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Automated assembly of a reference taxonomy for phylogenetic data synthesis
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Methods
Biodiversity Data Journal 5: e12581
https://doi.org/10.3897/BDJ.5.e12581 (22 May 2017)
https://doi.org/10.3897/BDJ.5.e12581 (22 May 2017)
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Article metadata
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Introduction
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The Open Tree of Life project
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Reference taxonomy requirements
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Related work
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Method
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Terminology
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Method overview
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Taxonomic sources
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Import and Normalization
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Aligning nodes across taxonomies
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Ad hoc adjustments
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Candidate identification
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Candidate selection
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Alignment heuristics
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Control flow for applying heuristics
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Failure to choose
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Redescriptions
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Merging unaligned source nodes
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Merging node data
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Final patches
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Assigning identifiers
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Results
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Summary of Open Tree Taxonomy
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Results of assembly procedure
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Evaluating the taxonomy relative to requirements
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OTU coverage
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Phylogenetically informed classification
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Taxonomic coverage
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Ongoing update
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Open data
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Discussion
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Community curation
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Comparison to other taxonomies
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Potential improvements and future work
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Data resources
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Conclusions
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Acknowledgements
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References
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