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.
  

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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.

Google Desktop for Linux Released

Google Desktop for Linux has been officially released. It's a real-honest-to-god native linux application, and doesn't use Wine like the Linux version of Picasa.

I've just installed it on Ubuntu Feisty Fawn from the Google Linux software repositories, and while it's currently only indexed about 1 % of my files, my initial tests suggest it is pretty slick ... a quick Ctrl-Ctrl, and up pops the search box. Apart from all the things I'd expect, like indexing the content of pdf files, directories like "/usr/man" are included on the default path list, so I presume it also looks inside man pages. One problem I've noticed so far in my very quick testing is that it seems to not follow symlinks to directories and won't let me add them as paths to index. The effect is that my "/home/perry/documents", which is actually a symlink to a larger partition, does not get indexed unless I add it to the path list with it's real path.

While there are already similar offerings for Gnome (eg Beagle) and KDE (eg Kat), my gut feeling is that Google Desktop will be my preferred option for the moment. Maybe one day we will get lucky, and Google will even make it FOSS (not holding my breath though).

SDF Public Access Unix celebrates 20 years

The Super Dimensional Fortress Public Access Unix has now been in operation for 20 years ! SDF is a non-commercial member supported BBS, which offers free accounts with Unix shell access, and a friendly and vibrant community.

I've been a 'lifetime' APRA member for a few years now, and have been using SDF for some lightweight web hosting (CGI in various flavours is supported). It's really handy to have a reliable shell account somewhere out in the aether to check network connectivity from, and my interactions with the community have always been fun. The photos in this post show one of my aging PCs, proudly displaying an SDF sticker.

To get a free account and check it out for yourself, telnet to sdf.lonestar.org and login as new.

Happy Birthday SDF !!


(yeh, I know I labeled this 'linux', and SDF actually runs on NetBSD. Different OS, similar audience).

Cleaning up the cesspool that is the PDB

Well .. maybe cesspool is a little strong ... there's a lot of great data in the Protein Data Bank, it's just that in the early days it was allowed to grow very large without enforcing better standardization of the data. Things that are being fixed include updating citations for structures from "To be published" to the actual publication if it exists (with PubMed ID), linking to sequence databases (ie UniProt), bringing atom names to standard IUPAC nomenclature (Hooray!!) and loads of other things I haven't mentioned. Don't fret ... none of the raw experimental data or coordinates are going to be changed :)

From the PDB remediation overview document (pdf):

When the RCSB PDB first addressed the remediation issues in 1998, it was with the intention of providing a uniform and consistent content across all formats. It was surprising and very disappointing to find that many PDB users at the time strongly objected to any changes in the released PDB entries, even if these changes addressed serious but correctable errors (e.g., consistency between chemical and coordinate sequence). As a result of this prevailing attitude toward changes in PDB format entries, the RCSB PDB released its corrections in a new set of mmCIF format data files and left the data in PDB file format unchanged. Since that initial release of mmCIF data, new data items and uniformity corrections have been added to the released mmCIF data files.

I've used coordinates from PDB format files for a lot of things over the years, but I've got to admit, I've never used an mmCIF file. The PDB file format is almost always supported by all legacy (and recent) structural biology analysis software, while using mmCIF is rarely an option (unless it's converted to PDB format first). If I'd known the mmCIF versions in the database have been 'remediated' I may have been more inclined to use them (or the somewhat equivalent XML/PDBML files) for some tasks, since the non-uniformity in atom naming in legacy PDB files can become a royal pain in the butt ....

Anyhow, everyone has until July 2007 to check out the new remediated files before the 'mainline' PDB changes over and provides these by default. All new structure releases will follow the remediated format after July. The old versions will still remain available ... but who would want them ... we are getting standardized goodness !!