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      Europe PMC: a full-text literature database for the life sciences and platform for innovation

      research-article
      Author(s): The Europe PMC Consortium 1 , 2 , 3 , 4 , * , †
      Publication date (Electronic):
      Journal: Nucleic Acids Research
      Publisher: Oxford University Press

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          Abstract

          This article describes recent developments of Europe PMC ( http://europepmc.org), the leading database for life science literature. Formerly known as UKPMC, the service was rebranded in November 2012 as Europe PMC to reflect the scope of the funding agencies that support it. Several new developments have enriched Europe PMC considerably since then. Europe PMC now offers RESTful web services to access both articles and grants, powerful search tools such as citation-count sort order and data citation features, a service to add publications to your ORCID, a variety of export formats, and an External Links service that enables any related resource to be linked from Europe PMC content.

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          Activities at the Universal Protein Resource (UniProt)

          emmanuel boutet, Claire O'Donovan (2014)
          The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequences and functional annotation. It integrates, interprets and standardizes data from literature and numerous resources to achieve the most comprehensive catalog possible of protein information. The central activities are the biocuration of the UniProt Knowledgebase and the dissemination of these data through our Web site and web services. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads.
          Article 0 comments Cited 576 times – based on 0 reviews     Review now
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            Gene Ontology Annotations and Resources

            Claire O'Donovan, emmanuel boutet, Jurg Bahler (2012)
            The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new ‘phylogenetic annotation’ process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.
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              Modeling sample variables with an Experimental Factor Ontology

              James P. Malone, Ele Holloway, Tomasz Adamusiak … (2010)
              Motivation: Describing biological sample variables with ontologies is complex due to the cross-domain nature of experiments. Ontologies provide annotation solutions; however, for cross-domain investigations, multiple ontologies are needed to represent the data. These are subject to rapid change, are often not interoperable and present complexities that are a barrier to biological resource users. Results: We present the Experimental Factor Ontology, designed to meet cross-domain, application focused use cases for gene expression data. We describe our methodology and open source tools used to create the ontology. These include tools for creating ontology mappings, ontology views, detecting ontology changes and using ontologies in interfaces to enhance querying. The application of reference ontologies to data is a key problem, and this work presents guidelines on how community ontologies can be presented in an application ontology in a data-driven way. Availability: http://www.ebi.ac.uk/efo Contact: malone@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (hwp): nar
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 28 January 2015
                Publication date (Electronic): 06 November 2014
                Publication date PMC-release: 06 November 2014
                Volume: 43
                Issue: Database issue , Database issue
                Pages: D1042-D1048
                Affiliations
                [1 ]European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                [2 ]The British Library, 96 Euston Road, London NW1 2DB, UK
                [3 ]Mimas, Roscoe Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
                [4 ]National Centre for Text Mining, School of Computer Science, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
                Author notes
                [* ]To whom correspondence should be addressed. Johanna McEntyre. Tel: + 44 1223 492 599; Fax: + 44 1223 494 468; Email: mcentyre@ 123456ebi.ac.uk
                Article
                DOI: 10.1093/nar/gku1061
                PMC ID: 4383902
                PubMed ID: 25378340
                SO-VID: f2e0d399-59a8-4bbc-aa3e-6d812eeee9ce
                Copyright © © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date accepted : 15 October 2014
                Date revision received : 09 October 2014
                Date received : 12 September 2014
                Page count
                Pages: 7
                Categories
                Subject: Database Issue
                Custom metadata
                cover-date 28 January 2015

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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