Delivering ELIXIR-UK

Lead Research Organisation: University of Edinburgh
Department Name: MRC Human Genetics Unit

Abstract

ELIXIR is a project that is designed to construct and operate a sustainable infrastructure for biological information in Europe. Owing to the dearth of individuals who can take advantage of large biological data sets, we have decided to focus the UK's ELIXIR node on training.

This is the century of biology, and genomics, transcriptomics, proteomics and metabolomics ('omics and bioinformatics) lie at its heart. The computer is an essential tool and now drives many critical aspects of the scientific process hence scientists need to know how to gain most advantage from it. Despite the central role of computing in science today:

- Most research scientists are ill-equipped to take advantage of the data 'bonanza' that is emanating from new technologies. Critical training needs across the community are, broadly, in the analysis and the interpretation of genome-scale data of many types, including next generation sequencing (NGS) data. Genomics is the area of greatest training need as it lies at the intersection of many fast-moving research disciplines.

- Many infrastructure technologists (career bioinformaticians) are ill-equipped to offer scalable, sustainable solutions for managing and interpreting data arising from this flood of technological advances. Critical training needs are in techniques and practices for data management, integration, compute and software, tools, services and standards.

The ELIXIR-UK Core Organisations are: the Universities of Oxford, Manchester, Liverpool, Birmingham, and Edinburgh; the NERC Environmental Omics Synthesis Centre; the Wellcome Trust Sanger Institute; the Genome Analysis Centre; and, University College London. Additional participating organisations are: the Software Sustainability Institute UK; the Hartree Centre; and the University of Dundee. Other organisations (UK and ELIXIR-wide) will be incorporated to provision training.

Technical Summary

The Node's training mission will be delivered in four ways:

(a) The organisation of training through ten cooperating Training Sectors where UK skills are strong, training needs have been identified, and training capabilities already exist. Each sector is led by established researchers in their fields, and many co-operations between the Sector Leads already exist. Each Sector Lead is responsible for: (i) representing the sector at initial Training the Trainers (TTT) events; (ii) organisation of an initial workshop that performs a training gap analysis for the sector, and (iii) fund-raising for resources that aim to plug these training gaps.

(b) These training gaps will also be filled by trainers' skills being developed by workshops that exchange ideas and best practice among sectors. ELIXIR-UK will be particularly supportive of training delivered at the
interface between different sectors. Existing training resources will be collated and new training materials
developed and disseminated at every opportunity.

(c) The development of a pilot Training e-Support Service platform that will seek, among other things, to offer the crucial means of registering and discovering training materials, face-to-face training opportunities
and training-relevant resources, and will progressively deliver forms of training online. A feasibility study will
be undertaken on whether pipelines could be developed to permit ELIXIR trainers to disseminate their own
training content on-line, whilst maintaining a separate copy in their home training institution.

(d) Development, management and monitoring of outcomes of the training activities through three posts who (i) support the Training Sector Leads, (ii) coordinate the redefinition of of training agendas with UK scientists, industry, grant-giving bodies and other ELIXIR Nodes, and (iii) will foster, mentor and support the community of trainings, across all sectors, in the UK and Europe.

Planned Impact

For Academic Impact please see 'Academic Beneficiaries'.

Industrial Impact.
Industry has a critical requirement for data sources, data integration, visualization and analysis tools, and for training related to these, across the broad spectrum of data types relevant to life sciences. The ELIXIR WP3 industry report refers to: protein and nucleotide sequencing; genomic information; genetic variation; small molecules; proteomics; transcriptomics; macromolecular structures; scientific literature analysis; ontologies or controlled vocabularies; and pathway and interaction information. In the pharmaceutical, consumer goods, consumer markets and agri-food sectors small molecule data, protein sequence and structure, as well as pathways are of critical importance. Genomic data, genomic variation, and links to phenotypes are important in plant and animal breeding. Food security can only be supported by scientifically driven research and by making the fruits of this research available to academic, governmental and industrial scientists. Scientists in large companies, medium and small size organizations can be overwhelmed by the complexity and volume of data. Repetition of in house custom solutions is not cost effective so a new landscape of pre-competitive collaborations is emerging. Training in understanding ranges of data types, interactions and agile integration are pre-requisites for efficient industrial research. Tools such as semantic web data integration techniques, controlled vocabulary / ontology definition and metadata capture are key for modern data driven biological research but adoption of these techniques in industry will require education and training. ELIXIR-UK will engage with industry in a number of ways:
- through industry organisations such as EFPIA, Pistoia (Pharma), and BioNOW (BioTech SMEs), systematically developing those links to inform its training content and training methods;
- awareness raising in industry of ELIXIR tools and resources, and providing training in them;
- packaging platform distributions such as BioLinux in other informatics sectors, such as cheminformatics;
- using industry for provisioning training and hosting training events;
- brokering access to high-end training needs in ICT literacy (e.g. HPC).

