Create Hyperlinks to Biological Databases and Resources

Generate urls and hyperlinks to commonly used biological databases and resources based on standard identifiers. This is primarily useful when writing dynamic reports that reference things like gene symbols in text or tables, allowing you to, for example, convert gene identifiers to hyperlinks pointing to their entry in the NCBI Gene database. Currently supports NCBI Gene, PubMed, Gene Ontology, CRAN and Bioconductor.


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biolink makes it easy to create hyperlinks to various online databases/resources for inclusion in dynamic reports written in Markdown, HTML or LaTeX.

It currently supports generating links for:

  • PubMed articles
  • Gene Ontologies
  • Kegg Pathways
  • Entrez genes
  • R packages on CRAN or Bioconductor
  • create an issue to request support for additional resources

Bold indicates support for data tags (see below).

Usage

Basic idea

link_entrez("4609")
## "<a href=\"https://www.ncbi.nlm.nih.gov/gene/4609\">4609</a>"
 
link_entrez("4609", text = "this gene")
## "<a href=\"https://www.ncbi.nlm.nih.gov/gene/4609\">this gene</a>"
 
link_entrez("4609", text = "this gene", format = "markdown")
## "[this gene](https://www.ncbi.nlm.nih.gov/gene/4609)"

Extended example

Note that `r link_pubmed("22952919", "this paper")` found that the ErbB
signaling pathway (`r link_kegg("hsa04012")`) and response to organic
substance process (`r link_go("GO:0010033")`) are enriched for a network
of oncogenes, including `r link_entrez("4609", "<symbol>")`.

⇣ generates ⇣

Data tags

For a few supported resources, specially formatted tags can be used to retrieve data from the corresponding resource. In the example above, link_entrez("4609", "<symbol>") produces MYC because the gene symbol was retrieved from NCBI.

See the package documentation for a complete list of supported data tags.

Installation

Install the released version of biolink from CRAN

install.packages("biolink")

or the development version from GitHub with

# install.packages("devtools")
devtools::install_github("aaronwolen/biolink")

News

biolink 0.1.5

  • Skip data tag tests on CRAN

biolink 0.1.4

  • Fix failed test caused by PubMed including an extra space in article title

biolink 0.1.3

  • Add support for name and definition gene ontology data tags

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("biolink")

0.1.6 by Aaron Wolen, a year ago


Browse source code at https://github.com/cran/biolink


Authors: Aaron Wolen [aut, cre]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports rentrez, xml2, DBI, RMySQL, glue, memoise

Suggests testthat, lintr, httr, covr


See at CRAN