Friday, 12 May 2017

Preprints and the ASAPBio "Central" Services

Jo McEntyre, EMBL-EBI; Thomas Lemberger, EMBO; Mark Patterson, eLife; Kristen Rattan, Collaborative Knowledge Foundation; Alfonso Valencia, Barcelona Supercomputer Centre. The use of preprints in the life sciences offers tantalising opportunities to change the way research results are communicated and reused, and the work of ASAPbio has been key in engaging the scientific community to promote their uptake. We fully support these goals, and consequently submitted a response to the recent ASAPbio Request for Applications (RFA). In light of ASAPbio’s understandable recent decision to suspend the RFA process for four months, we are making our proposal public here, to encourage and contribute to ongoing, open discussions on these matters.
Our consortium is led by the European Bioinformatics Institute (EMBL-EBI), with collaborators in the Collaborative Knowledge Foundation, the Barcelona Supercomputer Centre, eLife and EMBO. We appreciate that not everyone interested in preprints will have time to read the full proposal, so we summarise some of the main points here.
We put in a response to the RFA because we share the excitement and enthusiasm that has emerged recently around the use of preprints in the biological sciences. The reason for our excitement is simple - alongside the rapid communication of research, we see massive potential for innovation based on preprint content. We envision that the best route to enable these goals is through a reasonable number of preprint servers and services, coordinated through the operation of agreed community standards. The standards will allow content to be federated and/or aggregated across servers, depending on the use cases. This model allows a diversity of approaches to addressing the opportunities and challenges that preprints bring.
Between us, we are developing infrastructure and services for publishing processes, article enrichment, text and data mining tools, bioinformatics, and mechanisms for data integration and discovery. But more important than our singular contributions, we are also embedded in broader researcher and developer communities that are as enthusiastic as we are about the opportunities for innovation that preprints offer. Alongside the core elements in the ASAPbio RFA, the fundamental theme of our proposal is therefore to enable those communities to engage with preprint content and contribute to moving scientific communication "beyond the PDF".
Our proposal is to combine existing and emerging open-source software and open data infrastructure to facilitate the ingestion of preprints from any source into a community archive and then share the content in different ways. This satisfies not only the scientific imperative of rapidly discoverable research results, but also creates a platform for innovation that has the promise to make information discovery faster and more effective in the future.
In short, the central services we envisage will enable any interested party to develop "plug-in" applications that can be used - optionally and in any order - in any part of the system. Some applications might work on individual documents prior to release (for example in quality control); others might work on the collection as a whole, post release; some might be fundamental "mission-critical" steps (like document conversions); and some might be more experimental. We propose to engage the developer and text- and data-mining communities through open challenges to invent new applications based on preprints. No-one knows where the next "killer app" will come from, so we want to foster broad participation and expose these developments to the wider scientific community.
The top priority is to support the uptake of preprints by the scientific community and ensure their citability and discoverability. But in order to realise transformative developments in the future, there are necessities beyond this.
Most critical among these is the ability to reuse preprints. By this, we mean not only that the content has a license that supports reuse (the CC-BY license), but also that the content is readily available as a whole, so that would-be application developers and text-miners do not have to struggle to gather content together. Most peer-reviewed literature is still subject to access and reuse restrictions and is highly distributed – with preprints we have a unique opportunity to support unrestricted and comprehensive reuse from the outset.
Secondly, quality metadata and the consistent application of standards are essential. We care about open standards like JATS for structuring the XML of full text articles, and are open to discussion about how this may evolve to support preprints in the future. Author names with ORCIDs, machine readable data citation, correctly identified institutions and funding sources are all critical for a connected research management ecosystem. Given these building blocks, others could develop tools that reduce the repetitive reporting burden on researchers, or services and indicators to give a wider stakeholder group a better understanding of the influence and impact of research. Finally, a governance structure that represents the interests of the community is a necessity, as services around preprints need to remain current and address evolving user needs over time. This approach to preprints infrastructure lends itself to reuse within different disciplinary contexts, providing a basis for cross-disciplinary standards of core elements, yet allowing adaptation by those communities according to their specific scientific requirements. Central services are a crucial part of biology today. It is hard to imagine how biology could progress without resources such as the wwPDB, or the International Nucleotide Sequence Database Collaboration. We are excited about preprints because they offer a tremendous opportunity to move science forward in parallel with these data resources, enabling integration of research outputs and knowledge discovery. We welcome comments and discussion as we move towards these shared goals, supporting science into the future.