Related Projects

Project Reference Relationship Related To Start End Award Value
BB/L005069/1 02/06/2014 31/12/2015 £1,031,385
BB/L005069/2 Transfer BB/L005069/1 01/01/2016 31/05/2018 £547,648
 
Description Improved understanding of the importance of training in Big Data life sciences, both in academia and in industry.
First Year Of Impact 2017
Sector Digital/Communication/Information Technologies (including Software),Education
Impact Types Cultural,Economic

 
Description FAIRsharing features in the Case Study report by the UK the Open Research Data Task Force.
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
URL https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/7753...
 
Description FAIRsharing is endorsed by the Research Data Alliance, as one of the few flagship outputs
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
URL https://www.rd-alliance.org/group/fairsharing-registry-connecting-data-policies-standards-databases-...
 
Description FAIRsharing is one of the elements mentioned in the "Framework for Discipline-specific Research Data Management" report by Science Europe.
Geographic Reach Europe 
Policy Influence Type Influenced training of practitioners or researchers
URL https://www.scienceeurope.org/wp-content/uploads/2018/01/SE_Guidance_Document_RDMPs.pdf
 
Description FAIRsharing is one of the resources recommended by the EU EOSC "Turning FAIR into Reality" report.
Geographic Reach Europe 
Policy Influence Type Influenced training of practitioners or researchers
 
Description FAIRsharing is one of the resources recommended by the UK Jisc "FAIR in Practice report".
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
 
Description FAIRsharing is recommended by major scholarly publishers and journals
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
URL https://fairsharing.org/communities#adopters
 
Description FAIRsharing is recommended by the STM association of scholarly publishers
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
URL https://www.stm-researchdata.org/
 
Description FAIRsharing is recommended in the "Horizon 2020 - Annotated Model Grant Agreement": guideline by the European Commission.
Geographic Reach Europe 
Policy Influence Type Influenced training of practitioners or researchers
URL https://ec.europa.eu/research/participants/data/ref/h2020/grants_manual/amga/h2020-amga_en.pdf
 
Description FAIRsharing is recommended in the "Sustainable and FAIR Data Sharing in the Humanities" report by the European Federation of Academies of Sciences and Humanities.
Geographic Reach Europe 
Policy Influence Type Influenced training of practitioners or researchers
URL https://doi.org/10.7486/DRI.tq582c863
 
Description FAIRsharing is recommended in the "Top 10 FAIR Data & Software Things" guideline by the Library Carpentry.
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
URL https://librarycarpentry.org/Top-10-FAIR/
 
Description FAIRsharing is recommended in the "Turning FAIR into Reality" report by the European Commission's Expert Group on FAIR Data.
Geographic Reach Europe 
Policy Influence Type Influenced training of practitioners or researchers
URL https://op.europa.eu/en/publication-detail/-/publication/7769a148-f1f6-11e8-9982-01aa75ed71a1/langua...
 
Description Nominated member of the FAIR European Data Champion Board
Geographic Reach Europe 
Policy Influence Type Membership of a guideline committee
URL https://www.fairsfair.eu/advisory-board/egfc
 
Description Nominated member of the GO-FAIR Executive Board
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
URL https://www.go-fair.org/go-fair-initiative/governance/executive-board/
 
Description EINFRA-EOSC - EOSC-Life
Amount £23,745,978 (GBP)
Funding ID 824087 
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 03/2019 
End 02/2023
 
Description FAIRplus
Amount £3,996,150 (GBP)
Funding ID 802750 
Organisation European Commission 
Department Innovative Medicines Initiative (IMI)
Sector Public
Country Belgium
Start 01/2019 
End 01/2022
 
Description ISA-InterMine: accelerating and rewarding data sharing
Amount £1,174,660 (GBP)
Funding ID 208381/A/17/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2018 
End 07/2021
 
Description The FAIRsharing service: supporting the research life-cycle
Amount £742,702 (GBP)
Funding ID 212930/Z/18/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2019 
End 07/2023
 
