Data from: Automated assembly of a reference taxonomy for phylogenetic data synthesis

Rees JA, Cranston KA

Date Published: June 16, 2017

DOI: http://dx.doi.org/10.5061/dryad.vk775

 

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Title README file for package
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Description Describes all files in package and provides external links to additional documentation.
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Title SILVA-to-NCBI mapping
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Description Contains a mapping of Genbank accession numbers to NCBI taxon ids and names. The accessions are those that are the reference sequences for SILVA clusters.
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Title OTT amendments
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Description The taxonomy amendments used in preparation of OTT. Includes all amendments in https://github.com/OpenTreeOfLife/amendments-1 at the time that we built the version of OTT described in the article. Each amendment is a json file that includes the change being proposed as well as sources that support the change.
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Title mapping of source ids to OTT ids
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Description Cumulative mapping of identifiers in sources to OTT identifiers. Format of each line is source:sourceid,OTTid.
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Title OTT version2.10
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Description This is the previous version of the Open Tree Taxonomy. It is included because we use the previous version during identifier assignment (ott2.10 required to build ott3.0). See the enclosed README for details on files and formats.
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Title OTT version 3.0
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Description Version of the Open Tree Taxonomy described in the manuscript. See the enclosed README for details on files and formats.
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Title separation taxonomy
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Description The 'separation taxonomy' described in the manuscript. Contains a list of taxa and a list of synonyms.
Download separation.tgz (729 bytes)
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When using this data, please cite the original publication:

Rees J, Cranston K (2017) Automated assembly of a reference taxonomy for phylogenetic data synthesis. Biodiversity Data Journal 5: e12581. http://dx.doi.org/10.3897/bdj.5.e12581

Additionally, please cite the Dryad data package:

Rees JA, Cranston KA (2017) Data from: Automated assembly of a reference taxonomy for phylogenetic data synthesis. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.vk775
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