https://github.com/cthoyt/biomodels-metadata-analysis

Generate a summary of metadata annotations in the BioModels database
https://github.com/cthoyt/biomodels-metadata-analysis

biomodels fair-data modeling reproducibility-crisis sbml systems-biology

Last synced: 13 days ago
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Generate a summary of metadata annotations in the BioModels database

• Host: GitHub
• URL: https://github.com/cthoyt/biomodels-metadata-analysis
• Owner: cthoyt
• Created: 2023-02-23T12:34:36.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2024-05-14T11:06:13.000Z (8 months ago)
• Last Synced: 2024-10-30T21:51:35.449Z (2 months ago)
• Topics: biomodels, fair-data, modeling, reproducibility-crisis, sbml, systems-biology
• Language: Python
• Homepage:
• Size: 224 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

        
# BioModels Metadata Analysis [![DOI](https://zenodo.org/badge/605565691.svg)](https://zenodo.org/badge/latestdoi/605565691)

[BioModels](https://www.ebi.ac.uk/biomodels/) is a [CC0 licensed](https://www.ebi.ac.uk/biomodels/termsofuse) repository

of mathematical models of biological and biomedical systems. It contains manually curated, non-curated, and

autogenerated models of varying quality. Most contain some model-level metadata.

This repo automatically downloads, parses, and summarizes the metadata across all applicable models

in BioModels. Currently, it generates 3 files:

1. [`tag_summary.tsv`](tag_summary.tsv) - summarizes what prefixes are used in model-level metadata

2. [`tag_prefix_summary.tsv`](tag_prefix_summary.tsv) - summarizes what prefixes are used in model-level metadata and in

   combination with what target prefixes

3. [`triples.tsv`](triples.tsv) - dump of all metadata statements as triples, normalized with

   the [Bioregistry](https://github.com/biopragmatics/bioregistry).

**Editorial**: While there might be subtle differences between the predicates in

the http://biomodels.net/biology-qualifiers/ and http://biomodels.net/model-qualifiers/ namespaces, it appears

that there is lots of duplicated information and not a standardized schema applied across BioModels.

## Rebuild

Dependencies and analysis are automated with `tox`. Run the following in the command line:

```shell

pip install tox

tox

```

## License

Code in this repository is licensed under the MIT License. Data in this repository is licensed under the CC0 License.

## Acknowledgements

The development of this repository is funded by the DARPA ASKEM program, grant number HR00112220036.