Title Continued improvements to the ISA toolkit 
Description Started in 2003 and first released in 2007, the ISA tools have been developed over time by the Oxford team and collaborators or directly contributed by partnering contributors, via the ISA Commons collaborative community. Short description of the developments and achievements of the resource over the last year: • Awarded Wellcome Trust funds (2018-2021), as collaborative project with the University of Cambridge's InterMine team to link the two resources and reward researchers for annotating and publish FAIR data; also, ISA is embedded in two ELIXIR Implementation Studies, on a Plant-focused data validation and on metabolomics. • With the uptake of ISA-Galaxy tools (https://github.com/ISA-tools/isatools-galaxy) and integration with the Galaxy Framework, ISA has struck a major milestone by showcasing how prospective data management can be done, demonstrating a full deposition workflow to Metabolights and creating training material (10.7490/f1000research.1115757.1). • Jupyter notebooks (https://github.com/ISA-tools/dtp-isa-exercises) have been developed as teaching material to showcase the use of ISA-API in various context to undergraduate and postgraduate courses on data readiness. 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? Yes  
Impact Community use and impact is tracked via the ISA Commons, which currently has over 40 international groups, projects, and organizations that use and contribute to the development of components of the ISA metadata tracking framework. Therefore, we can say that the ISA user base ranges from hundreds to thousands of researchers from increasingly diverse domains (ranging from -omics, cell-based research, biomedical nanotechnology, plant phenotyping, toxicology, biodiversity, metagenomics, stem cell research, system biology, neuroscience, microbial science and immunology), and goes beyond researchers, curators, others resource developers and service providers, to also include journals. For example, ISA is used by the University of Oxford' GigaScience and underpins Springer Nature's Scientific Data data journal, supporting intelligent data sharing and credit; ISA is used to describe the experiment and to provide browse and search functionality for Scientific Data's content (http://scientificdata.isa-explorer.org). The ISA framework is currently embedded in a number of UK, EC and NIH and pharma funded infrastructure and research projects; here are exemplars from the ELIXIR UK Node and other Nodes: o EMBL-EBI MetaboLights' new web-based submission relies on ISA-JSON format to build web component and on the ISA-API to validate, convert experiments represented in ISA objects. o BBSRC-funded COPO infrastructure relies on the ISA API, ISA-JSON serialization and on the ISA configurations to support plant-based experiment molecular profiling experiments; it also used the ISAconverter to deposit to the ENA database. o ELIXIR-UK Node partners, University of Birmingham and Imperial College London use ISA Galaxy Tools, ISA-API and ISA validator - as part of their work in the UK Phenome Centre - to collect data prospectively but also organise public deposition to repositories. o ELIXIR Plant Community's MIAPPE standards and BrAPI rely on availability of ISA parsers and validation tools in the context of data validation programs. 
URL http://isa-tools.org
 
Title Continued improvements to the ISA toolkit and the new Datascriptor component 
Description Started in 2003 and first released in 2007, the ISA tools (http://isa-tools.org) have been developed over time by the Oxford team and collaborators or directly contributed by partnering contributors, via the ISA Commons collaborative community (https://www.isacommons.org). Key work over the last year is the development of a new component, the Datascriptor: https://datascriptor.org, as part of the Wellcome Trust award (2018-2021), a collaborative project with the University of Cambridge's InterMine team. Leveraging our experience and links with the communities, we are designing an open-source web-based tool - part of an ecosystem of existing annotation and authoring systems - to help researchers to use community standards to describe their (meta)data at the source, and capitalize on their effort to accelerate the creation of a data article. In addition major advances have been made to the ISA API also working with the ELIXIR Plant and Metabolomics communities. 
Type Of Material Improvements to research infrastructure 
Year Produced 2019 
Provided To Others? Yes  
Impact Community use and impact is tracked via the ISA Commons, which currently has over 40 international groups, projects, and organizations that use and contribute to the development of components of the ISA metadata tracking framework. Therefore, we can say that the ISA user base ranges from hundreds to thousands of researchers from increasingly diverse domains (ranging from -omics, cell-based research, biomedical nanotechnology, plant phenotyping, toxicology, biodiversity, metagenomics, stem cell research, system biology, neuroscience, microbial science and immunology), and goes beyond researchers, curators, others resource developers and service providers, to also include journals. For example, ISA is used by the University of Oxford' GigaScience and underpins Springer Nature's Scientific Data data journal, supporting intelligent data sharing and credit; ISA is used to describe the experiment and to provide browse and search functionality for Scientific Data's content (http://scientificdata.isa-explorer.org). The ISA framework is currently embedded in a number of UK, EC and NIH and pharma funded infrastructure and research projects; here are exemplars from the ELIXIR UK Node and other Nodes: (i) EMBL-EBI MetaboLights' new web-based submission relies on ISA-JSON format to build web component and on the ISA-API to validate, convert experiments represented in ISA objects. (ii) BBSRC-funded COPO infrastructure relies on the ISA API, ISA-JSON serialization and on the ISA configurations to support plant-based experiment molecular profiling experiments; it also used the ISAconverter to deposit to the ENA database. (iii) ELIXIR-UK Node partners, University of Birmingham and Imperial College London use ISA Galaxy Tools, ISA-API and ISA validator - as part of their work in the UK Phenome Centre - to collect data prospectively but also organise public deposition to repositories. (iv) ELIXIR Plant Community's MIAPPE standards and BrAPI rely on availability of ISA parsers and validation tools in the context of data validation programs. 
URL https://datascriptor.org
 
