Swiss National Science Foundation joins Europe PMC

We're delighted to announce that the Swiss National Science Foundation joins Europe PMC as a new funder. This brings the Europe PMC funder family to 29 members.

The Swiss National Science Foundation (SNSF) supports basic science in all academic disciplines, from history to medicine and the engineering sciences. The SNSF is Switzerland’s foremost research funding organisation and finances over 3,200 projects involving 14,800 researchers each year.

Researchers funded by the Swiss National Science Foundation 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:

http://europepmc.org/Joining

Unlocking the open - Europe PMC integrates with Unpaywall

It’s always frustrating to hit a paywall when you stumble across an exciting article.

Until recently, for many of us the only legal way of getting hold of the publication was to purchase the paper in question. But that is no longer the case for millions of scientific publications thanks to Unpaywall - a free, open-source tool launched by ImpactStory - a nonprofit dedicated to making scholarly research more open, accessible, and reusable.

With Unpaywall you can find free versions of the full text research papers scattered around the internet. Unpaywall harvests legally-uploaded content from over 50,000 open data sources, including open repositories, open access and hybrid journals, as well as services like DOAJ, Crossref, and even Europe PMC.

In Europe PMC, free full text is already available for 4.6 million out of 33 million records. As for the rest, an open access copy may exist in a different repository, or reside on the publisher’s website. However, users have no way of knowing that the article they are interested in may be available elsewhere. And that happens more often than you think. According to a recent study, nearly half of all scientific articles requested by Unpaywall users are already available from one of the open sources.

We believe in the power of open science, but to unlock its true potential open content needs to be easily discovered. To help address this issue, Europe PMC has teamed up with Unpaywall to help users get open access to publications easily.

You can now see the iconic green Unpaywall logo on the full text link on the Europe PMC website whenever a free version of the paper can be found using the Unpaywall service.

Here is how we do it. If a paper is available in Europe PMC, the full text link will bring you right to it.

If, however, we do not have the free full text, we use the publication’s DOI to search for an open copy via the Unpaywall API. We then use the URL returned by the API as the full text link, which appears on the article’s abstract page, like in the following example:

Whenever possible, the link will bring you directly to the PDF version of the paper in question.

According to our estimations, this service will help users discover 2.7 million open access publications in addition to the 4.6 million free full text already available in Europe PMC.

Our goal is to build a system that helps you navigate the open content effortlessly. We hope that with this new tool many more of us in and out of academia will be able to read the research literature without any barriers.

Why every researcher should care about open citations

What happens when you cite someone’s research?

As you write a research publication you include references to the work of your fellow researchers. Once the article is published in a scientific journal the readers may view the reference list to verify cited information or perhaps discover additional studies relevant to their topic. But have you ever wondered what happens with citation data that you produce and how it is being used by others?

Once the article is accepted for publication, many journal publishers will submit the article record to Crossref in order to obtain a DOI for the paper. This record will include article metadata: author names, affiliations, article title, journal name, etc. Often the publisher will also submit the references of articles in their journals to access the Cited-By Service provided by Crossref. This citation data is not released automatically - by default the references are hidden from the public eye and can only be obtained from Crossref with specific consent from the publisher.

Why do we need citations to be open?

Open citation data can be put to a good use. It improves the discoverability of the scholarly content and helps to trace knowledge back to its sources. It allows the discovery of connections within scientific research, demonstrating how a single finding may be used by scholars in different disciplines and countries. It can reveal shared authorship or common funding. Citation data is used to calculate citation rates, and can help create new transparent indicators for research evaluation.

Setting citations free: the Initiative for Open Citations

Despite its potential, the bulk of citation data has been difficult to find and access until recently. With the launch of the Initiative for Open Citations (I4OC) on April 6th, 2017 much of the previously unavailable citation data has been liberated. The I4OC has encouraged many scholarly publishers to make the references they deposit with Crossref open. Thanks to their efforts, the share of freely available citation data in Crossref has grown from 1% to over 50% (as of February 2018).

via https://i4oc.org/

What free tools are built on open citation data?

Europe PMC hosts an extensive collection of biomedical research papers, which is supplemented by an open citation network - freely available without subscription. The citation data is mainly determined from the Europe PMC content and is further supplemented with metadata supplied by Crossref. Since the launch of the I4OC the number of citations added monthly to Europe PMC via Crossref has nearly doubled. While 7.1 million references were ingested from May to October in 2016, this number has grown to 14.9 million references for the same period in 2017. As of February 2018 the Europe PMC citation network contains 316,930,434 citation links for 12.8 million citing records - nearly 44% of the 29 million journal articles.

