Identifying ELIXIR Core Data Resources

Durinx, Christine; McEntyre, Johanna; Appel, Ron D.; Apweiler, Rolf; Barlow, Mary; Blomberg, Niklas; Cook, Charles E.; Gasteiger, Elisabeth; Kim, Jee-Hyub; López, Rodrigo; Redaschi, Nicole; Stockinger, Heinz; Teixeira, Daniel; Valencia, Alfonso

doi:10.12688/f1000research.9656.2

Cited by 63 publications

(58 citation statements)

References 3 publications

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“…The PDB is a primary data archive central to biomedicine worldwide, on par with the International Nucleotide Sequence Database Collaboration responsible for nucleic acid sequence data. Both have been classified by the European ELIXIR partnership as Core Data Resources that are “absolutely critical for the integrity and advancement of life science research,” adding that “If for any reason we were to lose access to these Core Data Resources, it would have a devastating effect not only on science, but also on medicine, industry, and innovation.”…”

Section: Overarching Valuementioning

confidence: 99%

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

et al. 2017

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The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open‐access, digital‐data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB data integrated with ∼40 external data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy.

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Section: Overarching Valuementioning

confidence: 99%

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

et al. 2017

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“…These metrics coming from the original data resources are normally not made publicly available and at present infeasible to retrieve. In fact, at present the first coordinated efforts to gather them in a standard manner are taking place in the context of the ELIXIR framework for European biological data resources [35].…”

Section: Discussionmentioning

confidence: 99%

Quantifying the impact of public omics data

Perez‐Riverol

Zorin

Dass

et al. 2018

Preprint

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The amount of omics data in the public domain is increasing every year [1, 2]. Public availability of datasets is growing in all disciplines, because it is considered to be a good scientific practice (e.g. to enable reproducibility), and/or it is mandated by funding agencies, scientific journals, etc. Science is now a data intensive discipline and therefore, new and innovative ways for data management, data sharing, and for discovering novel datasets are increasingly required [3, 4]. However, as data volumes grow, quantifying its impact becomes more and more important. In this context, the FAIR (Findable, Accessible, Interoperable, Reusable) principles have been developed to promote good scientific practises for scientific data and data resources [5]. In fact, recently, several resources [1, 2, 6] have been created to facilitate the Findability (F) and Accessibility (A) of biomedical datasets. These principles put a specific emphasis on enhancing the ability of both individuals and software to discover and re-use digital objects in an automated fashion throughout their entire life cycle [5]. While data resources typically assign an equal relevance to all datasets (e.g. as results of a query), the usage patterns of the data can vary enormously, similarly to other "research products" such as publications. How do we know which datasets are getting more attention? More generally, how can we quantify the scientific impact of datasets?Recently, several authors [7][8][9] and resources [10] pointed out the importance of evaluating the impact of each research product, including datasets.

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“…There are some promising indicators, including a 2017 meeting between several major funding organizations who came to a strong consensus that core data resources for the life sciences should be supported through a coordinated international effort to both ensure long-term sustainability and appropriately align funding with scientific impact (Anderson et al, 2017). A project is underway called ELIXIR Core Data Resources (Durinx et al, 2017), defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. The Global Sustainability Coalition for Open Science Services (SCOSS) 3 is an international group of leading aca-demic and advocacy organizations that came together in 2016 to help secure the vital infrastructure underpinning Open Access and Open Science, for which SPARC Europe is a founding member.…”

Section: Dr Danny Kingsley Cambridge University Librarymentioning

confidence: 99%

JLSC Board Editorial 2018

Clement

Agate

Searle

et al. 2018

Journal of Librarianship and Scholarly Communication

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The current scholarly communication landscape is populated by a variety of actors and powered by an ever-increasing array of complementary and competitive systems for the production, publication, and distribution of scholarship. Recent years have also seen increasing numbers of proposals to recast these systems in ways that better align with the needs and values of the academy and its scholars. In this editorial, members of the Editorial Board of the Journal of Librarianship and Scholarly Communication consider the present environment and contemplate the future of academy-owned and -supported scholarly communication, as well as the role of libraries in that future.

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Identifying ELIXIR Core Data Resources

Cited by 63 publications

References 3 publications

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

Quantifying the impact of public omics data

JLSC Board Editorial 2018

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