Title Re-launching BioSharing as FAIRsharing and improving it 
Description FAIRsharing, now is a curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resource more discoverable, more widely adopted and cited. 
Type Of Material Improvements to research infrastructure 
Year Produced 2011 
Provided To Others? Yes  
Impact Launched in 2011, as BioSharing and re-launched as FAIRsharing in 2017, this resource is at the epicentre of FAIR-enabling activities, delivering guidance, tools and services with and for a variety of stakeholders. As these activities mature, we will implement them in, or connect them to, the FAIRsharing resource itself. FAIRsharing has a growing userbase encompassing institutions, libraries, journal publishers, infrastructure programmes, societies and other organizations or projects that in turn serve and guide individual researchers or other stakeholders on research data management matters. 
URL https://fairsharing.org/communities
 
Title Redevelopment of the FAIRsharing resource 
Description Funded by the new Wellcome Trust award (2019-2023), we are in the process or redesign and redeveloping FAIRsharing as an open source system, with new and friendly features to grow, access and use the content. 
Type Of Material Improvements to research infrastructure 
Year Produced 2019 
Provided To Others? Yes  
Impact Work has just started, but to ensure continued impact in the stakeholder community, FAIRsharing redevelopment and it is guided by a new Advisory Board, organised in a small group of Executive Advisors and a larger group of Stakeholder Advisors that represent the users and adopters: https://fairsharing.org/communities#governance 
 
Description ELIXIR Interoperability Platform and FAIRsharing 
Organisation ELIXIR
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Run by Prof. Sansone group, FAIRsharing (https://fairsharing.org) is a resource on standards, repositories, and data policies endorsed by a growing number of stakeholder communities, including major publishers, funders, libraries and FAIR-supporting organizations. FAIRsharing is part of the ELIXIR Recommended Interoperability Resources (RIRs) to facilitate interoperability and reusability of life science data and support the principles of FAIR data management.
Collaborator Contribution The ELIXIR Recommended Interoperability Resources have been selected by external panel of reviewers, based on the selection criteria published in the Call for RIR application, which measure how they facilitate scientific research and how they improve FAIRness of life science data.
Impact FAIRsharing is and will continue to be used by and further linked to other ELIXIR registries and services.
Start Year 2018
 
Description ELIXIR Interoperability Platform and ISA 
Organisation ELIXIR
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution ISA is part of the ELIXIR Recommended Interoperability Resources (RIRs) to facilitate interoperability and reusability of life science data and support the principles of FAIR data management.
Collaborator Contribution The ELIXIR Recommended Interoperability Resources have been selected by external panel of reviewers, based on the selection criteria published in the Call for RIR application, which measure how they facilitate scientific research and how they improve FAIRness of life science data.
Impact ISA is and will continue to be used by and further developed with ELIXIR communities, especially with Plant and Metabolomics use cases.
Start Year 2018
 
Description ELIXIR Metabolomics Community 
Organisation ELIXIR
Department ELIXIR UK
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution My team has contributed ISA-related work to the ELIXIR Metabolomics use case, activities and reports.
Collaborator Contribution We have gained more visibility for the ISA work and now ISA-Tab is a formal format used by the Galaxy analysis toolkit for metabolomics applications.
Impact The ISA framework as the basis for the metadata standards used by this ELIXIR Metabolomics Community and the tools are embedded in the EBI MetaboLights databases, as well as in other international metabolomics resources.
Start Year 2017
 
