Searching bioinformatic databases with YubNub

You may already be familiar with YubNub; it describes itself as “the social command line for the web”. Most commands consist of two (or more) words … one for the search engine, the other for the query.

For example, typing:

gg open science on friendfeed

into the YubNub search box searches Google for “open science on friendfeed“, via YubNub.

I thought I’d highlight a few life science- and bioinformatics-related YubNub commands I find myself using quite often in my day-to-day work. Some are commands I created, others someone else created. This is the beauty of YubNub … often someone has already made the ‘obvious’ command … it’s worth just trying to search with a command you expect to exist, since it often does.

Onward, with the list:

  • pubmed — Searches PubMed
  • hubmed — Searches HubMed (Alf Eatons featureful alternative interface to PubMed)
  • gopubmed — Searches GoPubMed (an ontology enhanced PubMed search)
  • doi — Redirects you based on a Digital Object Identifier (DOI), via
  • pdb — Searches the Protein DataBank for 3D structures. Usually the search term should be a 4 letter pdb code.
  • uniprot — Searches the Uniprot database (use an accession, id or keyword as the query).
  • ihop — Searches iHOP, information Hyperlinked over Proteins, for views of the biomedical literature guided by gene networks. Nothing to do with pancakes (or prayer).

There is also a class of more general, non-biomedical commands which I often use:

  • gg — The Google.
  • gimThe Google Image Search.
  • wp — Good ol’ Wikipedia.
  • ucc — The universal currency converter at Use it like ucc 399 aud usd, to convert $399 Australian dollars to US dollars. Then, if you have your cash in Australian dollars, weep about the recent drop in the exchange rate 😛
  • man — Like *nix man ‘manual pages’, but for YubNub commands. Eg, man ucc will give the manual page describing how to used the ucc command.
  • ls — A bit like the *nix shell ls, this command lists existing YubNub commands that contain your query in their name, description or url. eg. searching ls protein gives you a short list of all the commands related to proteins.

I’ve installed the YubNub opensearch plugin so I can search directly from the search box (or location bar) in Firefox. Maybe one day Ubiquity will fulfill this purpose, since in many way it is the natural progression of the YubNub idea. But for the moment YubNub is the fastest, most streamlined way I’ve found to quickly fire off a search when I need to hunt down a reference, protein sequence or 3D structure. Nothing like instant gratification 🙂

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