Acromine: a new tool is featured on Europe PMC labs

There is a new prototype tool available for browsing on Europe PMC labs: Acromine. Developed and hosted by the National Centre for Textmining, University of Manchester, Acromine suggests expansions of acronyms and presents articles specific to those expansions. The new tool is presented on an interface similar to the look and feel of Europe PMC.

For example, the expansions returned for the acronym ‘AD’ are given via the link: http://www.nactem.ac.uk/acromine/#page=1&query=AD

The list of terms was generated based on the occurrences of the acronyms and their expansions in full text articles on Europe PubMed Central. American and British alternative spelling variants are also factored when expansions are suggested.

We hope that this new tool will be of benefit, and we look forward to receiving your feedback.

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Wellcome Trust supports open access award programme

The Wellcome Trust has joined with the Public Library of Science and Google to launch the Accelerating Science Award Program (ASAP) to recognise the use of scientific research, published through open access, that has led to innovations in any field that benefit society.This new, innovative programme recognises individuals who have used, applied or remixed scientific research - published through open access - to innovate and make a difference in science, medicine, business, technology or society as a whole. Potential nominees include individuals, teams or groups of collaborators (such as scientists, researchers, educators, social services, technology leaders, entrepreneurs, policy makers, patient advocates, public health workers and students) who have used scientific research in transformative ways. 

It shows how the unrestricted exchange of information can advance science and medicine and benefit society. It also aspires to encourage a new generation of individuals to embrace the use of scientific research published through open access.

"The Wellcome Trust is proud to sponsor ASAP, and in doing so, recognise those who have maximised the impact of scientific research published through open access," said Robert Kiley, Head of Digital Services at the Wellcome Trust. "We are eager to see real case studies that showcase the unique value of open access, and through these stories, inspire greater support for open access."

Three top awards of $30 000 each will be presented. The nomination period is open from 1 May to 15 June 2013. Winners will be announced in Washington, DC, in October 2013, at an Open Access Week kick-off event hosted by SPARC and the World Bank. 

ASAP is sponsored by 24 global organisations that value the transformative impact of applying scientific research, published through open access, to extend the reach of science and medicine.

Find more about ASAP on the ASAP website or follow the conversation on Twitter with #SciASAP.

Yorkshire Cancer Research joins Europe PMC

On May 1st 2013 Yorkshire Cancer Research (YCR) became the newest member of the Europe PMC Funders’ Group, and we’re delighted to have them on board. YCR fund cancer research that is carried out by world-class scientists and clinicians across Yorkshire, and provide information to help local people beat cancer.

Closing the gap between the research they fund, and the people - whether in Yorkshire or Uruguay - who might need to read it, scientists and clinicians funded by YCR will now make their published research articles freely available from Europe PMC as soon as possible, and in any event within six months of publication.

For more information about joining Europe PMC, visit our website:  

http://europepmc.org/Joining or email Cecy Marden at c.marden[at]wellcome.ac.uk.

The Importance of Jargon

by Ian Le Guillou, Department of Biochemistry, University of Cambridge

Although contradictory to the hopes of the Access to Understanding competition, writing about the work described in 'NLK is a Novel Therapeutic Target for PTEN Deficient Tumour Cells' made me realise the importance of scientific jargon. Yes, it makes research very difficult to understand for anyone outside of that specialism, but it exists for a reason.

My article was 800 words long and yet I barely covered the contents of the paper's abstract, which also has the aim of summarising the work for an interested audience. The abstract was only 155 words: a five-fold compression through the use of jargon. This means that scientists in the field can take in the important points and decide whether to read further in less than 30 seconds – an important issue when there are thousands of research papers published every day.

Scientific jargon is so compact because the words have very precise meanings that do not need to be explained to those in the know. The PTEN paper was probably the closest fit to my own research of the papers in the competition, but still far enough that I had to look up several terms. However, this helped when writing about it because I knew which were the complicated sections. That meant I could make an extra effort when explaining it to other people. The familiarity is key: after using the same jargon every day among colleagues, it is far from easy to switch it off. It takes a concerted effort to avoid slipping into your usual vernacular and to explain each concept from its basics.

Scientists are increasingly being expected to interact with the public as part of their duty. Researchers are being given media training or being offered public engagement courses to help with this, but it is no easy task. There are few professions that are expected to balance the deeply specialised vocabulary of their peers with an expectation to be public facing.

I see the Access to Understanding competition as part of the movement to bring science into the 21^st century, where Web 2.0 has democratised information. The media are no longer the gatekeepers; everyone can publish and everyone can access. The public no longer rely as much on journalists to learn about the latest developments; instead they can go straight to the source. Social media and blogs allow scientists to explain the significance of what they do and directly connect with people who are interested in their research.

Although jargon is important and necessary for scientists to communicate among themselves, it creates a barrier to the outside world. We can't blame scientists for using jargon, but the public want to hear from them. It will take a lot of practice to explain in plain language but hopefully that way everyone will have a greater access to understanding.

Note: Ian was one of the winners (awarded joint second place) of the 2013 Access to Understanding science-writing competition for his entry 'Another brick in the wall', which describes research published in the article 'NLK is a novel therapeutic target for PTEN deficient tumour cells'.

See also guest posts by competition winners Emma Pewsey (first place) and Claire Sand (joint second place) for their reflections on Access to Understanding.