Description ELIXIR Metabolomics Community 
Organisation ELIXIR
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution My team has contributed ISA-related work to the ELIXIR Metabolomics use case, activities and reports.
Collaborator Contribution We have gained more visibility for the ISA work and now ISA-Tab is a formal format used by the Galaxy analysis toolkit for metabolomics applications.
Impact The ISA framework as the basis for the metadata standards used by this ELIXIR Metabolomics Community and the tools are embedded in the EBI MetaboLights databases, as well as in other international metabolomics resources.
Start Year 2017
 
Description FAIRsharing and Data Stewardship Wizard 
Organisation Czech Technical University in Prague
Country Czech Republic 
Sector Academic/University 
PI Contribution The Data Stewardship Wizard (DSW) is a tool for data management planning. Prof. Sansone's group runs FAIRsharing, a community-recognized curated, informative and educational resource that interlinks community standards to databases, repositories and data policies (by funders and policies). We have worked with the DSW team to surface the right level of information from FAIRsharing to the DSW users, via the respective tools' APIs.
Collaborator Contribution The DSW has accessed relevant FAIRsharing content and displaied for selection to the users, when they define a data management plan.
Impact The questioning in the Data Stewardship Wizard is modelled after the conversation a researcher could have with a data management expert; most questions are closed questions with a limited set of possible answers. Answers on standards and repositories are obtained from linked services, such as FAIRsharing, as illustrated in this figure: https://datascience.codata.org/articles/10.5334/dsj-2019-059/dsj-18-954-g1.png/?action=download
Start Year 2019
 
Description FAIRsharing and terms4FAIRskill initiative 
Organisation Dutch Techcentre for Life Sciences
Country Netherlands 
Sector Charity/Non Profit 
PI Contribution The terms4FAIRskills project aims to create a formalised terminology that describes the competencies, skills and knowledge associated with making and keeping data FAIR. When mature, this terminology will apply to a variety of use cases, including: - To assist with the creation and assessment of stewardship curricula; - To facilitate the annotation, discovery and evaluation of FAIR-enabling materials (e.g. training) and resources; - To enable the formalisation of job descriptions and CVs with recognised, structured competencies. Prof. Sansone and Dr. Peter McQuilton have co-founded the initiative and, with other members of the group, we provide ontology expertise and have built and mantain the OWL file.
Collaborator Contribution Each partner contribute use cases for the terminology and hands-on work to build the classification.
Impact The OWL version of the terminology, plus related files, are available at: https://github.com/terms4fairskills/FAIRterminology
Start Year 2019
 
Description FAIRsharing and terms4FAIRskill initiative 
Organisation ELIXIR
Department ELIXIR UK
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution The terms4FAIRskills project aims to create a formalised terminology that describes the competencies, skills and knowledge associated with making and keeping data FAIR. When mature, this terminology will apply to a variety of use cases, including: - To assist with the creation and assessment of stewardship curricula; - To facilitate the annotation, discovery and evaluation of FAIR-enabling materials (e.g. training) and resources; - To enable the formalisation of job descriptions and CVs with recognised, structured competencies. Prof. Sansone and Dr. Peter McQuilton have co-founded the initiative and, with other members of the group, we provide ontology expertise and have built and mantain the OWL file.
Collaborator Contribution Each partner contribute use cases for the terminology and hands-on work to build the classification.
Impact The OWL version of the terminology, plus related files, are available at: https://github.com/terms4fairskills/FAIRterminology
Start Year 2019
 
Description FAIRsharing and terms4FAIRskill initiative 
Organisation The Committee on Data for Science and Technology (CODATA)
Country United Kingdom 
Sector Private 
PI Contribution The terms4FAIRskills project aims to create a formalised terminology that describes the competencies, skills and knowledge associated with making and keeping data FAIR. When mature, this terminology will apply to a variety of use cases, including: - To assist with the creation and assessment of stewardship curricula; - To facilitate the annotation, discovery and evaluation of FAIR-enabling materials (e.g. training) and resources; - To enable the formalisation of job descriptions and CVs with recognised, structured competencies. Prof. Sansone and Dr. Peter McQuilton have co-founded the initiative and, with other members of the group, we provide ontology expertise and have built and mantain the OWL file.
Collaborator Contribution Each partner contribute use cases for the terminology and hands-on work to build the classification.
Impact The OWL version of the terminology, plus related files, are available at: https://github.com/terms4fairskills/FAIRterminology
Start Year 2019
 