Citation data in Europe PMC can be accessed programmatically using the citations or references modules of the RESTful or SOAP APIs. Each module returns bibliographic information: article identifier, title, author’s list, publication year, citation counts, etc. In combination with other services within Europe PMC developers’ suite, such as the Annotations API or Grants API, it represents a powerful tool for citation analysis.

Website users can access reference lists and cited-by information for a particular article in the Citation tab.

They can also use advanced search settings to retrieve publications that have been cited a certain number of times, or to access papers co-cited together.

An important thing to mention here, is that citation information is matched to Europe PMC records based on available metadata. This means that if a citation can be confidently identified, it will appear as a publication link. Readers can thus follow the reference trail through the citation network, and find research relevant to their area.

Open citation data also enables development of the powerful discovery tools. For example, in Europe PMC it is possible to sort search results by the number of citations to find the most highly cited articles on a particular topic. Citation counts for each paper are also displayed in the results list.

The cited-by information available via the Citations tab is also represented visually in a citation graph. Readers can view citation graphs on the abstract or full text page of the publication. The graph shows how frequently a paper has been referenced over time. Hovering over individual graph points brings up the number of citations for each year.

Another Europe PMC feature built using open citation data are author profiles. An author profile provides a graphical overview of the author's academic output. It is generated automatically for every researcher with a public ORCID record and ‘claimed’ works available in Europe PMC. The profile contains a publication graph showing the number of papers for any given year and a yearly citation count. Open access articles are highlighted in blue, with a darker shade representing articles licensed for reuse.

Each individual record in the profile is also displayed in the publication list together with the already familiar citation graph based on open citations. Users can sort the list by date or times cited, to see which of the works had higher impact in terms of citations.

The number of author profiles in Europe PMC is growing constantly and currently combines information for more than 650,000 biomedical researchers and over 5 million articles. To help users easily retrieve author information we have implemented a Suggested Authors feature. For an author search that matches a researcher with ORCID, a user will see a suggested authors box at the top of their results list. It will display author information for the two most prolific researchers, including their affiliation (if available), the number of publications and the number of citations. Users can then go directly to the profile page of the author using the link provided.

Taking action

Citations stitch together the global web of scholarly knowledge. To make the most of the open citations, please support the I4OC in their bold ambition: to make all citation data freely available for reuse. Get the word out about the initiative, ask journals in which you publish or do peer review to open up their citations, and finally - use the open citations in your own research and demonstrate the value of the open scholarship.

Get the essence: introducing search snippets

Reading scientific papers can be very time consuming. So you should not waste a minute searching for the relevant literature. Thanks to the cutting-edge search technologies Europe PMC helps you find facts and evidence in research publications in a blink of an eye. Search results now display snippets - highlights from the article matching your query. For every result you can see up to two snippets, separated by an ellipsis. 



Why is it important? The search term appears in context, so you can judge whether it is a negligible mention or an essential reference. This means that when sorting results by date or citation count rather than relevance, you can easily identify articles to add to your reading list thanks to the snippets shown. Not only that, but you can also quickly navigate to the place in the text, where your keywords appear. If your search terms appear in the abstract, they will be highlighted in yellow once you open the page.



To locate the keywords found in the full text take advantage of the snippet links on the abstract page. They will take you directly to the mention, saving you time of scanning through the text.



Next step? Letting the AI to read the paper for you. Learn about advances in text-mining for biomedical discovery from our recent post. We wish you happy reading!

Looking back, looking forward: a year in review

As 2017 concludes, we reflect on Europe PMC’s landmark achievements. Let’s take a closer look at the highlights of this year.

Cutting-edge search and viewing mechanisms

Search results now display snippets - fragments of the publication text that contain matches to your query. Snippets highlight the search term in its context, making it easier to identify the relevant content you were looking for. The snippet link on the article abstract allows you to navigate directly to where your  search terms appear in the full text. Another new feature is the publication year filter, so that you can limit your search results to a particular year, or even a year range.

In addition to these search improvements we have focused on the abstract and full text display. We have added a citation graph to the publication pages, showing how frequently the article was referenced over time. The graph is a visual representation of the “cited by” information available via the Citations tab. The redesigned affiliation view helps you navigate through the list of authors, highlighting those that belong to the same institution.

User services

Last year we introduced Author Profile pages based on publicly available ORCID data. This year we have made them more discoverable thanks to the “Suggested Authors” feature. An author search in Europe PMC now brings up a Suggested Authors box linking to matching researchers that have an ORCID iD. The box displays up to the two most prolific researchers and links to their Author Profile page. Currently, there are over 600,000 biomedical researchers life science researchers actively publishing and using their ORCIDs, having claimed about 4.7 million articles available in Europe PMC.

