For twenty years we have had some sort of desktop access to the scientific literature. At first we only had abstracts of articles, and accessed them through fairly clunky interfaces (anyone remember BIDS?). The introduction of PubMed in 1997 improved the interface, but still had only abstracts. These days, in most research institutes and universities, the full-text of a huge proportion of the world’s scientific research is available through a simple web interface.
That availability has changed the way we use the literature. Long gone is the idea of the one-off “literature search”, an attempt to provide a comprehensive list of papers on a specific topic. Searching is no longer something you have to sit down and plan. More often we just use a quick search on PubMed or Google to answer a question, such as “what genes affect xxx process”, and may do this many times in a day.
But PubMed and similar systems are not very good at answering questions; they were designed as ways to find articles. In fact the whole scholarly publication system is not set up in a way that facilitates answering questions. Journal articles are blocks of text – descriptions of methods, results and discussion – with images and figures interlaced. They are not machine-readable databases of facts. Scientific literature is not part of the semantic web.
Text-mining and semantic technology sets out to remedy, or perhaps side-step, this. Software like Textpresso has been going a few years and has powered a query system for a limited range of subject domains (including Drosophila). Now UKPMC has launched a new feature – Evidence Finder – that helps you to ask questions across the whole of PubMedCentral – that’s over 400k articles, or 10,004,566 sentences about genes, proteins, diseases & metabolites. This new tool has been developed by UKPMC Labs
UKPMC Labs is a new component of the UKPMC website, which will showcase novel applications based on UKPMC content.
Evidence Finder is not as slick as Textpresso. The results you get come as a list of articles, not an answer to your question.
The exact question you ask can affect your results – “affects”, “controls” and “regulates” all give different results. I still have the feeling that I am searching, not mining. On the plus side, on the page of results there is a box with some alternative questions that you might have wanted to ask.
Added 17 Feb 2012
Thanks to UKPMC for pointing out I had misunderstood how Evidence Finder is intended to work. First you should search for the disease, gene, protein or other entity that you are interested in. Then choose a question from the list on the right, to further refine your search.
The title “Evidence Finder” suggests to me that the tool is aimed at clinical questions and evidence-based medicine, a bit like PubMed’s Clinical Queries. I like the simplicity of the interface, and I appreciate there is a balance between creating a powerful interface with bells and whistles and keeping it simple to use. It is also much harder to tailor an interface that has to cope with a very wide range of topics.
But it is early days and Evidence Finder look promising. Try it out and give them feedback.
Oh, and try to make sure that all your research goes into UKPMC so that it can be part of the evidence base!