Description FAIRsharing and terms4FAIRskill initiative 
Organisation University of Edinburgh
Department Digital Curation Centre (DCC)
Country United Kingdom 
Sector Academic/University 
PI Contribution The terms4FAIRskills project aims to create a formalised terminology that describes the competencies, skills and knowledge associated with making and keeping data FAIR. When mature, this terminology will apply to a variety of use cases, including: - To assist with the creation and assessment of stewardship curricula; - To facilitate the annotation, discovery and evaluation of FAIR-enabling materials (e.g. training) and resources; - To enable the formalisation of job descriptions and CVs with recognised, structured competencies. Prof. Sansone and Dr. Peter McQuilton have co-founded the initiative and, with other members of the group, we provide ontology expertise and have built and mantain the OWL file.
Collaborator Contribution Each partner contribute use cases for the terminology and hands-on work to build the classification.
Impact The OWL version of the terminology, plus related files, are available at: https://github.com/terms4fairskills/FAIRterminology
Start Year 2019
 
Description FAIRsharing and the Centre for Open Science 
Organisation Center for Open Science (COS)
Country United States 
Sector Private 
PI Contribution The Center for Open Science (COS, cos.io) is a non-profit technology company with a mission to increase the openness, integrity, and reproducibility of research. It works to achieve this mission through meta-scientific research to quantify the barriers to reproducibility, advocacy and outreach to stakeholder organizations to remove those barriers, summarized in the Transparency and Openness Promotion (TOP) guidelines (cos.io/top), and builds infrastructure to enable these solutions (osf.io). Based in Pro. Sansone group in Oxford, FAIRsharing (fairsharing.org) is a curated, informative and educational resource on data and metadata standards, inter-related to repositories and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resources more findable, more widely adopted and cited. In this context, the organizations are carrying out a joint project to increase the number and the clarity of journal and research funder policies that effectively incentivize data sharing, among other goals. The TOP Guidelines consist of eight specific standards that funder and publishers of scientific research can use to implement better research practices. The FAIRsharing registry exists to bring clarity and discoverability to existing data policies. By working together these two organizations will classify the recommendations these policies contain, to improve their definition, comparability and ultimately clarity of guidance to the users (authors and awardees). Initially, an exemplar set of policies, already in FAIRsharing, has been commonly curated and their compliance to the TOP Data Transparency standard assessed; a mechanism will be developed to display the level of compliance in FAIRsharing. Progressively, the work will expand to cover more policies; additional sorting and discovery features will be added to help users to find and compare policies.
Collaborator Contribution COS team has developed the TOP standard and calculated the score of these policies.
Impact A growing number of policies (from funders and journals: https://fairsharing.org/policies/) have a TOP Level Data Transparency score visible in their FAIRsharing record; for example here is the PLOS record in FAIRsharing https://fairsharing.org/FAIRsharing.t2exm showing a TOP Level Data Transparency: 2.
Start Year 2019
 
Description FAIRsharing, Datacite and major scholarly publishers 
Organisation Cambridge University Press
Country United Kingdom 
Sector Private 
PI Contribution DataCite is a leading global non-profit organization, that provides persistent identifiers (DOIs) with a focus on research data. DataCite's portfolio of services provide the means to create, find, cite, connect, and use research. Based in my group, FAIRsharing is a curated, informative and educational resource on data and metadata standards, inter-related to repositories and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resources more findable, more widely adopted and cited. Both organizations aim to advance and enable FAIR research data. This joint effort between DataCite and FAIRsharing is set to improve, in collaboration with several leading publishers, the criteria used by journal publishers for the recommendation of research data repositories for the benefit of the broader research community. Our contribution has been to bring together publishers (Cambridge University Press, eLife, Elsevier, EMBO Press, F1000, Oxford University Press's GigaScience, PLOS, Springer Nature's Scientific Data, Taylor and Francis, Hindawi, and Wiley) that were part of the FAIRsharing network. We have also lead the discussion that has resulted in the proposed criteria, and written the article and run a survey to collect community feedback.
Collaborator Contribution Datacite has assisted with the discussion and dissemination of the work.
Impact Pre-print article: https://doi.org/10.17605/OSF.IO/N9QJ7 Blog post from a some of the participating publishers: - eLife https://elifesciences.org/inside-elife/7b9ba7ef/elife-latest-criteria-for-data-repository-selection - Elsevier https://www.elsevier.com/connect/share-your-thoughts-to-make-data-sharing-simpler-and-more-efficient?sf224886680=1&utm_campaign=MCRED_CMRE_DataElsevier&sf224890780=1 - F1000 https://blog.f1000.com/2019/11/29/data-repository-selection-criteria-that-matter-request-for-comments/ - GigaScience http://gigasciencejournal.com/blog/fairsharing-data-repository-selection/ - Hindawi https://about.hindawi.com/blog/data-repository-selection-criteria-that-matter-request-for-comments/ - Wiley https://www.wiley.com/network/researchers/latest-content/data-repository-selection-criteria-that-matter-we-want-to-hear-from-you - PLOS https://blogs.plos.org/plos/2019/11/request-for-comments-on-data-repository-selection-criteria-that-matter/ Taylor & Francis https://librarianresources.taylorandfrancis.com/data-repository-selection-criteria-that-matter/ - Cambridge University Press https://www.cambridge.org/core/blog/2019/12/10/openresearch-selecting-a-data-repository-criteria-that-matter - Springer Nature https://researchdata.springernature.com/users/69696-varsha-khodiyar/posts/57690-data-repository-selection-request-for-comments
Start Year 2019
 
