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R package to make phenotypic traits from the Phenoscape Knowledgebase available from within R.
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hlapp Enables switching to POST for JSON-returning queries
This had already been enabled for CSV returning queries.

Note that most KB API methods returning JSON do not actually support
POST at this point. However, the expectation is that for those that do
not, it is hardly possible to create a query URL (for a GET request)
that is too long. The one triggering the issue (/term/labels, see #113)
does support POST.

Fixes #113.
Latest commit 466773a Oct 18, 2019
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RPhenoscape: Semantically rich phenotypic traits from the Phenoscape Knowledgebase

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  • Author: Hong Xu, Hilmar Lapp
  • Maintainer: Hilmar Lapp

Most of the services provided with the Phenoscape Knowledgebase web API return data in JSON format, plain text (usually tab-delimited), and NeXML. This package facilitates interfacing with the Phenoscape Knowledgebase for searching ontology terms, retrieving term info, and querying data matrices.


The development version of RPhenoscape is available on Github. It has not yet been released to CRAN. To install RPhenoscape from Github, use the install_github() function in the remotes package (which can be installed from CRAN using install.packages()):

remotes::install_github("phenoscape/rphenoscape", build_opts=c("--no-manual"))

The custom build_opts parameter ensures that the vignette(s) will be built and installed as well. (The default for build_opts will skip building vignettes.) Building vignettes requires recent versions of the knitr and rmarkdown packages to be installed.

Once installed, the package can be loaded ("attached") as any other R package:


Package Usage Information

The functionality and operations of the RPhenoscape package can be viewed on the dedicated package website:

Use cases described there include the following:

  • Using Ontotrace to obtain a character matrix
  • Obtaining the character matrices for studies published for a taxonomic clade
  • Subsetting matrices by taxonomic subgroup or anatomical part
  • Searching for details for a given taxon

Phenoscape Knowledgebase

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