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| Content | |
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| Description | Europe PMC: a full-text literature database for the life sciences and platform for innovation |
| Contact | |
| Research center | European Bioinformatics Institute |
| Authors | Europe PMC Consortium |
| Primary citation | Europe PMC Consortium (2015) [1] |
| Release date | 2007 |
| Access | |
| Website | europepmc |
Europe PubMed Central (Europe PMC) is an open-access repository that contains millions of biomedical research works. It was known as UK PubMed Central until 1 November 2012. [2]
Europe PMC provides free access to more than 9.3 million full-text biomedical and life sciences research articles and over 43.3 million citations. [3] Europe PMC contains some citation information and includes text mining based marked up text that links to external molecular and medical datasets. [1] [4] The Europe PMC funders group requires that articles describing the results of biomedical and life sciences research they have supported be made freely available in Europe PMC within 6 months of publication to maximise the impact of the work that they fund. [5]
The Grant Lookup facility allows users to search for information in a wide variety of different ways on over 101,900 grants awarded by the Europe PMC funders. [6] [7]
Most content is mirrored from PubMed Central, which manages the deposit of entire books and journals. [8] Additionally, Europe PMC offers a manuscript submission system, Europe PMC plus, [9] which allows scientists to self-deposit their peer-reviewed research articles for inclusion in the Europe PMC collection. [10]
The Europe PMC project was originally launched in 2007 as the first 'mirror' site to PMC, which aims to provide international preservation of the open and free-access biomedical and life sciences literature. It forms part of a network of PMC International [11] (PMCI) repositories that includes PubMed Central Canada. Europe PMC is not an exact "mirror" of the PMC database but has developed some different features. [1] [4] On 15 February 2013 CiteXplore was subsumed under Europe PubMed Central. [12]
The resource is managed and developed by the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), on behalf of an alliance of 27 biomedical and life sciences research funders, led by the Wellcome Trust. [5]
Europe PMC is supported by 27 organisations: Academy of Medical Sciences, Action on Hearing Loss, Alzheimer's Society, Arthritis Research UK, Austrian Science Fund (FWF), the Biotechnology and Biological Sciences Research Council, Blood Cancer UK, Breast Cancer Now, the British Heart Foundation, Cancer Research UK, the Chief Scientist Office of the Scottish Executive Health Department, Diabetes UK, the Department of Health, the Dunhill Medical Trust, the European Research Council, Marie Curie, the Medical Research Council, the Motor Neurone Disease Association, the Multiple Sclerosis Society, the Myrovlytis Trust, the National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), Parkinson's UK, Prostate Cancer UK, Telethon Italy, the Wellcome Trust, the World Health Organization and Worldwide Cancer Research (formerly Association for International Cancer Research). [13]
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization, clinical effects of mutations as well as similarities of biological sequences and structures.
PubMed is a free database including primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval.
The Wellcome Trust is a charitable foundation focused on health research based in London, United Kingdom. It was established in 1936 with legacies from the pharmaceutical magnate Henry Wellcome to fund research to improve human and animal health. The aim of the Trust is to "support science to solve the urgent health challenges facing everyone." It had a financial endowment of £29.1 billion in 2020, making it the fourth wealthiest charitable foundation in the world. In 2012, the Wellcome Trust was described by the Financial Times as the United Kingdom's largest provider of non-governmental funding for scientific research, and one of the largest providers in the world. According to their annual report, the Wellcome Trust spent GBP £1.1 billion on charitable activities across their 2019/2020 financial year. According to the OECD, the Wellcome Trust's financing for 2019 development increased by 22% to US$327 million.
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, USA.
The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust.
A health or medical library is designed to assist physicians, health professionals, students, patients, consumers, medical researchers, and information specialists in finding health and scientific information to improve, update, assess, or evaluate health care. Medical libraries are typically found in hospitals, medical schools, private industry, and in medical or health associations. A typical health or medical library has access to MEDLINE, a range of electronic resources, print and digital journal collections, and print reference books. The influence of open access (OA) and free searching via Google and PubMed has a major impact on the way medical libraries operate.
