Searching biological databases from the Firefox search bar

There is currently no "Google for Bioinformatics", and so biologists/bioinformaticians typically need to search a number of separate databases to find the data the desire. While the Biobar Firefox extension helps search for a dizzying array of biological databases (individually), I think sometimes it offers too much, and contains too many databases that I rarely if ever use. As useful as it is, most of the time I keep the Biobar toolbar hidden to reclaim the screen real-estate.

Instead, I prefer the more lightweight "search plugins" to fully fledged extentions (accessed via the little search box up near the URL location bar). Here are some Firefox search plugins for common 'bioinformatic' search engines which I found scattered across the far reaches of the web:

• HubMed is a clean and slick interface to search the PubMed database, with some features that the NCBI search doesn't have. You may already be familiar with it, but sadly the majority of life scientists appear not to know about it / use it. I prefer HubMed to the regular NCBI Entrez interface. You can install the HubMed Firefox search plugin at HubMed.
• In case you want the plain vanilla NCBI PubMed interface, the UCSF library provides a PubMed search plugin.
  
• The Mycroft project by Mozilla seems to be an official repository of firefox search plugins. On Mycroft, I found plugins for searching SwissProt, the Protein Data Bank (PDB).

I also wanted some that couldn't find, so I made them. Here are Firefox search plugins for Uniprot and Pfam:

Here is the code for the Pfam one, as an example:

<?xml version="1.0" encoding="UTF-8"?>
<OpenSearchDescription xmlns="http://a9.com/-/spec/opensearch/1.1/"
                      xmlns:moz="http://www.mozilla.org/2006/browser/search/">
 <shortname>Pfam</shortname>
 <description>Search the Pfam database</description>
 <image width="16" height="16">data:image/x-icon;base64,AAABAAEAICAAAAAAAACoCAAAFgAAACgAAAAgAAAAQAAAAAEACAAAAAAAgAQAAAAAAAAAAAAAAAAAAAAAAAAAAAAA%2F%2F%2F%2FAMWLMwDew54AjEcBAO22WwD658kAoWclAMSdbADYn0gA1LKBALiLVADt1rMA%2FffkAKp0PACcXQ0AtnomAMiXVwDxvmsA0ZY4ALuJQwDjqk8AzqZ3AKVoFQD27dkA2LuRAJJRFACVVAEA5s6lALyVYgCbXR0Aq3ElAPPhvwClbDIAzqBkAL2BLgDFkEAAtYJKAPS9YACQTwkA%2Fu3QALJxHgDZnD8A5bJfAMWTTwD%2B89cAnmIUAOiwVQDXtYkAl1gXAN6%2FlgDsuWYAxJpeAN6kTADoz60AwYg6AL6RWwDQrH0Ay6NwAMmPOQCNTgEAllcMAKVtIwDNlD4A9uPGAPfAZgCocjEAxp1mAJhYBQDZv5sAi0oLAKxvHgDUmkIAt4hIAJpeFACoaxoAn2EOAKBlGQDwuF4Aun8qALJ2JQCocDgA3KFEAJRSCAD%2B9twAjksFAJVWEQDt2rcAkFEOAMKVXQD57M4AklACAKBfGACkaigA%2BvDWAPXnyQDr068A7bNWALeHTQD24sEAu5NdAJlZCgDgxqEA6rZjALyOWADcvZIAzZE4ANi5jQDEmGIAj0oAAJVWBgDl0KoA67NaAMCELwDChzQA8%2BLDAJhZEgClbS4AqnM1AOSpSwDy3L4Ai0cFAJxfEQCiYxQAnWAbAJteIQChZikAx402ANyhSAD669EA8Ni2AJBNAgCXVwIAzqt6AOjTsACSUwUAl10WAKhpGADutl0A5a9UAMugbgCSUAwA1rB%2FAOCmSgD86s4A9ujGAI1MAgCbYBUApmoZAK9yHwCjai8AqHAmANWzhADFnm8Ajk8EAI9LCADlzasAk1MBAKBeDgCfZBYAm2AeAKpzOQDQlD0At4ROALuQXQD879QA%2BujLAJFPAACVVgMAmFcFAJRTFQCVVhgAmFsYAKVmFwDZtocA9L1jAPK7YQDLkDsAvJNdAMeVUAD77c8AkFEFAOGqUQDhqE8A3J9CAM2TOgD57NAA9OTHAPThwACPUAIAjk0HAOXNpwCWWAQA27uTAJ9jGACkZhUApmkbAKNsJADwul8A77dbAO60WQDRq38A67RYAOmxVwDPqXkA36ZNANmeRgC%2BlmEA%2FOvQAPvqzAD86MkA7di2AI1KAQCPTAEAjUoFAI9OAACOTQMA6NCrAJJOAgCRUQEAk1QDAJZVAwCTVQYAklENAJRWCACYWAcAmFcKAJtdDwCYWRkAnmMWANW0iQDyvWIA07ODAOu2XADnsFcAuHsmALh%2BKQDcpEsAtIJIALuTXACOSwMAkE0HAI9NCQCSUQUAkE8MAJhZAwCcXw8Anl8RAPK7XwDtuFwA7bVWAP745QD66s4A%2BebJAJBPAwCQUQMAPuWfn5%2Bfn5MfJIjln%2BWfLkIZgdGmwX0un5%2Bf5eWf9s%2FlwETAwMCp3EznUNjdRET1nY2jDLTROINERETARERE75%2FARMDARETdbgUmfz29wMCphNRWyV5v1sCERERERERkn8BEwMBERIT%2Bf7DGt5XznanARNvymdPx3cBERERERO%2BfwETAwMD1RBvgsbDHTj96kqjARKiNWd6oqUREREREZJ%2FARMDARERERNyHT3DHinBP4p2onaBJg4RERERERESyn8BEwMBERERERN08xM1O%2BcY1S5LkA5x5hERERERERLKfwETAwERERERERMCd8yMvxunGajQY6FWEREREREREsp%2FARMDAREREREREwMCoW%2FcTYQXHUhF1G4TARERERESyn8BEwMBERERERPVEwIQ8RguzKshOjw%2Fc9cBERERERO%2BfwETAwEREREREqYSd8UIy0LuOO8jnudj1REREREREsp%2FARMDAwMBERMCE1B7Mpga0kQhYieqLW4TARERERETvn8BEwMDAwMCEGydiV1rSWml1VRvblO2HqMBEREREwGSfwETAwEREqRsnjIHSkIJovoOEwIT%2FiYTAREREREREZJ%2FARMDAwETA2EO0kHMWdIOEhMCEW60C%2FoRERERERERkn8BEwMDARBtWYy1gDlUbhKlEhDzjtou9wERERERERLKfwETAwMBEW10NhZvahEREwJ1T7PmvooOERERERERE75%2FARMDARPWdSjlWnYTAwN3%2Fw87H%2BcutG%2FVERERERMDvn8BEwMDAwN1NfKeERIT%2B4jv5ik7LR9vARPVEREREwO%2BfwETAwETAW0JFqp2dtVAVTgXGCXvbwEREREREREREsp%2FARMDAwIRbB%2Ftrq2VI%2BIpOLxCH%2F4SERERERERERESyn8BEwMBEwBs9vKWGLLj6BQIPvahERESpREREREREwO%2BfwETAwEREhJKkugZACnJcg6jAwEREREREREREREREZJ%2FARMDAwETAWykiQP3ReEMa2oREqURERERERERERESyn8BEwMBE9dxuyncUYNAGKGZ28Bup9URE9URERERERO%2BfwETAwMD1G55BcdXfbCDQBrTM5NX1RKlEREREREREZJ%2FARMDARESo4euHGxvYljC6Bvy%2FIYOERERERERERMBkn0T1wMBERBsXR731RIRbBCXZgZBf7tepRMDAwMDAwLKfwET1RMDAncPplL2oRPXd2jE6IChzoZ3AwMDAwMDA759EwMBEREQbTEHLUJqdwITAnW1RHFSY1oTARERERERk5UTAwMDAhN29gPjGSHv%2F3UTAhL305jbWwITAwMBERGTFn%2BXln5%2Bf5UqXKzMSZzfC5eXCn0p%2Brqzl5Z%2Bfn5%2F2HQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 </image>
 <url type="text/html" method="GET" template="http://www.sanger.ac.uk/cgi-bin/Pfam/qquerypfam.pl?">
   <param name="terms" value="{searchTerms}">
 </url>
</opensearchdescription>

