Phylesystem: a git-based data store for community curated phylogenetic estimates [article]

Emily Jane B. McTavish, Cody E. Hinchliff, James F. Allman, Joseph W. Brown, Karen A. Cranston, Mark T. Holder, Jonathan A. Rees, Stephen A. Smith
2015 bioRxiv   pre-print
Phylogenetic estimates from published studies can be archived using general platforms like Dryad or TreeBASE. Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy and reusability of the phylogenetic statements. Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves
more » ... e ability of other researchers to reuse phylogenetic estimates. Because the process of curating a published phylogenetic estimate is not error-free, retaining a full record of the provenance of edits to a tree is crucial for openness, allowing editors to receive credit for their work, and making errors introduced during curation easier to correct. Here we report the development of software infrastructure to support the open curation of phylogenetic data by the community of biologists. The backend of the system provides an interface for the standard database operations of creating, reading, updating, and deleting records by making commits to a git repository. The record of the history of edits to a tree is preserved by git's version control features. Hosting this data store on GitHub provides open access to the data store using tools familiar to many developers. We have deployed a server running the "phylesystem-api", which wraps the interactions with git and GitHub. The Open Tree of Life project has also developed and deployed a JavaScript application that uses the phylesystem-api and other web services to enable input and curation of published phylogenetic statements.
doi:10.1101/013862 fatcat:jejnnmktnfhd5gypxbihwp6zyy