Jan 16, 2015

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

BioRxiv : the Preprint Server for Biology
Emily Jane B. McTavishStephen A. Smith

Abstract

Motivation Phylogenetic estimates from published studies can be archived using general platforms like Dryad ([Vision, 2010][1]) or TreeBASE ([Sanderson et al ., 1994][2]). 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. 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. Results 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 recor...Continue Reading

  • References
  • Citations

References

  • We're still populating references for this paper, please check back later.
  • References
  • Citations

Citations

  • This paper may not have been cited yet.

Mentioned in this Paper

Study
Environmental Infrastructure
Catheter Tip
Trees (plant)
Research Personnel
Gene Deletion
Phylogenetic Analysis
Apis mellifera filamentous virus
Biologic Preservation
Alpha 1-Antitrypsin

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Related Papers

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Yanchao Wang, Rajshekhar Sunderraman
Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Sheau-Ling HsiehFeipei Lai
© 2020 Meta ULC. All rights reserved