To add this to your list of search engines, you also need to put the appropriate "link" tag in the head of an html page that you want the search plugin to be detected from, like this:

<link rel="search" href="opensearch_uniprot.xml"
   type="application/opensearchdescription+xml"
   title="Uniprot" />
<link rel="search" href="opensearch_pfam.xml"
   type="application/opensearchdescription+xml"
   title="Pfam" />

OpenSearch plugins are also partially supported by some versions of Internet Explorer, but I haven't tested it (there is no POST support for OpenSearch plugins in IE 7). [insert obligatory Firefox fanboy stab at IE here].

Chances are, you'd like to make one to search your favorite database. Here is the documentation I used for creating OpenSearch plugins for Firefox:

• "Creating OpenSearch plugins for Firefox" at the Mozilla Developer Centre, and some blog posts here and here.
• "The data: URI kitchen" is a useful web-based tool for encoding images a base64 (you need this to embed icons using the Image tag).
• There is also this "add to search bar" extension, which I didn't use in the end.
  

---

Edit: Argghh .. looks like this code is showing up fine on the web page, but is a bit broken when displayed from the RSS feed in akregator .. I assume other feed readers may also be having trouble .. Anyone know a reliable way to post code in Blogger ? Wordpress is starting to look attractive ...

A simple but useful application for Google Co-op On-the-fly Custom Search

My del.icio.us linkstream is a bit like a window into my stream of consciousness.

I've always wanted to be able to 'search outward' from just my delicious links ... a recent post from Alf about Google Co-op 'on-the-fly' search engines just triggered a simple but really useful idea; make a Google Co-op search of my delicious linkstream ... this way I can search just within pages I've deemed worthy of bookmarking.

After a bit of wrangling with the various ways of getting data out of delicious (see my own comments to this post), I found this script for generating an html page of links from delicious. This page contains all my delicious links, not just the most recent ones (it seems you can only get a subset of the most recent links without authenticating with delicious, hence the PHP script using the delicious API).

So, after hosting the PHP script revealing all my links, I can point the Google Co-op Custom Search Engine to that page, and search away ! It's a nice way of using search to 'retrace' my steps, since it should generally restrict results to the parts of the web I've already seen and rated as worthy of re-examination.