rotl: study_external_IDs – R documentation

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study_external_IDs

Get external identifiers for data associated with an Open Tree study

Description

Data associated with studies contributing to the Open Tree synthesis may be available from other databases. In particular, trees and alignments may be available from treebase and DNA sequences and bibliographic information associated with a given study may be available from the NCBI. This function retrieves that information for a given study.

Usage

study_external_IDs(study_id)

Arguments

study_id

An open tree study ID

Value

A study_external_data object (which inherits from a list) which contains some of the following.

doi, character, the DOI for the paper describing this study

external_data_url, character, a URL to an external data repository (e.g. a treebase entry) if one exists.

pubmed_id character, the unique ID for this study in the NCBI's pubmed database

popset_ids character, vector of IDs for the NCBI's popset database

nucleotide_ids character, vector of IDs for the NCBI's nucleotide database

Examples

## Not run: 
flies <- studies_find_studies(property="ot:focalCladeOTTTaxonName", value="Drosophilidae")
study_external_IDs(flies[2,]$study_ids)

## End(Not run)

rotl

Interface to the 'Open Tree of Life' API

v3.0.11

BSD_2_clause + file LICENSE

Authors

Francois Michonneau [aut, cre] (<https://orcid.org/0000-0002-9092-966X>), Joseph Brown [aut] (<https://orcid.org/0000-0002-3835-8062>), David Winter [aut] (<https://orcid.org/0000-0002-6165-0029>), Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>)

Initial release