PubMed Central (PMC) is a free digital repository that archives open access full-text scholarly articles that have been published in biomedical and life sciences journals. As one of the major research databases developed by the National Center for Biotechnology Information (NCBI), PubMed Central is more than a document repository. Submissions to PMC are indexed and formatted for enhanced metadata, medical ontology, and unique identifiers which enrich the XML structured data for each article. Content within PMC can be linked to other NCBI databases and accessed via Entrez search and retrieval systems, further enhancing the public's ability to discover, read and build upon its biomedical knowledge.
Biomedical text mining refers to the methods and study of how text mining may be applied to texts and literature of the biomedical domain. As a field of research, biomedical text mining incorporates ideas from natural language processing, bioinformatics, medical informatics and computational linguistics. The strategies in this field have been applied to the biomedical literature available through services such as PubMed.
David J. Lipman is an American biologist who from 1989 to 2017 was the director of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. NCBI is the home of GenBank, the U.S. node of the International Sequence Database Consortium, and PubMed, one of the most heavily used sites in the world for the search and retrieval of biomedical information. Lipman is one of the original authors of the BLAST sequence alignment program, and a respected figure in bioinformatics. In 2017, he left NCBI and became Chief Science Officer at Impossible Foods.
The Cambridge Biomedical Campus is the largest centre of medical research and health science in Europe. The site is located at the southern end of Hills Road in Cambridge, England.
The National Centre for Text Mining (NaCTeM) is a publicly funded text mining (TM) centre. It was established to provide support, advice and information on TM technologies and to disseminate information from the larger TM community, while also providing services and tools in response to the requirements of the United Kingdom academic community.
COSMIC is an online database of somatically acquired mutations found in human cancer. Somatic mutations are those that occur in non-germline cells that are not inherited by children. COSMIC, an acronym of Catalogue Of Somatic Mutations In Cancer, curates data from papers in the scientific literature and large scale experimental screens from the Cancer Genome Project at the Sanger Institute. The database is freely available to academic researchers and commercially licensed to others.
The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of sequence assembly and other metadata related to sequencing projects. The archive is composed of three main databases: the Sequence Read Archive, the Trace Archive and the EMBL Nucleotide Sequence Database. The ENA is produced and maintained by the European Bioinformatics Institute and is a member of the International Nucleotide Sequence Database Collaboration (INSDC) along with the DNA Data Bank of Japan and GenBank.
Sir Shankar Balasubramanian is an Indian-born British chemist and Herchel Smith Professor of Medicinal Chemistry in the Department of Chemistry at the University of Cambridge, Senior Group Leader at the Cancer Research UK Cambridge Institute and Fellow of Trinity College, Cambridge. He is recognised for his contributions in the field of nucleic acids. He is scientific founder of Solexa and biomodal.
Timothy John Phillip Hubbard is a Professor of Bioinformatics at King's College London, Head of Genome Analysis at Genomics England and Honorary Faculty at the Wellcome Trust Sanger Institute in Cambridge, UK. From 1 March 2024, Hubbard became the director of Europe's Life Science Data Infrastructure ELIXIR.
Alexander George Bateman is a computational biologist and Head of Protein Sequence Resources at the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL) in Cambridge, UK. He has led the development of the Pfam biological database and introduced the Rfam database of RNA families. He has also been involved in the use of Wikipedia for community-based annotation of biological databases.
Sarah Amalia Teichmann is a German scientist who is head of cellular genetics at the Wellcome Sanger Institute and a visiting research group leader at the European Bioinformatics Institute (EMBL-EBI). She serves as director of research in the Cavendish Laboratory, at the University of Cambridge and a senior research fellow at Churchill College, Cambridge.
Duncan Odom is a research group leader at the German Cancer Research Center (DKFZ) in Heidelberg, and the Cancer Research UK Cambridge Institute at the University of Cambridge. Previously he was as an associate faculty member at the Wellcome Trust Sanger Institute from 2011 to 2018.
Kathryn Rachel Ayscough is a professor of molecular cell biology and head of the department of biomedical science at the University of Sheffield. She was awarded the 2002 Society for Experimental Biology President's Medal. Her research investigates the role of the actin cytoskeleton in membrane trafficking and cell organisation.
Biocuration is the field of life sciences dedicated to organizing biomedical data, information and knowledge into structured formats, such as spreadsheets, tables and knowledge graphs. The biocuration of biomedical knowledge is made possible by the cooperative work of biocurators, software developers and bioinformaticians and is at the base of the work of biological databases.