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Published byVeronica Short Modified over 6 years ago
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ELIXIR Core Data Resources and Deposition Databases
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Open data requires infrastructure
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Data infrastructure for the next 20 years
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Why do we need indicators?
Life Science Community Science policy actions: towards long term preservation of, and access to, biological data Build trust in a broad user base, in particular for new or occasional users Resource managers Build capacity across partners regarding effectiveness and excellence in resource management Indicators allowing life-cycle management based on objective criteria
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What are ELIXIR Core Data Resources?
A set of data resources that are of fundamental importance to the broad life science community and the long-term preservation of biological data They provide complete collections of generic value to life science, and show high levels of usage, scientific quality and service
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Indicators that support decision making
A carefully chosen set of indicators, reflecting the multiple facets of bioinformatics resources Impact Scientific focus Indicators that support decision making Scientific impact Community Legal & funding infrastructure Quality Scientific focus and quality of science Community served Quality of service Legal and funding infrastructure and governance Impact and translational stories
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1. Scientific focus and quality of science
Measuring what? Inherent scientific quality of the resource, its uniqueness and comprehensiveness Indicators: Archives vs knowledge bases Scope statement: scientific coverage and comprehensiveness International dimension Staff effort: including curation effort
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2. Community served Community Measuring what? Usage of the resource
Indicators: Overall usage: access via web browser and other methods Potential usage Usage in research as measured through citation in the literature: the resource name, data of a resource Dependency of other resources
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3. Quality of service Quality
Measuring what? Service levels and reliability Indicators: Use of persistent and unique identifiers Data throughput: number of entries, depositions Technical performance: uptime, response time Use of community-recognized standards for (meta)data Links to documentation of provenance Data availability - access services and formats Customer service: helpdesk, user feedback, training activities
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Legal & funding infrastructure
4. Legal and funding infrastructure, and governance Legal & funding infrastructure Measuring what? Soundness of the legal, funding and governance structure guaranteeing its long-term stability Indicators: Scientific Advisory Board Legal framework supporting Open Science Privacy policy Ethics policy Sustainable support and funding
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5. Impact and translational stories
Measuring what? Is the resource meeting its objective of fulfilling a specific need of the scientific community Indicators: Counterfactual analysis Accelerating science Translational data
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Benchmarking FAIR against our indicators
Core resources are Findable Accessable Interoperable Reusable FAIR Principles Core Data Resource Indicators 1 Science 2 Community 3 Service 4 Governance 5 Impact a b c d e f g Findable: F1 F2 F3 F4 Accessible: A1 A1.1 A1.2 A2 Interoperable: I1 I2 I3 Re-usable: R1 R1.1 R1.2 R1.3 Core resources address scientific need, community and impact Core resource indicators support decisions on value
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For more details
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Process to identify ELIXIR Core Data Resources
ELIXIR Scientific Advisory Board Advises on the process Comments the overall list of ELIXIR CDRs ELIXIR Nodes ELIXIR Hub ELIXIR Director Heads of Nodes Committee Submit Case Document(s) Hub Checks application Director Informs HoNs Committee of applications Establishes the list of ELIXIR Core Data Res. Reviews and adds to the list Panel of independent experts Review the applications
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Themes arising, for discussion
Scope Breadth of coverage and community served Knowledgebases and deposition databases (archives) Nested resources When many resources coordinate under an “umbrella” resources e.g. InterPro Consortium (14 protein family databases) Licensing and reuse “Terms of use” “Public domain” Creative commons licenses that support open science: CC0, CC-BY, CC-BY-SA Other
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Initial set of Core Data Resources
ArrayExpress ChEBI ChEMBL EGA ENA Ensembl Ensembl Genomes Europe PMC Human Protein Atlas The IMEx Consortium (IntAct and MINT) InterPro PDBe PRIDE STRING db UniProt
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Emerging requirement: Deposition Databases
To respond to funders and journals regarding data management policies and plans An ELIXIR Deposition Database is defined as being part of an ELIXIR Node portfolio of services accepting deposition of experimental data from an international community of researchers beyond the funding envelope of the database itself meeting the technical quality and governance criteria expected of ELIXIR Core Data Resources, but may be at an earlier stage of development, meeting an emerging scientific requirement, or may be narrower in scope.
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Initial set of ELIXIR Deposition Databases
ArrayExpress BioModels EGA ENA IntAct MetaboLights PDBe PRIDE BioSamples BioStudies EVA EMDB
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Summary & Future Another round of CDR selection in 2018
CDR Forum within Data Platform realise the shape of the data infrastructure publication on vital statistics Feeding into the Global Data Resource Coalition
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