The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

Drysdale, Rachel; Cook, Charles E.; Petryszak, Robert; Baillie-Gerritsen, Vivienne; Barlow, Mary; Gasteiger, Elisabeth; Gruhl, Franziska; Haas, Jürgen; Lanfear, Jerry; López, Rodrigo; Redaschi, Nicole; Stockinger, Heinz; Teixeira, Daniel; Venkatesan, Aravind; Forum, Elixir Core Data Resource; Blomberg, Niklas; Durinx, Christine; McEntyre, Johanna

doi:10.1093/bioinformatics/btz959

Cited by 49 publications

(37 citation statements)

References 35 publications

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“…UniProt additionally integrates, interprets, and standardizes data from multiple selected resources to add biological knowledge and associated metadata to protein records and acts as a central hub from which users can link out to 180 other resources. In recognition of the quality of our data, and the service we provide, UniProt was recognised as an ELIXIR Core Data Resource in 2017 ( 1 ) and received the CoreTrustSeal certification in 2020. The data resource fully supports the Findable, Accessible, Interoperable and Reusable (FAIR) data principles ( 2 ), for example by making data available in a number of community recognised formats, such as text, XML and RDF and via Application Programming Interfaces (API)s and File Transfer Protocol (FTP) downloads, providing stable and traceable identifiers for protein sequence and protein sequence features and by fully evidencing our data sources throughout.…”

Section: Introductionmentioning

confidence: 99%

UniProt: the universal protein knowledgebase in 2021

Bateman¹,

Martin²,

Orchard³

et al. 2020

Nucleic Acids Research

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The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.

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Section: Introductionmentioning

confidence: 99%

UniProt: the universal protein knowledgebase in 2021

Bateman¹,

Martin²,

Orchard³

et al. 2020

Nucleic Acids Research

Self Cite

5,314

3,195

View full text Add to dashboard Cite

show abstract

“…In addition, HPA’s massive collection of images has supported a multitude of publications and become a citizen science resource for developing AI classification learning models 52 , 53 . The HPA is sustained through community contribution to ELIXIR 54 , that allows scientists from academia and industry to explore spatio-temporal aspects of the human proteome 55 – 57 .…”

Section: Hpp Structure and Achievementsmentioning

confidence: 99%

A high-stringency blueprint of the human proteome

et al. 2020

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The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP’s tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.

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“…While the IMEx Consortium is a global effort with contributing members from Europe, North America and Australasia, its common rigorous curation rules and standards have allowed IMEx to be selected as one of the Core Data Resources of the European Life Sciences Infrastructure for Biological Information (ELIXIR) 15 , which are considered essential for the long-term preservation of biological data. At the same time the IMEx Consortium continues to provide an enhanced service to both research funders and data users 16 .…”

Section: The Imex Consortiummentioning

confidence: 99%

Towards a unified open access dataset of molecular interactions

et al. 2020

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The International Molecular Exchange (IMEx) Consortium provides scientists with a single body of experimentally verified protein interactions curated in rich contextual detail to an internationally agreed standard. In this update to the work of the IMEx Consortium, we discuss how this initiative has been working in practice, how it has ensured database sustainability, and how it is meeting emerging annotation challenges through the introduction of new interactor types and data formats. Additionally, we provide examples of how IMEx data are being used by biomedical researchers and integrated in other bioinformatic tools and resources.

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The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

Abstract: Supplementary information Supplementary data are available at Bioinformatics online.

Cited by 49 publications

References 35 publications

UniProt: the universal protein knowledgebase in 2021

UniProt: the universal protein knowledgebase in 2021

A high-stringency blueprint of the human proteome

Towards a unified open access dataset of molecular interactions

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