We have also made it easier to manage your accounts in Europe PMC. User accounts allow you to save frequently run searches. You can sign in using your ORCID, Twitter, and Europe PMC Plus credentials, or create a separate Europe PMC account. If you have several accounts due to multiple sign-ins you can now merge them to have all your saved searches in one place.

Integrated research data

Data integration is a unique feature of Europe PMC. To help researchers navigate the data-rich literature we have developed the SciLite tool. It highlights text-mined biological terms (annotations) in scientific articles and links them to related data records in public resources. Since its launch in July last year, the SciLite application has expanded to cover both abstracts and open access full text articles. The list of SciLite annotations has also broadened with the new providers joining the scheme. In addition to core named entities (gene/protein names, organisms, diseases, chemicals, Gene Ontology terms, database accession numbers), phosphorylation events, and gene functions, users can find gene-disease associations from Open Targets and DisGeNET, as well as protein-protein interactions from the IntAct database. We have added a new feature to the SciLite tool and you can now see a list of individual terms for each annotation type.

To make it easier to access all primary data associated with a study, Europe PMC has integrated with the BioStudies database. BioStudies acts as a data container, combining supplemental data and linked data residing in public repositories in a single location. Linked data is identified by text-mined accession numbers for over 20 major data resources in the life sciences, including ENA, PDBe, and UniProt. Over a million Europe PMC articles now have corresponding BioStudies records, which can be explored by clicking on the BioStudies link on the abstract pages.

Support for text and data mining

We want to make the most of having 1.8 million open access articles and 4.5 million full text articles in Europe PMC. We encourage text mining groups and developers to develop new technologies, which can improve information retrieval and researcher workflows. All open content in Europe PMC can be accessed via APIs or via the FTP site. This year we have added the literature-data crosslinks and supplementary data files (including figures for open access articles) to the list of content available for bulk download. We have also expanded the Europe PMC programmatic tools suit with the Annotations API, which allows retrieval of all text-mined annotations from Europe PMC and other providers. The API provides the means for a wider community of biomedical scientists to exploit the results of text-mining in their own research.

User community

We envision Europe PMC as an innovation platform, open for new developments coming from the community itself. We continuously undertake outreach and engagement efforts to foster a collaborative community of Europe PMC users and stakeholders. We have expanded Europe PMC user support with online training covering different aspects of the service, from literature and data search to programmatic access. We have set up a public developer forum for discussions, questions and suggestions about Europe PMC web services. Join the group to connect with the Europe PMC developers and other power users.

Among other community news, our family of 28 funders was joined by the Wellcome Trust/DBT India Alliance, who became a member of Europe PMC so that the research they fund can be archived in Europe PMC, supporting their open access policies. Over 2300 grants have been added by our funders since the spring and the database now includes more than 60,000 grants, crosslinked to the articles they supported.

It is critical to us to understand the needs of our user community and their goals, and manage Europe PMC services accordingly. At the beginning of this year we conducted a user research study to gain a better understanding of literature search behaviour and published a user research report. In the Summer we conducted a user survey with over 300 participants. The feedback we have received from the user research and survey will inform next year’s development.

After looking back at Europe PMC accomplishments, we are looking forward to the new and exciting goals for 2018. You can see what’s in store for 2018 on the Europe PMC roadmap. As always, we welcome your feedback. Leave a comment, send us an e-mail, or connect with us via Twitter. We wish you all happy holidays. Season’s greetings from Europe PMC!

PubMed Central Canada is retiring: response from Europe PMC

The PubMed Central International (PMCI) network is a collaborative effort between the PMCI repositories, publishers, and funding organisations that wish to preserve and provide free access to journal articles authored by the researchers they support. For many years, the PMCI network has consisted of three nodes, PMC USA, Europe PMC and PMC Canada. As of the 23rd February 2018, this network will reduced to two nodes following the decision by the Canadian Institutes of Health Research (CIHR) and the National Research Council (NRC) to close down PMC Canada.

Europe PMC is committed to the PMCI collaboration, and will continue to provide a world-class service, as it has done for the past decade, with funds secured until 2021. The funding of Europe PMC is shared across twenty eight international life science funding organisations, providing a resilient sustainability model for this key research infrastructure (1).

The European Bioinformatics Institute (EMBL-EBI), which runs Europe PMC, and the NCBI, which runs PMC USA, have a long history of collaboration in the provision of open life sciences data resources, starting with the International Nucleotide Sequence Database Collaboration (INSDC). The PMCI network is well-aligned with these resources, and plays an integral part in fulfilling our shared goals to enable international open science.

(1). https://www.biorxiv.org/content/early/2017/04/27/110825

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.