ELIXIR‐EXCELERATE: establishing Europe's data infrastructure for the life science research of the future

Hancock, John M.; Blomberg, Niklas; Brunak, Søren; Capella-Gutiérrez, Salvador; Durinx, Christine; Evelo, Chris T.; Goble, Carole; Gut, Ivo; Ison, Jon C.; Keane, Thomas; Leskošek, Brane; Matyska, Luděk; McEntyre, Johanna; Miguel, Celia María Gonzalo; Navarro, Arcadi; Newhouse, Steven; Nyrönen, Tommi; Palagi, Patricia M.; Persson, Bengt L.; Pommier, Cyril; Rambla, Jordi; Roos, Marco; Rustici, Gabriella; Smith, Andrew; Valencia, Alfonso; Gelder, Celia W.G. van; Vondrášek, Jiřı́; Willassen, Nils Peder; Arenas, Juan Jesús; Parkinson, Helen; Finn, Robert D.; Beltrán, Sergi; Matalonga, Leslie; Hurst, Hannah; Kersey, Paul J.; Lappalainen, Ilkka; Kahlem, Pascal; Saunders, Gary; Sarntivijai, Sirarat; Drysdale, Rachel; Tedds, Johnathan; Lanfear, Jerry; Harrow, Jennifer

doi:10.15252/embj.2020107409

Cited by 24 publications

(18 citation statements)

References 9 publications

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“…ELIXIR has brought Europe’s national centers and core bioinformatics resources into a single, coordinated infrastructure since its launch in December 2013. ELIXIR AAI 15 is an identity and access management service portfolio used for authenticating data users and managing their access rights in services. ELIXIR AAI provides an implementation of a GA4GH Passport Broker (see Passport system components ) that authenticates a data user with their ELIXIR identity and assembles their visas from various assertion repositories for delivery to downstream Passport Clearinghouses for the purpose of enforcing access to services.…”

Section: Resultsmentioning

confidence: 99%

GA4GH Passport standard for digital identity and access permissions

et al. 2021

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Section: Resultsmentioning

confidence: 99%

GA4GH Passport standard for digital identity and access permissions

et al. 2021

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“…Tools of particular interest span the fields of computer vision, optical character recognition, handwriting recognition, named entity recognition and language translation. Workflow technologies from the ELIXIR Research Infrastructure [19], including Galaxy [20], Common Workflow Language [21], Research Object Crates (RO-Crates) [22,23] and WorkflowHub [24], and selected tools are integrated in a cloud-based workflow platform for natural history specimens-the 'Specimen Data Refinery' [1] that will become one of the main services to be offered by the planned DiSSCo research infrastructure [5]. The tools themselves, implemented with findable, accessible, interoperable, and reusable (FAIR) characteristics [25] are packaged into canonical workflow component libraries [26], rendering them reusable, and interoperable with one another.…”

Section: The Specimen Data Refi Nery: a Canonical Workfl Ow Framework...mentioning

confidence: 99%

The Specimen Data Refinery: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections

et al. 2022

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A key limiting factor in organising and using information from physical specimens curated in natural science collections is making that information computable, with institutional digitization tending to focus more on imaging the specimens themselves than on efficiently capturing computable data about them. Label data are traditionally manually transcribed today with high cost and low throughput, rendering such a task constrained for many collection-holding institutions at current funding levels. We show how computer vision, optical character recognition, handwriting recognition, named entity recognition and language translation technologies can be implemented into canonical workflow component libraries with findable, accessible, interoperable, and reusable (FAIR) characteristics. These libraries are being developed in a cloud- based workflow platform—the ‘Specimen Data Refinery’ (SDR)—founded on Galaxy workflow engine, Common Workflow Language, Research Object Crates (RO-Crate) and WorkflowHub technologies. The SDR can be applied to specimens’ labels and other artefacts, offering the prospect of greatly accelerated and more accurate data capture in computable form. Two kinds of FAIR Digital Objects (FDO) are created by packaging outputs of SDR workflows and workflow components as digital objects with metadata, a persistent identifier, and a specific type definition. The first kind of FDO are computable Digital Specimen (DS) objects that can be consumed/produced by workflows, and other applications. A single DS is the input data structure submitted to a workflow that is modified by each workflow component in turn to produce a refined DS at the end. The Specimen Data Refinery provides a library of such components that can be used individually, or in series. To cofunction, each library component describes the fields it requires from the DS and the fields it will in turn populate or enrich. The second kind of FDO, RO-Crates gather and archive the diverse set of digital and real-world resources, configurations, and actions (the provenance) contributing to a unit of research work, allowing that work to be faithfully recorded and reproduced. Here we describe the Specimen Data Refinery with its motivating requirements, focusing on what is essential in the creation of canonical workflow component libraries and its conformance with the requirements of an emerging FDO Core Specification being developed by the FDO Forum.

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“…The EGA has implemented solutions to address these needs. First, the EGA supports linking of EGA user identities to identities issued by the ELIXIR ( 15 ) AAI service ( 16 , 17 ). Once linked, ELIXIR credentials can be used with EGA services.…”

Section: Accessing Data At the Egamentioning

confidence: 99%

The European Genome-phenome Archive in 2021

Freeberg

Fromont

D’Altri

et al. 2021

Nucleic Acids Research

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The European Genome-phenome Archive (EGA - https://ega-archive.org/) is a resource for long term secure archiving of all types of potentially identifiable genetic, phenotypic, and clinical data resulting from biomedical research projects. Its mission is to foster hosted data reuse, enable reproducibility, and accelerate biomedical and translational research in line with the FAIR principles. Launched in 2008, the EGA has grown quickly, currently archiving over 4,500 studies from nearly one thousand institutions. The EGA operates a distributed data access model in which requests are made to the data controller, not to the EGA, therefore, the submitter keeps control on who has access to the data and under which conditions. Given the size and value of data hosted, the EGA is constantly improving its value chain, that is, how the EGA can contribute to enhancing the value of human health data by facilitating its submission, discovery, access, and distribution, as well as leading the design and implementation of standards and methods necessary to deliver the value chain. The EGA has become a key GA4GH Driver Project, leading multiple development efforts and implementing new standards and tools, and has been appointed as an ELIXIR Core Data Resource.

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ELIXIR‐EXCELERATE: establishing Europe's data infrastructure for the life science research of the future

Abstract: A new inter‐governmental research infrastructure, ELIXIR, aims to unify bioinformatics resources and life science data across Europe, thereby facilitating their mining and (re‐)use.

Cited by 24 publications

References 9 publications

GA4GH Passport standard for digital identity and access permissions

GA4GH Passport standard for digital identity and access permissions

The Specimen Data Refinery: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections

The European Genome-phenome Archive in 2021

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