DatabaseLinke.R

A set of functions to parse and open (search query) links to genomics related and other websites for R. Useful when you want to explore e.g.: the function of a set of differentially expressed genes.

DOI

DatabaseLinke.R – Parse links to databases from your list of gene symbols

A set of functions to parse and open (search query) links to genomics related and other websites for R. Useful when you want to explore e.g.: the function of a set of differentially expressed genes.

Get the DatabaseLinke.R

[TOC]

Summary

A set of functions to parse links to genomics related websites.

It can do 3 things:

  1. Parse (and store) the links for a vector of gene symbols
  2. Parse the links, and open them in the default browser (beware for 20+ genes)
  3. Parse the link, and write open commands into an (executable) bash script, which you can later open in batches.

Note: It typically parses query (search) links, instead direct links

List of Databases

Species specific

Install

  1. Install package

Install directly from GitHub via devtools with one R command:

# install.packages("devtools"); # If you don't have it.
require("devtools")
devtools::install_github(repo = "vertesy/DatabaseLinke.R")

Usage

1) Simply load the package:

require("DatabaseLinke.R ")

Then call user setup script (every time before using)

source("https://raw.githubusercontent.com/vertesy/DatabaseLinke.R/master/R/DatabaseLinke.Setup.Global.Variables.R")

2) Alternative

Directly source it from the web in R:

   source("https://raw.githubusercontent.com/vertesy/DatabaseLinke.R/master/R/DatabaseLinke.R")
   source("https://raw.githubusercontent.com/vertesy/DatabaseLinke.R/master/R/DatabaseLinke.Setup.Global.Variables.R")

You can also download and source.

Test it!

# Dummy
geneSymbols = c('Sox2', 'Actb'); 

# Test Helper
openURLs.1by1("http://www.google.com/search?as_q= Sox2 ")

# Test
link_GeneCards(geneSymbols); link_GeneCards(geneSymbols, Open = TRUE)
link_ensembl_zebra(geneSymbols); link_ensembl_zebra(geneSymbols, Open = TRUE)
link_ensembl_mice(geneSymbols); link_ensembl_mice(geneSymbols, Open = TRUE)
link_ensembl_mice(geneSymbols); link_ensembl_mice(geneSymbols, Open = TRUE)
link_ensembl(geneSymbols); link_ensembl(geneSymbols, Open = TRUE)
link_ensembl.grc37(geneSymbols); link_ensembl.grc37(geneSymbols, Open = TRUE)
link_uniprot_mice(geneSymbols); link_uniprot_mice(geneSymbols, Open = TRUE)
link_uniprot_human(geneSymbols); link_uniprot_human(geneSymbols, Open = TRUE)
link_uniprot_zebrafish(geneSymbols); link_uniprot_zebrafish(geneSymbols, Open = TRUE)
link_String(geneSymbols); link_String(geneSymbols, Open = TRUE)
qString(geneSymbols); qString(geneSymbols, Open = TRUE)
link_pubmed(geneSymbols); link_pubmed(geneSymbols, Open = TRUE)
link_wikipedia(geneSymbols); link_wikipedia(geneSymbols, Open = TRUE)
link_google(geneSymbols); link_google(geneSymbols, Open = TRUE)
link_HGNC(geneSymbols); link_HGNC(geneSymbols, Open = TRUE)
qHGNC(geneSymbols); qHGNC(geneSymbols, Open = TRUE)
link_wormbase(geneSymbols); link_wormbase(geneSymbols, Open = TRUE)
link_MGI.JAX(geneSymbols); link_MGI.JAX(geneSymbols, Open = TRUE)

Use details

Default species is typically mice

You can use the functions in 3 ways:

  1. Open the link in your web browser:

    link_String("Mecom")

  2. Writes the link in a bash script, called run.sh:

    link_String("Mecom", writeOut = T)
    • use, if you have too many links to open at once
    • When you run the script, it opens all the links as tabs in your default browser (on OS X / *nix).
    • Comment out some lines if its too much
    • More precisely, it will write the links to BashScriptLocation in an executable format.

Writing to file

Using link_String("Mecom", writeOut = T), in your bash script, you will find:

open 'http://string-db.org/newstring_cgi/show_network_section.pl?identifier=Mecom&species=10090'

link_String("Mecom", writeOut = F, Open=F)

Writes the link to the screen. You get:

http://string-db.org/newstring_cgi/show_network_section.pl?identifier=Mecom&species=10090

as a character vector, so you can write out in a column of your gene-table.

