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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
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Phylesystem: a git-based data store for community-curated phylogenetic estimates
Emily Jane McTavish1, Cody E Hinchliff2, James F Allman3
1Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA, Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany.
Bioinformatics (Oxford, England)
|May 6, 2015
Summary
This study introduces open-source software for curating phylogenetic data, enhancing reproducibility and reuse. The system uses git for version control and GitHub for open access, facilitating community-driven data improvement.
Area of Science:
- Evolutionary Biology
- Bioinformatics
Background:
- Archiving phylogenetic estimates is crucial for research transparency and reproducibility.
- Existing platforms require data editing and taxonomic mapping for improved reusability.
- Tracking curation provenance is essential for acknowledging contributions and correcting errors.
Purpose of the Study:
- To develop software infrastructure for community-driven open curation of phylogenetic data.
- To enhance the accuracy and reusability of published phylogenetic estimates.
- To provide a transparent and version-controlled system for managing phylogenetic data.
Main Methods:
- Developed a backend system using git for version control of phylogenetic data.
- Utilized GitHub for hosting the data store, enabling open access.
- Deployed a server running the 'phylesystem-api' to manage git and GitHub interactions.
- Created a JavaScript web application for input and curation of phylogenetic statements.
Main Results:
- Established a software infrastructure supporting open curation of phylogenetic data.
- Implemented a system that preserves the history of edits through git's version control.
- Provided open access to the data store via GitHub.
- Deployed a functional web application for phylogenetic data curation.
Conclusions:
- The developed system facilitates open and collaborative curation of phylogenetic data.
- Enhanced data accuracy and reusability through version control and community input.
- Promotes transparency and reproducibility in phylogenetic research.
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