Tuesday, 14 November 2017

Harness the power of text-mining for biomedical discovery: introducing Europe PMC Annotations API

We are excited to announce the launch of Europe PMC Annotations API, which provides programmatic access to annotations text-mined from biomedical abstracts and open access full text articles. The Annotations API is a part of Europe PMC’s programmatic tools suit and is freely available on the Europe PMC website: https://europepmc.org/AnnotationsApi.

The exponential growth in scientific data and scholarly content cannot be addressed by conventional means of information discovery. Text-mining offers a practical solution to scale information extraction and advance biomedical research. However its application is still limited, partially due to the technical know-how needed to set up a text-mining pipeline. Nonetheless, even non-specialists can capitalize on the text-mining outcomes. Making the text-mining outputs openly available can enable a broad audience of researchers and developers to address current challenges in biomedical literature analysis. For that reason, Europe PMC has established a
community annotation platform. It consolidates text-mined annotations from various providers and makes them available both via the Europe PMC website as text highlights using the SciLite application, and now programmatically, with the Europe PMC Annotations API.

What types of annotations are available via the API?

The text-mining platform hosts a variety of annotation types, including the following:
  • Named entities: gene/protein names, organisms, diseases, Gene Ontology terms, chemicals and accession numbers.
  • Biological events: protein phosphorylation
  • Relationships: gene-disease associations
  • Text phrases: GeneRIF (Gene Reference into Function), as well as protein-protein interactions.

The number and diversity of annotation types available to users grows as the new providers join the scheme. Currently annotations are contributed by a number of providers, including Europe PMC’s own text-mining pipeline for named entities, the Swiss Institute of Bioinformatics for gene function annotations, DisGeNET and the Open Targets Platform for gene-disease relations, IntAct for manually curated protein-protein interactions, and NaCTEM for phosphorylation events.

What can you do using the Annotations API?

The Annotations API offers diverse functionality for various user workflows. It is possible to retrieve all mentions of chemical entities found in results section, or recall all articles that discuss involvement of FFA2 protein in diabetes. Users can combine a number of parameters (such as annotation type, annotation provider, or even article section) to specify their query. The filter parameter allows the user to switch between two options: retrieving only specified annotations for each article, or retrieving all the annotations limited to the list of articles that contain the specified annotation. Output formats include XML, ID_LIST, JSON and JSON-LD, which produces a linked data representation of the annotations for annotations exchange across different platforms, making it easier to consume the data.

The following modules are available for the Annotations API:
  • get /annotationsByArticleIds: Get the annotations contained in the list of articles specified by the user. The user can specify article iDs, annotation type, annotation provider, or article section.
  • get /annotationsByEntity: Get the annotations of the articles which have at least one annotation tagging the specified entity (e.g. BRCA1, metformin, or cancer).
  • get /annotationsByProvider: Get the annotations of the articles which have at least one annotation provided by the specified provider (e.g. Open Targets).
  • get /annotationsByRelationship: Get the annotations of the articles which have at least one annotation tagging two specified entities relating to each other (i.e. NRGN-schizophrenia for gene-disease relationship).
  • get /annotationsBySectionAndOrType: Get the annotations of the articles which have at least one annotation of a type inside an article section (e.g. all organisms annotations in “Materials and Methods” section). The user can also choose to specify only the annotation type or only the article section.

Advancing science with text-mining

Systematic analysis of research literature offers immense potential for advancing scientific knowledge. However, extracting facts and evidence is a difficult, time-consuming and laborious task. That’s where text-mining comes into play, helping to advance the discovery process. Our goal in developing the Annotations API was to make text-mining outputs available to a wider community of biomedical scientists, and we hope that with this new tool anyone will be able to harness the power of text-mining for the benefit of their own research.

Thursday, 31 August 2017

Wellcome Trust/DBT India Alliance joins Europe PMC

We're delighted to announce that the Wellcome Trust/DBT India Alliance joins Europe PMC as a new funder. This brings the Europe PMC funder family to 28 members.

Wellcome Trust/DBT India Alliance logo

The Wellcome Trust/DBT India Alliance is an equal partnership initiative between the Wellcome Trust (UK) and the Department of Biotechnology (Government of India). The broad aim of the India Alliance is to build excellence in the Indian biomedical scientific community by supporting future leaders in the field.

Researchers funded by the Wellcome Trust/DBT India Alliance will join thousands of others who 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:

Wednesday, 19 July 2017

Blow your own trumpet: build an academic CV with ease

Whether applying for a postdoc, a grant, or a tenure position, you will need to compile a publication list every now and then. There can be many ways to do so, from maintaining an Excel sheet, to building your profile on a faculty page. One option, however, requires minimum effort from your side and keeps a stable record of all your achievements. It is our all-time favourite – an ORCID iD. Getting one is easy: you register with the ORCID foundation at www.orcid.org.
How does it help you to maintain a publication list? Very simple - we have already taken care of that. We automatically generate Author Profiles for biomedical researchers based on their ORCID record. You can find yours under the following link: europepmc.org/authors/[your ORCID iD]. We list all your publications in Europe PMC that you have claimed and made public in your ORCID profile, conveniently linking to abstracts and free full text. There are links to your ORCID and ImpactStory pages to help keep all related information in one place.
We know that showing impact is important, so you can see citation counts for every paper and even sort papers in your profile by “times cited” to see which of your works made the biggest impact. All citations come from open sources and no subscription is required. The other option is to sort your publication list by date, to display the most recent publications first.
Do you fancy something more visual than a dry list? Download a publication graph from your Author Profile. It shows your academic output year by year as well as your yearly citation rate. An extra touch for open science champions – open access papers are marked blue on the publication graph. Looks neat, doesn’t it?
If at this point you are wondering how long it will take you to add all your publications, no worries. We know how busy and stressful academic research can be. That’s why we made sure that you won’t spend much time and effort updating the list. We have teamed up with ORCID and developed a simple tool that allows you to claim your published papers found in Europe PMC to your ORCID. It works like a charm: authorise the tool, scroll through suggested items, pick your contributions from the list – and voila – they are added to your record. Nowadays more and more publishers will make your job even easier – by adding your newly published manuscript to your ORCID record on your behalf. All you need to do is to provide your ORCID ID upon submission.

You can link to your Author Profile page from your institutional or personal website, or attach the graph image to your application. The link to your profile will also appear whenever people search for your work on Europe PMC, helping to promote the science you do.
With an author profile that lists all your publications it is easy to get credit where it’s due, and keep your academic CV in check. Try it for yourself with Europe PMC.

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!

Tuesday, 20 December 2016

Europe PMC - a year in review

This has been a very busy and fruitful year for Europe PMC. With holidays approaching we take a look back at some of the Europe PMC achievements and milestones of 2016.
We kicked off in January with a new, mobile-friendly homepage and information pages. The final design was based on user research in which we gathered lots of feedback from you to come up with design concepts, which were thoroughly tested again before release. We still have work to do on improving these pages and we intend to chip away with making them better, based on feedback, throughout 2017.
Our spring was focussed on the migration of manuscript submission services from JISC to the EMBL-EBI. We installed a database (developed by JISC) that contains information on all the grants awarded by the funders of Europe PMC. This information is important to us to authorize the upload of manuscripts from grant holders, but we also make the data discoverable on the Europe PMC website via the grant finder, or programmatically via the GRIST API. Over 2500 grants have been added by our funders since the spring and the database now includes more than 56,000 grants, crosslinked to the articles they supported.
Summer was a hot time for us. One of the key objectives for Europe PMC is to enable application developers and text miners to reuse the open access full text content, in order to find innovative approaches to searching, filtering and reading the scientific literature. Towards this goal, in July we launched SciLite - a tool that allows text-mined terms to be displayed as an overlay on research articles. For Europe PMC users, SciLite makes it easier to scan articles for key concepts and provides deep links with related data. For text miners, it is an opportunity to showcase their work to a wider public. SciLite is based on the Web Annotation Data Model and is open to any text-mining group. So far, SciLite operates on articles with a CC-0, CC-BY or CC-BY-NC licence, and has contributions from the National Centre for Text Mining (NaCTeM) and the Bibliomics and Text Mining group at the University of Applied Sciences, Geneva, as well as from the core Europe PMC text-mining pipeline; the number of contributors is set to grow in 2017. All the full text annotations are available via a SPARQL API.
As a part of our mission to deliver a world-class service for all of our users, we took a major step towards improving our search by migrating Europe PMC indexing to Solr in the late summer. This has already significantly improved the speed with which we can return search results, as well as making our indexing of new content more efficient. As well as these basics, Solr comes with some useful features built-in, such as filters, auto-suggestions, and snippets, which we plan to start exploiting next year. Other search improvements introduced in 2016 include the addition of reverse sort orders for “date” and “times cited”, so that you can see results ranked by “oldest first” or “least cited”, and the ability to search by embargo date (as well as their display on abstract pages).
Finally, for the summer, our family of 27 funders was joined by the Academy of Medical Sciences (AMS), who became a member of Europe PMC so that the research they fund can be archived in Europe PMC, supporting their open access policies.
We are always open to new opportunities to improve on existing services. This year our External Link providers, who link out from the content in Europe PMC to their resources, can now display an image alongside the link itself. Already the iconic Altmetric donut is apparent on articles under the “External Links” tab, the CitePeer icon alerts users to alternative reference lists on the Related Articles tab, and the ImpactStory badge can be seen on the Author Profile pages. The Author Profile pages are generated for every researcher with a paper in Europe PMC listed in their ORCID profile, and their number has been constantly growing throughout the year. Currently, there are about 350,000 life science researchers actively publishing and using their ORCIDs, having claimed about 3.5 million articles available in Europe PMC.
Our autumn has been about building a program of community engagement and starting research projects with users that will inform next year’s development. The Europe PMC team has now expanded to include a community manager. We hope that this will help us to connect and reach out to all of our stakeholders, create opportunities for networking and discussions, as well as to identify useful synergies. It’s critical to us to understand the needs of our user community and their goals, and manage Europe PMC services accordingly. Finally, as part of our community engagement, we aspire to be open about our development plans in order to gain feedback at the earliest opportunity. So we have concluded this year with the publication of a roadmap that summarizes our recent accomplishments and highlights our near-term development plans, which we will update quarterly on the Europe PMC website. As always, we welcome your feedback. Leave a comment, send us an e-mail, or connect with us via Twitter.
We are looking forward to 2017 and wish all our users happy holidays. Season’s greetings from Europe PMC!