Annual Scientific Report 2015

Literature Services
The EMBL-EBI Literature Services team runs Europe PMC, the database for
full-text life-science literature and platform for text-based innovation. Linking
research articles with the underlying supporting data, and using articles to
provide biological context across all data resources, are critical to data-driven
discovery. To achieve this, we work collaboratively with other service providers,
publishers and databases, and engage with the scientific community and our
users. In this regard, the databases developed at EMBL-EBI and more widely
through ELIXIR are of primary importance.
The core of our work is providing fast, reliable and
powerful access to the literature, and to place those
article narratives in the wider context of related data
and credit systems, such as article citations. We engage
with individual scientists, text miners, developers and
database managers to understand how layers of value
can be built upon the basic article content. Our team
provides the infrastructure that enables individuals
to enrich the literature, either manually or using
computational methods, and to publish the results,
maximising the usefulness of the core content. This
allows the widest possible reuse of publicly funded
experimental data.
Europe PMC grows at a rate of over 1 million abstracts
and around 300 000 full-text articles per year, and as of
December 2015 offered more than 30.5 million abstracts
and around 3.5 million full-text research articles from
PubMed and PubMed Central. It also includes metadata
for Agricola (agricultural science records), biological
patents and clinical guidelines. This year we added
a new section to Europe PMC that contains a small
collection of books and documents, extending the scope
of full-text clinical guidelines in particular.
Europe PMC layers article-citation networks, links
articles to underlying databases and makes text-mined
terms of biological interest discoverable. It provides
programmatic access via REST and SOAP web services,
and allows users to bulk-download open-access articles
via FTP (of which there are now over 1 million). Users
can also search over 50 000 biomedical research grants
that have been awarded to approximately 20 000 PIs
supported by Europe PMC’s 27 funders. These funders
include the World Health Organisation, the European
Research Council and many national funding agencies
and charities, led by the Wellcome Trust. Europe PMC is
developed by EMBL-EBI, the University of Manchester
(Mimas and NaCTeM) and the British Library.
Major achievements
In 2015 use of Europe PMC continued to increase
with more than 10 million unique IP addresses visiting
the website during the year. Programmatic access via
RESTful web services in particular also increased,
serving on average 24 million requests per month in
XML and JSON formats.
We focused on improving the user experience of Europe
PMC, based on user research and direct feedback. We
launched a new, responsive website design , which offer
improved navigation and ease of use on mobile devices
and smaller screens. We also introduced user accounts
that enable users to log in with an ORCID, Twitter or
Europe PMC account and save their favourite searches.
Future developments will allow people to use their
accounts to further customize their experience.
Our integration with ORCIDs – unique identifiers for
researchers – continued to be central to developments
on Europe PMC. We launched a new author profile
page, which provides a graphical overview of an author’s
publications and their citation rate over time (see
Figure), as well as citations over time of individual
articles. The page can be downloaded for use in other
documents, such as CVs. Over 200 000 unique ORCIDs
are now associated with over 2.2 million articles in
Europe PMC, many of whom used the Europe PMC
claiming tool to add articles to their ORCID record. We
improved ways to find ORCID-related information on
the website: it is now possible to type in an ORCID in the
main search box and find individual authors by name;
in addition, the author field in the Advanced Search
now includes suggestions for the author’s ORCID and
affiliation. All the data used to develop these features
on the website are also available via web services. Via
our collaboration in the EU-funded THOR project, we
also began to explore how datasets may be claimed to an
ORCID record.
In the area of text mining, we continued to improve
access to content for text-mining groups, and our
collaborations in this regard are informing the
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2015 EMBL-EBI Annual Scientific Report