Description FAIRsharing, Datacite and major scholarly publishers 
Organisation Datacite
Sector Charity/Non Profit 
PI Contribution DataCite is a leading global non-profit organization, that provides persistent identifiers (DOIs) with a focus on research data. DataCite's portfolio of services provide the means to create, find, cite, connect, and use research. Based in my group, FAIRsharing is a curated, informative and educational resource on data and metadata standards, inter-related to repositories and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resources more findable, more widely adopted and cited. Both organizations aim to advance and enable FAIR research data. This joint effort between DataCite and FAIRsharing is set to improve, in collaboration with several leading publishers, the criteria used by journal publishers for the recommendation of research data repositories for the benefit of the broader research community. Our contribution has been to bring together publishers (Cambridge University Press, eLife, Elsevier, EMBO Press, F1000, Oxford University Press's GigaScience, PLOS, Springer Nature's Scientific Data, Taylor and Francis, Hindawi, and Wiley) that were part of the FAIRsharing network. We have also lead the discussion that has resulted in the proposed criteria, and written the article and run a survey to collect community feedback.
Collaborator Contribution Datacite has assisted with the discussion and dissemination of the work.
Impact Pre-print article: https://doi.org/10.17605/OSF.IO/N9QJ7 Blog post from a some of the participating publishers: - eLife https://elifesciences.org/inside-elife/7b9ba7ef/elife-latest-criteria-for-data-repository-selection - Elsevier https://www.elsevier.com/connect/share-your-thoughts-to-make-data-sharing-simpler-and-more-efficient?sf224886680=1&utm_campaign=MCRED_CMRE_DataElsevier&sf224890780=1 - F1000 https://blog.f1000.com/2019/11/29/data-repository-selection-criteria-that-matter-request-for-comments/ - GigaScience http://gigasciencejournal.com/blog/fairsharing-data-repository-selection/ - Hindawi https://about.hindawi.com/blog/data-repository-selection-criteria-that-matter-request-for-comments/ - Wiley https://www.wiley.com/network/researchers/latest-content/data-repository-selection-criteria-that-matter-we-want-to-hear-from-you - PLOS https://blogs.plos.org/plos/2019/11/request-for-comments-on-data-repository-selection-criteria-that-matter/ Taylor & Francis https://librarianresources.taylorandfrancis.com/data-repository-selection-criteria-that-matter/ - Cambridge University Press https://www.cambridge.org/core/blog/2019/12/10/openresearch-selecting-a-data-repository-criteria-that-matter - Springer Nature https://researchdata.springernature.com/users/69696-varsha-khodiyar/posts/57690-data-repository-selection-request-for-comments
Start Year 2019
 
