ArticleBioinformatics (Oxford, England)2015
Phylesystem: a git-based data store for community-curated phylogenetic estimates.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
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- A complete and dynamic tree of birds.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Is variation in female aggressiveness acrossProceedings. Biological sciences · 2025Article
- More social species live longer, have longer generation times and longer reproductive windows.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Article
- DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life.Systematic biology · 2024Article
- Genomic Assessment of the Contribution of theInternational journal of molecular sciences · 2023Article
- Genetic sex determination, sex chromosome size and sex-specific lifespans across tetrapods.Journal of evolutionary biology · 2023Article
- The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data.BMC microbiology · 2022Article
- Quantifying research interests in 7,521 mammalian species with h-index: a case study.GigaScience · 2022Article
- OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life.Systematic biology · 2021Article
- Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life.BMC bioinformatics · 2021Article
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- The evolution of multicellular complexity: the role of relatedness and environmental constraints.Proceedings. Biological sciences · 2020Article
- Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion.PLoS computational biology · 2019Article
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- To increase trust, change the social design behind aggregated biodiversity data.Database : the journal of biological databases and curation · 2018Article
- TreeToReads - a pipeline for simulating raw reads from phylogenies.BMC bioinformatics · 2017Article
- Automated assembly of a reference taxonomy for phylogenetic data synthesis.Biodiversity data journal · 2017Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationPhylogenetic 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.
resultsHere, 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 (http://github.com/) 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. AVAILABILITY AND IMPLEMENTATION: Source code for the web service layer is available at https://github.com/OpenTreeOfLife/phylesystem-api. The data store can be cloned from: https://github.com/OpenTreeOfLife/phylesystem. A web application that uses the phylesystem web services is deployed at http://tree.opentreeoflife.org/curator. Code for that tool is available from https://github.com/OpenTreeOfLife/opentree. CONTACT: mtholder@gmail.com.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.