Freelancing science » PubMed

Semi-automated workflows – Taverna Interaction Service

Pawel Szczesny — Wed, 12 Mar 2008 15:56:15 +0000

I was still thinking about recent Neil’s wondering about possibility of automating every scientific workflow, when I saw this (Bioinformatics Advance Access abstract):

The Taverna Interaction Service: enabling manual interaction in workflows by Anders Lanzén and Tom Oinn

Taverna is an application that eases the integration of tools and databases for life science research by the construction of workflows. The Taverna Interaction Service extends the functionality of Taverna by defining human interaction within a workflow and acting as a mediation layer between the automated workflow engine and one or more users.

I have not tried it yet but this Taverna plugin is very likely an answer to doubts I often have when automation of bioinformatics workflows is discussed: we shouldn’t always remove ourselves from the workflow, as interaction with software can be often critical in making a discovery. For example conscious decision about which sequences should go in during PSI-BLAST search can dramatically influence quality of resulting profile. So I agree with Neil that not every workflow can be automated, but more importantly not every workflow should be. Possibility of wrapping one’s mind around a problem is gone when there’s no feedback loop on the process.

Mining PubMed – another tools available

Pawel Szczesny — Wed, 05 Mar 2008 15:37:20 +0000

There are two new tools available that mine semantically PubMed abstracts, e-LiSe and Anne O’Tate. First one was made by my colleagues from Institute of Biochemistry and Biophysics in Warsaw, while the second is from University of Illinois, Chicago. Female-sounding names is not the only thing that makes them look similar, they both provide analogous functionality, like keywords or author names associated with user query.

There’s quite a lot of third party interfaces to PubMed (see David Rothman’s excellent list), so I couldn’t resist to run few queries on both servers and compare them to GoPubmed, which currently wins hands down in terms of features and interface. I wasn’t surprised to see that results overlap significantly, although not completely. Each of servers found valuable keywords other two did not have – that’s understandable, they use different algorithms. I wonder if we will see a meta-server of PubMed data-miners, like there are for protein structure prediction (for example meta.bioinfo.pl). In theory, exhaustive search for meaningful keywords by different methods and then their classification and analysis should work better than any single method, but this is just a guess.

Publishers, please provide images in the journal’s feed

Pawel Szczesny — Tue, 23 Oct 2007 19:45:25 +0000

Currently almost all scientific journals provide a RSS feed of their content. I am very grateful for that, as many other scientists. However, I see a large disproportion between what I would like to scan through and what I’m actually able to. Abstracts, which are usually provided in these feeds, look almost exactly the same, and after thirty or fifty I’m not really sure if I understand what I read (most likely even Robert Scoble would have the same problem, although at a different level). Biochemistry journal found a solution (see below) – providing images instead of abstracts in the feed (in fact, they used this approach on their homepage long before RSS feeds became a standard). It’s simple, very effective and I have no idea at all why it’s not more popular. So here I’m asking – publishers of scientific journals: please give me images in the journal’s feed. I don’t mind having also the abstracts, but visual summary would be much more useful. In return I promise read these feeds instead of relying on Pubmed searches or my colleagues recommendations and GR shared items.

Healia and third party PubMed/Medline tools

Pawel Szczesny — Mon, 01 Oct 2007 18:58:10 +0000

David Rothman describes Healia, easy to use interface to the PubMed. But it’s just one of many third party PubMed/Medline tools David had described. Check out his posts related to the one about Healia.

clipped from davidrothman.net

Healia’s PubMed search (currently in beta) might be one of the best interfaces available for clinicians who don’t have the search skills to effectively search PubMed through its native interface.

Some notable features:

Automatic “AND”
By default, Healia inserts a boolean “AND” between all search terms (as Google does). While the expert searcher might find this unpleasantly limiting, it is a familiar behavior for many clinical searchers who view Google as their ideal, preferred search interface.