Dryad
Published June 16, 2017 | Version v1
Dataset Open

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

Authors/Creators

  • 1. Duke University

Description

Taxonomy and nomenclature data are critical for any project that synthesizes biodiversity data, as most biodiversity data sets use taxonomic names to identify taxa. Open Tree of Life is one such project, synthesizing sets of published phylogenetic trees into comprehensive summary trees. No single published taxonomy met the taxonomic and nomenclatural needs of the project. Here we describe a system for reproducibly combining several source taxonomies into a synthetic taxonomy, and we discuss the challenges of taxonomic and nomenclatural synthesis for downstream biodiversity projects.

Notes

README file for package
Describes all files in package and provides external links to additional documentation.
SILVA-to-NCBI mapping
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.
accessions.tgz
OTT amendments
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.
amendments.tgz
mapping of source ids to OTT ids
Cumulative mapping of identifiers in sources to OTT identifiers. Format of each line is source:sourceid,OTTid.
by_qid.tgz
OTT version2.10
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.
ott2.10.tgz
OTT version 3.0
Version of the Open Tree Taxonomy described in the manuscript. See the enclosed README for details on files and formats.
ott3.0.tgz
separation taxonomy
The 'separation taxonomy' described in the manuscript. Contains a list of taxa and a list of synonyms.
separation.tgz

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: 1208809

Files

README.txt

Files (223.1 MB)

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md5:273ed30ccc51bbf18cc410cf34038444
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md5:318ce3ebb20046553d98eae918e5a75e
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Additional details

Related works

Is cited by
10.3897/bdj.5.e12581 (DOI)