Annual Scientific Report 2015

development of Europe PMC as a platform for
application development based on full text. We
contributed gene–disease associations text mined
from both abstracts and open-access text articles to
the Centre for Therapeutic Target Validation (Open
Targets) platform, launched in December 2015. For any
given gene–disease association, articles are provided
ranked by relevance. We now text mine 19 accession
number types, adding resources such as the Gene
Ontology, European Genome-phenome Archive (EGA)
and ProteomeXchange to the list. This latter work of
detecting data citations is particularly important to
support literature-data integration, is contributing to
our understanding of the impact of data resources in
research, and is a key indicator for defining ELIXIR
Core Resources.
We now have 26 providers of external links from articles
to websites of interest. This year we have added Publons,
a small company that develops systems of credit for peer
review, and Kudos, a company offering lay descriptions
of research articles. The biggest supplier of links is now
Wikipedia, with over 500 000 links to Wikipedia pages
from articles in Europe PMC.
Future plans
In 2016 we plan to release a new system for displaying
results from third-party application developers and
text miners. Working with key communities across
ELIXIR and beyond, we will develop the means to
show text-mined annotations on open access articles
on the Europe PMC website and share these results
widely, for example to journals or other applications
such as bibliographic reference managers. Using a
Johanna McEntyre
Literature Services
PhD in plant biology, Manchester
Metropolitan University, 1990. Editor,
Trends in Biochemical Sciences, Elsevier,
1997. Staff Scientist, NCBI, National Library
of Medicine, NIH, US, 2009.
At EMBL-EBI since 2009.
variety of user-based research approaches, we will
continue to improve the experience on the website, and
in particular we expect to change the article pages and
search experience for the better over the course of the
year. We will be begin to support an author manuscript
submission system, which has previously been hosted
by our Jisc collaborators. A component of this is an
Awarded Grants database containing all awards from
the 27 Europe PMC funders since they joined. A new,
integrated grant search will be released, showing the
crossover between grants and the research outputs (in
the form of articles) they funded.
Selected publications
Europe PMC Consortium (2015) Europe PMC: a
full-text literature database for the life sciences
and platform for innovation. Nucleic Acids Res.
43:D1042-D1048
Kafkas Ş, Kim JH, Pi X, McEntyre JR (2015) Database
citation in supplementary data linked to Europe
PubMed Central full text biomedical articles. J. Biomed.
Semantics 6:1
McEntyre J, Sarkans U, Brazma A (2015) The BioStudies
database. Mol. Syst. Biol. 11:847
EuropePMC launched author profiles in
2015, which draws on ORCIDs to provide
a graphical representation of an author’s
publications and citation rate over time.
http://europepmc.org
2015 EMBL-EBI Annual Scientific Report 120