My reflections on the Access to Understanding competition

By Claire Sand, Institute of Pharmaceutical Science, King's College London

The Access to Understanding competition had instant appeal for me because it seemed to combine my two greatest interests – science and writing. I have always been fascinated with the human body (particularly in disease), and am currently working on my PhD in cardiovascular research, but having been an avid reader all my life, I have an equally strong interest in language and semantics. I’ve often thought of medical journalism as a potential future career option, but never had the opportunity to test my skills and gain feedback from readers outside of academic science. Placing in the top three has provided me with validation that this is a viable path to take, and I feel encouraged and inspired to pursue this type of writing further.

Coming from a family of non-scientists I have always been keen to share exciting discoveries (whether my own or others’) in terms that won’t be off-putting. In addition to the personal satisfaction that can be gained from sparking scientific interest in non-experts, I also believe that this type of public engagement is essential on a number of other levels. I have often found non-scientists to be refractory to hearing about research because they have preconceived notions that they won’t understand, or that they are being patronised. Science as a profession (and especially animal research) seems to be shrouded in mystery, and is generally viewed at best with disinterest, and at worst with suspicion.

When people ask me what I do for a living, my reply of “I work in medical science” is often met with “Oh right” and a rapid change of subject – people don’t seem to have a concept of what this job actually involves, and are usually not particularly keen to find out, or don’t know what questions to ask. At first this reaction surprised me: medical breakthroughs always elicit great public excitement (and praise of doctors), but I am becoming increasingly aware of an information ‘black hole’ in medical progress; many people are entirely unaware of the years of lab work that go into understanding a disease and developing new drugs to target it. This is, more than anything, the result of poor communication by scientists. In a time where money for research is more and more difficult to come by, we as scientists should be trying to get people excited about our research. Raising awareness of the origin of medicines, and engaging with both the public and policy makers is the only way to ensure the future of scientific funding. I am hopeful that down the line the efforts of public engagement schemes like Access to Understanding will demystify the process of medical research and will open more doors into the extraordinary and awe-inspiring world of science.

Note: Claire was one of the winners (awarded joint second place) of the 2013 Access to Understanding science-writing competition for her entry 'Blood vessels from skin: the new frontier in tissue engineering', which describes research published in the article 'Direct reprogramming of fibroblasts into endothelial cells capable of angiogenesis and reendothelialization in tissue-engineered vessels'.

Institutional and Subject-Specific Repositories: Responding to HEFCE’s Call for Advice on Open Access

Earlier this month HEFCE invited advice on developing their open access policy in the post-2014 Research Excellence Framework (REF).

Both EMBL-EBI, who run the Europe PubMed Central (Europe PMC) service, and the UK members of the Europe PMC Funders’ Group, strongly support HEFCE’s movement towards requiring that all outputs submitted to the post-2014 REF are published open access. However, both groups also have concerns about HEFCE’s exclusive focus on institutional repositories (IRs), and recommend that in addition to IRs HEFCE also include subject repositories, such as Europe PMC, as a valid archive for research submitted to the post-2014 REF.

You can read the full EMBL-EBI response here, and the full Europe PMC Funders’ Group response here.

Why I entered the Access to Understanding competition

By Emma Pewsey, Department of Materials Science, University of Cambridge.

I’m a relative newcomer to biosciences – at school, physics and chemistry were more my thing. However, starting a PhD on the corrosion of metal implants in the human body meant I needed to brush up on my biology. It was time to hit the medical journals.

It was easy enough to find papers. However, it was much harder to determine whether they were relevant. Abstracts seemed to compete with each other in squeezing the most technical terms into one sentence. I was lucky – I had plenty of time to go and learn what they meant. Most people don’t.

Once I’d broken through the jargon, I found many of the papers really interesting. I like interesting facts, and the majority of research papers are full of them. Therefore, it’s a shame that they’re so inaccessible to most people.

So I love the idea behind the Access to Understanding competition. I was surprised to learn at the awards ceremony how many non-scientists nowadays need to access research papers – from patient groups to teachers. My own participation in science outreach events has also shown me how much general interest there is in science. And making research more accessible should be a priority for all researchers – after all, who wouldn’t prefer their work to be read by thousands of people, rather than just a couple?

The competition also gave me an excuse to try some science writing – something I’d been meaning to do for ages.

Looking down the list of articles to choose from, I saw one I had to write about. Cortical thickness mapping to identify focal osteoporosis in patients with hip fracture? Yes please.

You see, I have a guilty not-so-secret. I love bones. They are the most fantastic objects in the universe. In particular, I love how they adapt to the forces which we place on them in our everyday lives to create a framework that supports our bodies that tries to be exactly as strong as it needs to be. But sometimes this goes wrong, and bones break. Thanks to the Access to Understanding competition, I got to read a fascinating piece of research that investigated why this happens in hips. If I hadn’t entered the competition, I wouldn’t have read it. I wouldn’t even have known it existed.

When I sent off my entry, I didn’t expect I’d hear anything back about it. I was just happy that I had a new set of interesting facts about hips to share with anyone looking for an interesting fact. I am delighted that winning has brought attention on the work done by Dr Poole’s group at Cambridge, and the range of work funded by Arthritis Research UK. And of course, I’m thrilled with the trophy that now sits in my living room!

My next writing challenge is completely different: a 60,000 word PhD thesis. I’ll make sure to include a lay summary!

 

Note: Emma recently won the 2013 Access to Understanding science-writing competition for her entry 'Hip, hip, hooray!' explaining research that investigated the causes of hip fracture in the elderly.