Components

  1. R script containing functions each of which operates on vectors of gene symbols.
  2. An executable bash script that you need to make. You can make it anywhere, but you need to specify it in the R-script’s BashScriptLocation variable.

List of Functions in DatabaseLinke.R (21)

Updated: 2023/11/27 20:46

  • 1 openURLs.1by1()

    Open URLs One by One. This function opens provided links sequentially with an optional delay between each. This can be useful for slower computers and to avoid triggering anti-robot measures in search engines.

  • GeneCards Link Generator. Generates GeneCards URLs for a given list of gene symbols.

  • Zebrafish Ensembl Link Generator. Generates the latest Ensembl (GRC38) URLs for a given list of zebrafish gene symbols.

  • Mouse Ensembl Link Generator. Generates the latest Ensembl (GRC38) URLs for a given list of mouse gene symbols.

  • Generate Zebrafish Ensembl Links. This function generates the latest Zebrafish Ensembl (GRC38) links for a list of gene symbols.

  • Generate Ensembl Links. This function generates the latest Ensembl (GRC38) links for a list of gene symbols.

  • Parse Ensembl GRC37 links. This function generates Ensembl GRC37 links for a list of gene symbols.

  • Parse UNIPROT Links for Mice Genes. This function generates UNIPROT links for a list of mouse gene symbols.

  • Parse UNIPROT Links for Human Genes. This function generates UNIPROT links for a list of human gene symbols.

  • Parse UNIPROT Links for Zebrafish Genes. This function generates UNIPROT links for a list of zebrafish gene symbols.

  • Parse STRING Database Links. This function generates links to the STRING protein interaction database for a list of gene symbols.

  • 12 qString()

    qString. Generates links to the STRING protein interaction database based on a given list of gene symbols. The function supports different organisms such as mice, humans, or “NA” for no specific organism.

  • link_pubmed. Generates links to the PUBMED database based on a given list of gene symbols and additional search terms.

  • link_wikipedia. Generates Wikipedia search query links based on a given list of gene symbols.

  • link_google. Parses Google search query links for a provided list of gene symbols. The “prefix” and “suffix” will be searched for together with each gene (e.g., “Human ID4 neurons”). Uses google=”http://www.google.com/search?as_q=”.

  • link_bing. Parses Bing search query links for a provided list of gene symbols.

  • 17 # qHGNC()

    HGNC link generator and web lookup. Parses HGNC links for a provided list of gene symbols.

  • link_wormbase. Generate Wormbase database links for a list of gene symbols.

  • link_MGI.JAX. Generate MGI JAX mouse genomics search query links for a list of gene symbols.

  • link_SNPedia_clip2clip. Generate SNPedia links from a list of rsIDs copied from an Excel column.

  • link_Franklin_clip2clip. Generate Franklin (Genoox) links from a list of coordinates.

Appendix

Google search URL / search query

String Meaning
as_oq This tells Google to find pages in which at least instance of nintendo OR wii is found
as_q This means that you look for both nintendo and wii in the same page
as_epq Google translates this as a Google search of “nintendo wii”, searches the exact phrase ‘nintendo wii’
num The number of results you want displayed, it ranges from 0 to 100. If you set num to 0 you will get the ‘No match found” message
safe If you set this to active the Google Safe Search is on and the adult material will be filtered
as_eq Use this to exclude a term from your search
as_qdr Shows only results that have been updated in the given time interval. Possible values: y (year), m6 (6 months), m3 (3 months).
as_sitesearch Limits the search to a specific domain or TLD (.us; .gov; .co.uk; .ro; etc)
as_occt This is set by default to ‘any’ but if you change it you can search in: title, url, links

Troubleshooting

If you encounter a bug, or something doesn’t work,

  1. please let me know by raising an issue on DatabaseLinke.R
  2. Fix by providing the missing function.
    • Try to source("https://raw.githubusercontent.com/vertesy/CodeAndRoll/master/CodeAndRoll.R") See details for CodeAndRoll
    • If still some functons are missing, try to install MarkdownReports: install.packages("devtools") devtools::install_github(repo = "vertesy/MarkdownReports") require("MarkdownReports") See details for MarkdownReports

Vertesy, 2021. Cite via: DOI