May 6, 2015

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

Bioinformatics
Emily Jane McTavishStephen A Smith

Abstract

Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). 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 the ability of other researchers to reuse phylogenetic estimates. As 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 i...Continue Reading

  • References10
  • Citations7

References

  • References10
  • Citations7

Citations

Mentioned in this Paper

Study
Environmental Infrastructure
Catheter Tip
Trees (plant)
Vision
Research Personnel
Gene Deletion
Acinetobacter sp. HYN18
Phylogenetic Analysis
Biologic Preservation

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