# Biomappings

> repository of community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources.

**Wikidata**: [Q111239110](https://www.wikidata.org/wiki/Q111239110)  
**Source**: https://4ort.xyz/entity/biomappings

## Summary
Biomappings is a repository of community-curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources. Developed by American chemist Charles Tapley Hoyt, it serves as a resource for linking biological identifiers across different databases and ontologies.

## Key Facts
- **Repository of biological mappings**: Stores equivalences and relationships between named biological entities not found in primary sources.
- **Created by Charles Tapley Hoyt**: An American chemist, biologist, and programmer, born in 1993.
- **Developed in Python**: Uses the general-purpose programming language Python, first released on February 20, 1991.
- **Part of the Biopragmatics Stack**: Integrated into the broader Biopragmatics ecosystem.
- **Open-source with CC0 License**: Released under the Creative Commons CC0 License, placing it in the public domain.
- **Maintained by INDRA team and Charles Tapley Hoyt**: Ongoing development and support.
- **7,410 records as of 2022-05-04**: Tracks the number of mappings available in the repository.
- **Depends on software**: Built using NetworkX, Requests, click, PyYAML, tqdm, and PyStow.
- **Latest stable version**: 0.3.1, released on 2023-08-14.
- **Described by source**: "Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings."

## FAQs
### Q: What problem does Biomappings solve?
A: Biomappings addresses the challenge of linking biological identifiers across different databases and ontologies, which are often not directly available from primary sources. It provides a centralized repository for community-curated and predicted mappings.

### Q: Who created Biomappings?
A: Biomappings was created by American chemist Charles Tapley Hoyt, who also serves as its primary developer and maintainer.

### Q: What programming language is Biomappings written in?
A: Biomappings is written in Python, a general-purpose programming language first released in 1991.

### Q: How many mappings does Biomappings contain?
A: As of 2022-05-04, Biomappings contains 7,410 records of biological mappings.

### Q: Is Biomappings open-source?
A: Yes, Biomappings is open-source and released under the Creative Commons CC0 License, placing it in the public domain.

## Why It Matters
Biomappings plays a critical role in the biomedical research community by providing a structured way to link biological entities across different databases and ontologies. This resource is essential for researchers, bioinformaticians, and developers who need to integrate data from multiple sources. By offering both curated and predicted mappings, Biomappings helps bridge gaps in biological knowledge that are not available from primary sources. Its open-source nature and community-driven approach ensure that it remains a valuable tool for the scientific community, facilitating more comprehensive and accurate biological research.

## Notable For
- **First release**: Version 0.0.1 was published on December 15, 2020.
- **Community-driven curation**: Combines both human-curated and machine-predicted mappings.
- **Integration with Biopragmatics**: Part of the broader Biopragmatics Stack, enhancing interoperability in biomedical data.
- **Public domain licensing**: Released under CC0, making it freely usable without restrictions.
- **Active maintenance**: Regular updates and improvements, with the latest stable version (0.3.1) released in August 2023.

## Body
### Overview
Biomappings is a repository designed to store and manage equivalences and relationships between named biological entities. It addresses the need for standardized mappings that are not readily available from primary sources, such as databases and ontologies.

### Development and Maintenance
Developed by Charles Tapley Hoyt, a biologist and programmer, Biomappings is written in Python. The project is maintained by the INDRA team and Hoyt, ensuring ongoing development and support. The repository is hosted on GitHub, with contributions from researchers like Amelia L. Hoyt, Benjamin M. Gyori, and Krishna Udaiwal.

### Licensing and Accessibility
Biomappings is released under the Creative Commons CC0 License, placing it in the public domain. This allows for unrestricted use, modification, and distribution. The source code is available on GitHub, and the project is part of the Biopragmatics Stack, which aims to improve interoperability in biomedical research.

### Technical Details
Biomappings depends on several software libraries, including NetworkX, Requests, click, PyYAML, tqdm, and PyStow. These tools support its functionality in data processing, web requests, and configuration management. The repository tracks 7,410 mappings as of 2022-05-04, demonstrating its growing utility in the biomedical field.

### Versions and Updates
Biomappings has undergone multiple releases, with the latest stable version being 0.3.1, published on August 14, 2023. Previous versions include 0.0.1 (December 15, 2020), 0.0.2 (December 16, 2020), and 0.1.0 (July 9, 2021), among others. Each update introduces new features and improvements, reflecting the project's active development cycle.

### Research and Applications
Biomappings is described in the academic literature as a tool for predicting and curating missing biomedical identifier mappings. Its applications include data integration, knowledge graph construction, and enhancing the accuracy of biological research. The project is supported by the Biosciences databases Wikiproject, indicating its relevance to the broader scientific community.

## References

1. [Release 0.0.1. 2020](https://github.com/biopragmatics/biomappings/releases/tag/v0.0.1)
2. [Release 0.0.2. 2020](https://github.com/biopragmatics/biomappings/releases/tag/v0.0.2)
3. [Release 0.0.3. 2020](https://github.com/biopragmatics/biomappings/releases/tag/v0.0.3)
4. [Release 0.0.4. 2021](https://github.com/biopragmatics/biomappings/releases/tag/v0.0.4)
5. [Release 0.1.0. 2021](https://github.com/biopragmatics/biomappings/releases/tag/v0.1.0)
6. [Release 0.1.1. 2021](https://github.com/biopragmatics/biomappings/releases/tag/v0.1.1)
7. [Release 0.1.2. 2021](https://github.com/biopragmatics/biomappings/releases/tag/v0.1.2)
8. [Release 0.2.0. 2022](https://github.com/biopragmatics/biomappings/releases/tag/v0.2.0)
9. [Release 0.3.0. 2023](https://github.com/biopragmatics/biomappings/releases/tag/v0.3.0)
10. [Release 0.3.1. 2023](https://github.com/biopragmatics/biomappings/releases/tag/v0.3.1)
11. [Release 0.3.2. 2023](https://github.com/biopragmatics/biomappings/releases/tag/v0.3.2)
12. [Release 0.3.3. 2023](https://github.com/biopragmatics/biomappings/releases/tag/v0.3.3)
13. [Release 0.3.4. 2023](https://github.com/biopragmatics/biomappings/releases/tag/v0.3.4)
14. [Release 0.3.5. 2023](https://github.com/biopragmatics/biomappings/releases/tag/v0.3.5)
15. [Release 0.3.6. 2023](https://github.com/biopragmatics/biomappings/releases/tag/v0.3.6)
16. [Release 0.3.7. 2023](https://github.com/biopragmatics/biomappings/releases/tag/v0.3.7)
17. [Release 0.4.0. 2025](https://github.com/biopragmatics/biomappings/releases/tag/v0.4.0)
18. [Source](https://biopragmatics.github.io/biomappings/)