Abstract
All species are hierarchically related to one another, and we use taxonomic names to label the nodes in this hierarchy. Taxonomic data is becoming increasingly available on the web, but scientists need a way to access it in a programmatic fashion that's easy and reproducible. We have developed taxize, an open-source software package (freely available from http://cran.r-project.org/web/packages/taxize/index.html) for the R language. taxize provides simple, programmatic access to taxonomic data for 13 data sources around the web. We discuss the need for a taxonomic toolbelt in R, and outline a suite of use cases for which taxize is ideally suited (including a full workflow as an appendix). The taxize package facilitates open and reproducible science by allowing taxonomic data collection to be done in the open-source R platform.
Highlights
Evolution by natural selection has led to a hierarchical relationship among all living organisms
There is no one authoritative taxonomic names source for all taxa - there are taxon specific sources that are used by many scientists
We provide a list of species names, some of which are misspelled, and we’ll call the application programming interfaces (API) with the tnrs function
Summary
Evolution by natural selection has led to a hierarchical relationship among all living organisms. The correct spellings are Helianthus annuus and Homo sapiens Another approach uses the Taxonomic Name Resolution Service via the Taxosaurus API http://taxosaurus.org/ developed by iPLant and the Phylotastic organization. In this example, we provide a list of species names, some of which are misspelled, and we’ll call the API with the tnrs function. A number of data sources in taxize provide the capability to retrieve higher taxonomic names, but we will highlight two of the more useful ones: Integrated Taxonomic Information System (ITIS) http:// www.itis.gov/ and National Center for Biotechnology Information (NCBI)[7]. There was only a single species in the family Asteraceae, so the data for Bellis perennis are carried over
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