Friday, 28 April 2017

Keeping track of published literature

Modern scientists are busier than ever. Their typical days are filled not only with experimental work, but also with teaching, supervising, mentoring, grant applications, budget planning… The list goes on and on. No wonder there is barely any time left to stay on top of the field. Keeping track of published literature is made easier by following these simple tips:

Newest first

Don’t get lost in the long list of publications. To find the most recent articles on Europe PMC, sort results by date. If you want to limit your search to a specific date range – last week or last month – set this in the advanced search.

Focus on what’s important

Citations are the currency of the academic world. Familiarise yourself with the most cited papers in your area by using “Times cited” as a sorting order. For your convenience, citation counts are displayed for each publication in the search results on Europe PMC.

Follow your colleagues

Are you already familiar with the experts in your field? Check for publications from a specific author by typing their last name into the search bar. For scientists with common last names, such as Smith or Wu, paste their unique ORCID ID into the search bar to match the author exactly.

Automate repetitive tasks

Don’t waste your time on a job that your computer can do for you. Doing the same search every now and then? Instead of typing a long query into the search bar every time, save your search and recall it with one click. In Europe PMC all of your saved searches appear in your account. Create an account or log in with ORCID or Twitter.

Stay alert

With a busy schedule, it is easy to miss an exciting discovery.  Any search, including those by keywords, author, or scientific journal, can be turned into an RSS feed on Europe PMC. This way, once an article on your topic is added to the database, you will be notified immediately.

Tuesday, 28 February 2017

Sort it out: Sorting your search results with Europe PMC


Imagine you are exploring a new topic. You start by searching for relevant papers in the field. You type your query, click the search button, and end up with thousands of scientific articles, waiting to be read. How do you identify which papers to focus on?


In Europe PMC, search results can be sorted differently to help you navigate through the literature. By default, results are sorted by relevance. But how is relevance defined? Let’s look at a search example: say we are interested in oxidative DNA damage. Once you type that string into a search box, the sorting algorithm ranks all your results and displays them in order. The algorithm takes into account how often search terms are found in the text. A document that mentions "DNA" ten times is likely to be more relevant to you than one with a single mention. The relevance score also depends on how many of the search terms a document contains. For instance, papers discussing "oxidative damage" or "DNA damage" are less appropriate than the ones specifically covering "oxidative DNA damage".
Rare terms will be more relevant than common ones. Note that we expand your search by including synonyms, so whenever you search for DNA damage, you will also discover articles mentioning genotoxic stress. You can switch off synonym expansion in the advanced search, or simply place your search terms in double quotes for an exact match, e.g. "oxidative DNA damage".



Scientific abstracts are ranked higher than articles, and papers are considered more relevant than books and other documents. Nonetheless, you can always change the type of content you are looking for via the "Popular content sets" on the right-hand side of the search results, or in the advanced search.



Using our relevance sorting, more recent publications will appear higher in the list, but if you want the latest papers over anything else, you can simply sort by date. For instance, if you are eager to see the latest manuscript from your collaborators, or the new publications from your favourite journal, just look at the most recent papers. What if, instead, you are interested in classic articles that have pioneered the field and laid the foundation for future research? Good news: you don't need to scroll to the last page of results. Simply search by date, in reverse order. Now you can see how a scientific field has progressed.



Another way to search for foundational articles is by sorting results by times cited. Citation counts can help you find experts in the field, or help you identify the most impactful works. When ordering results by times cited, the number of citations is displayed for each paper.



With Europe PMC you can find research that matters with the click of a button. Sorting has never been easier!