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Open Access literature databases!

There, that’s grabbed your attention, hasn’t it? No? Strangely, talking to most researchers about publication databases and repositories has them either nodding off or suddenly remembering an urgent meeting. In this guest post, Mohammed Tasab, Engagement Officer at UK PubMed Central explains why PIs should care about UK PubMed Central, the UK’s database of open access articles.

It can be quite easy to forget how daily access to online articles, reviews and other sources of information is part of the typical scientist’s daily routine. It’s as natural as brushing your teeth. Frankly, you’re more concerned about how much longer it will take your post-doc to finish the final damned experiment for this latest paper. You already have a journal in mind, and have written the outline and the introduction. So why should you, as principle investigator, care about yet another information repository? But think back to the days when you had to spend hours in the library hunting for relevant papers, and it’s not hard to see how things have improved in the last decade. Today you have access to hundreds of thousands of published peer-reviewed articles on your desk. You still have piles of paperwork, but no longer have to hunt through acres of photocopied articles each time you need a paper. Obviously, the more content you can access in one place the better. This simple idea was the driving force towards the creation of NCBI PubMed and now UK PubMed Central (UKPMC).

UKPMC is designed as a sophisticated online resource with new functionality, additional content and other tools, as demanded by PIs who advised the project. Eight of the UK’s leading research funding bodies, working with the British Library, The University of Manchester and the European Bioinformatics Institute, put a considerable amount of time and money into developing and maintaining this free new repository. The aim was to promote access to the widest possible amount of scientific and medical literature, in the shortest time possible.

Currently, UKPMC provides access to a huge number of published articles, clinical guidelines, UK bioscience theses and research reports. A single UKPMC search queries PubMed, Agricola, Patents, Chinese Biological Abstracts and Citeseer abstracts, in addition to almost two million full text articles. This is certain to expand in size. On top of this, advanced textmining features allow the user to find “bioentities” (species, genes, proteins, chemicals, etc) from which you can link out to related information in other databases. More is to come in the way of evidence extraction, which can search full text for semantic concepts, for example “ligand binding proteins”.

Beyond the literature mining capabilities, special tools within the Grant Reporting System (UKPMC+) allow PIs to link their grants to published articles, submit manuscripts to the repository, report grant outcomes and view their citation counts. These features will make it much easier to measure and report research output. It’s an important step towards building a seamless portal linking academics to the world of professional scientific publishing and to research funders.

The value of a more integrated system is not lost on leading academics. Professor Dame Nancy Rothwell believes that new online resources, such as UKPMC, must adapt to suit researcher requirements. This also means that it is extremely important for researchers to be involved in the development of resources.

UKPMC is very much a user-led resource that is still in development, so criticisms and suggestions for change or additional tools are essential. Such resources cannot be improved without constant feedback. Please contact ukpmc@bl.uk or use the feedback button provided to give your opinion.

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Mohammed Tasab is currently the Engagement Officer for UK PubMed Central working in the Faculty of Life Sciences at the University of Manchester. He holds a doctorate in molecular cell biochemistry, an MSc degree in Industrial Biotechnology and a BSc in Genetics. An experienced researcher, he has worked over fifteen years in several areas of biochemical research including procollagen biosynthesis, disulphide bonding in proteins and angiogenesis. Outside of academia he has also spent time working for in the medical communications industry and as a science teacher. He enjoys dabbling in small business, blogging, and various social networking tools.