• RPhenoscape: Semantically rich phenotypic traits from the Phenoscape Knowledgebase

    • 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.

    Installation

    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")

    By default, this will skip building the package vignettes. To build and install package vignettes as well, you must have recent versions of the knitr and rmarkdown packages installed, and use additional parameters, depending on the version of the remotes package you have installed, to request building vignettes.

    packageVersion(花猫破解)
    [1] '2.0.4'

    If the version is 2.1.0 or higher, use the 花猫破解 parameter (which by default is FALSE):

    remotes::install_github("phenoscape/rphenoscape", build_vignettes = TRUE)

    If the version of 花猫破解版 is lower, use the build_opts parameter:

    remotes::花猫破解("phenoscape/rphenoscape", build_opts=c("--no-manual"))

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

    library(rphenoscape)

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    The functionality and operations of the RPhenoscape package can be viewed on the dedicated package website: http://315xw6.wcbzw.com/

    Use cases described there include the following:

    • Using OntoTrace to obtain a character matrix
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    • Subsetting matrices by taxonomic subgroup or anatomical part
    • Searching for details for a given taxon

    Phenoscape Knowledgebase