Johanna McEntyre

Johanna McEntyre

Team Leader - McEntyre team: Literature services

Jo has been Team Leader for Literature Services at EMBL-EBI since 2009. She is the PI for Europe PMC - the database of abstracts and full-text articles for the life sciences. Prior to joining EMBL-EBI, Jo was a staff scientist at the NCBI, National Library of Medicine, NIH, USA, and was the Editor at Trends in Biochemical Sciences (TiBS), Elsevier. Jo is active in the Force 11 Data Citation Implementation Group, and is interested in text mining as a means to improve the integration of literature with public data resources.She holds a PhD in plant biology from Manchester Metropolitan University.

ORCID iD: 0000-0002-1611-6935

Tel:+ 44 (0) 1223 492 599 / Fax:+ 44 (0) 1223 494 468

McEntyre team

EMBL-EBI Literature Services, led by Dr Johanna McEntyre, runs Europe PMC, the database of life sciences research articles. As the scientific literature is increasingly linked to data outputs, one of the key work programs of the Literature Services team is to integrate textual content with databases, in particular with those databases developed at EMBL-EBI, but also more widely through the development of data sharing processes with collaborating organisations. 

About Europe PMC

Europe PMC is a unique, free, information resource for biomedical and health researchers, featuring more than 30 million abstracts and over 3 million full-text research articles from PubMed and PubMed Central; biological patents; clinical guidelines; PhD theses; and research reports. Content in Europe PMC is linked to public databases such as UniProt, Protein Data Bank (PDBe), and the European Nucleotide Archive (ENA), text-mining technologies are used to highlight keywords such as gene names, organisms and diseases. Europe PMC layers citation networks, links to underlying databases, and makes text-mined terms of biological interest discoverable. We are a major integrator of ORCIDs, with over 2 million articles in Europe PMC now claimed by at least one ORCID. These enrichments are available for browsing and filtering search results on the website and have led to the development of features such as a citation count sort order for results lists and data citation information. Programmatic access is provided via SOAP and REST web services, and Open Access articles are available for bulk download by FTP.

Users can also search 50,000 biomedical research grants awarded to the 25,000 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, and are led by the Wellcome Trust.

Europe PMC is developed by EMBL-EBI, the University of Manchester (NaCTeM), Jisc, and the British Library.

Publications

2016

Overview of the interactive task in BioCreative V.
Wang Q, S Abdul S, Almeida L, Ananiadou S, Balderas-Martínez YI, Batista-Navarro R, Campos D, Chilton L, Chou HJ, Contreras G, Cooper L, Dai HJ, Ferrell B, Fluck J, Gama-Castro S, George N, Gkoutos G, Irin AK, Jensen LJ, Jimenez S, Jue TR, Keseler I, Madan S, Matos S, McQuilton P, Milacic M, Mort M, Natarajan J, Pafilis E, Pereira E, Rao S, Rinaldi F, Rothfels K, Salgado D, Silva RM, Singh O, Stefancsik R, Su CH, Subramani S, Tadepally HD, Tsaprouni L, Vasilevsky N, Wang X, Chatr-Aryamontri A, Laulederkind SJ, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Wu CH, Hirschman L, Arighi CN.
Database : the journal of biological databases and curation Volume 2016 (2016) p.

Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources.
Bousfield D, McEntyre J, Velankar S, Papadatos G, Bateman A, Cochrane G, Kim JH, Graef F, Vartak V, Alako B, Blomberg N.
F1000Research Volume 5 (2016) p.

The EMBL-EBI channel.
McEntyre J, Birney E.
F1000Research Volume 5 (2016) p.52

2015

Section level search functionality in Europe PMC.
Kafkas Ş, Pi X, Marinos N, Talo' F, Morrison A, McEntyre JR.
Journal of biomedical semantics Volume 6 (2015) p.7

The BioStudies database.
McEntyre J, Sarkans U, Brazma A.
Molecular systems biology Volume 11 (2015) p.847

Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.
Kafkas Ş, Kim JH, Pi X, McEntyre JR.
Journal of biomedical semantics Volume 6 (2015) p.1

Europe PMC: a full-text literature database for the life sciences and platform for innovation.
Europe PMC Consortium.
Nucleic acids research Volume 43 (2015) p.D1042-8

2013

Application of text-mining for updating protein post-translational modification annotation in UniProtKB.
Veuthey AL, Bridge A, Gobeill J, Ruch P, McEntyre JR, Bougueleret L, Xenarios I.
BMC bioinformatics Volume 14 (2013) p.104

Database citation in full text biomedical articles.
Kafkas Ş, Kim JH, McEntyre JR.
PloS one Volume 8 (2013) p.e63184

2011

UKPMC: a full text article resource for the life sciences.
McEntyre JR, Ananiadou S, Andrews S, Black WJ, Boulderstone R, Buttery P, Chaplin D, Chevuru S, Cobley N, Coleman LA, Davey P, Gupta B, Haji-Gholam L, Hawkins C, Horne A, Hubbard SJ, Kim JH, Lewin I, Lyte V, MacIntyre R, Mansoor S, Mason L, McNaught J, Newbold E, Nobata C, Ong E, Pillai S, Rebholz-Schuhmann D, Rosie H, Rowbotham R, Rupp CJ, Stoehr P, Vaughan P.
Nucleic acids research Volume 39 (2011) p.D58-65

2009

Finding query suggestions for PubMed.
Lu Z, Wilbur WJ, McEntyre JR, Iskhakov A, Szilagyi L.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium Volume 2009 (2009) p.396-400

2006

Biocurators: contributors to the world of science.
Bourne PE, McEntyre J.
PLoS computational biology Volume 2 (2006) p.e142

2004

Patterns and clusters within the PSM column in TiBS, 1992-2004.
McEntyre JR, Gibson TJ.
Trends in biochemical sciences Volume 29 (2004) p.627-633

2001

PubMed: bridging the information gap.
McEntyre J, Lipman D.
CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne Volume 164 (2001) p.1317-1319

PubMed Central decentralized.
Sequeira E, McEntyre J, Lipman D.
Nature Volume 410 (2001) p.740

Guide to the draft human genome.
Wolfsberg TG, McEntyre J, Schuler GD.
Nature Volume 409 (2001) p.824-826

2000

This round's on TiBS.
McEntyre J.
Trends in biochemical sciences Volume 25 (2000) p.581

1998

Linking up with Entrez.
McEntyre J.
Trends in genetics : TIG Volume 14 (1998) p.39-40

1995

Ready for a motif submission? A proposed checklist.
Bork P, Ouzounis C, McEntyre J.
Trends in biochemical sciences Volume 20 (1995) p.104

1994

I think therefore I publish.
Boguski M, McEntyre J.
Trends in biochemical sciences Volume 19 (1994) p.71

Services

Team members

Shaojiang Cai
Guilherme Formaggio De Mello
Yuci Gou
Florian Graef
Audrey Hamelers
Kathryn Holmes
Michele Ide-Smith
Senay Kafkas
Jyothi Katuri
Oliver Kilian
Jee-Hyub Kim
Nikos Marinos
Michael Parkin
Xingjun Pi
Frances Rogers
Francesco Talo
Vid Vartak
Aravind Venkatesan