is released under CC0 1.0.