Description FAIRsharing, Datacite and major scholarly publishers 
Organisation Elsevier
Country Netherlands 
Sector Private 
PI Contribution DataCite is a leading global non-profit organization, that provides persistent identifiers (DOIs) with a focus on research data. DataCite's portfolio of services provide the means to create, find, cite, connect, and use research. Based in my group, FAIRsharing is a curated, informative and educational resource on data and metadata standards, inter-related to repositories and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resources more findable, more widely adopted and cited. Both organizations aim to advance and enable FAIR research data. This joint effort between DataCite and FAIRsharing is set to improve, in collaboration with several leading publishers, the criteria used by journal publishers for the recommendation of research data repositories for the benefit of the broader research community. Our contribution has been to bring together publishers (Cambridge University Press, eLife, Elsevier, EMBO Press, F1000, Oxford University Press's GigaScience, PLOS, Springer Nature's Scientific Data, Taylor and Francis, Hindawi, and Wiley) that were part of the FAIRsharing network. We have also lead the discussion that has resulted in the proposed criteria, and written the article and run a survey to collect community feedback.
Collaborator Contribution Datacite has assisted with the discussion and dissemination of the work.
Impact Pre-print article: https://doi.org/10.17605/OSF.IO/N9QJ7 Blog post from a some of the participating publishers: - eLife https://elifesciences.org/inside-elife/7b9ba7ef/elife-latest-criteria-for-data-repository-selection - Elsevier https://www.elsevier.com/connect/share-your-thoughts-to-make-data-sharing-simpler-and-more-efficient?sf224886680=1&utm_campaign=MCRED_CMRE_DataElsevier&sf224890780=1 - F1000 https://blog.f1000.com/2019/11/29/data-repository-selection-criteria-that-matter-request-for-comments/ - GigaScience http://gigasciencejournal.com/blog/fairsharing-data-repository-selection/ - Hindawi https://about.hindawi.com/blog/data-repository-selection-criteria-that-matter-request-for-comments/ - Wiley https://www.wiley.com/network/researchers/latest-content/data-repository-selection-criteria-that-matter-we-want-to-hear-from-you - PLOS https://blogs.plos.org/plos/2019/11/request-for-comments-on-data-repository-selection-criteria-that-matter/ Taylor & Francis https://librarianresources.taylorandfrancis.com/data-repository-selection-criteria-that-matter/ - Cambridge University Press https://www.cambridge.org/core/blog/2019/12/10/openresearch-selecting-a-data-repository-criteria-that-matter - Springer Nature https://researchdata.springernature.com/users/69696-varsha-khodiyar/posts/57690-data-repository-selection-request-for-comments
Start Year 2019
 
Description FAIRsharing, Datacite and major scholarly publishers 
Organisation European Molecular Biology Organisation
Department EMBO Press
Country Germany 
Sector Academic/University 
PI Contribution DataCite is a leading global non-profit organization, that provides persistent identifiers (DOIs) with a focus on research data. DataCite's portfolio of services provide the means to create, find, cite, connect, and use research. Based in my group, FAIRsharing is a curated, informative and educational resource on data and metadata standards, inter-related to repositories and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resources more findable, more widely adopted and cited. Both organizations aim to advance and enable FAIR research data. This joint effort between DataCite and FAIRsharing is set to improve, in collaboration with several leading publishers, the criteria used by journal publishers for the recommendation of research data repositories for the benefit of the broader research community. Our contribution has been to bring together publishers (Cambridge University Press, eLife, Elsevier, EMBO Press, F1000, Oxford University Press's GigaScience, PLOS, Springer Nature's Scientific Data, Taylor and Francis, Hindawi, and Wiley) that were part of the FAIRsharing network. We have also lead the discussion that has resulted in the proposed criteria, and written the article and run a survey to collect community feedback.
Collaborator Contribution Datacite has assisted with the discussion and dissemination of the work.
Impact Pre-print article: https://doi.org/10.17605/OSF.IO/N9QJ7 Blog post from a some of the participating publishers: - eLife https://elifesciences.org/inside-elife/7b9ba7ef/elife-latest-criteria-for-data-repository-selection - Elsevier https://www.elsevier.com/connect/share-your-thoughts-to-make-data-sharing-simpler-and-more-efficient?sf224886680=1&utm_campaign=MCRED_CMRE_DataElsevier&sf224890780=1 - F1000 https://blog.f1000.com/2019/11/29/data-repository-selection-criteria-that-matter-request-for-comments/ - GigaScience http://gigasciencejournal.com/blog/fairsharing-data-repository-selection/ - Hindawi https://about.hindawi.com/blog/data-repository-selection-criteria-that-matter-request-for-comments/ - Wiley https://www.wiley.com/network/researchers/latest-content/data-repository-selection-criteria-that-matter-we-want-to-hear-from-you - PLOS https://blogs.plos.org/plos/2019/11/request-for-comments-on-data-repository-selection-criteria-that-matter/ Taylor & Francis https://librarianresources.taylorandfrancis.com/data-repository-selection-criteria-that-matter/ - Cambridge University Press https://www.cambridge.org/core/blog/2019/12/10/openresearch-selecting-a-data-repository-criteria-that-matter - Springer Nature https://researchdata.springernature.com/users/69696-varsha-khodiyar/posts/57690-data-repository-selection-request-for-comments
Start Year 2019
 
Description FAIRsharing, Datacite and major scholarly publishers 
Organisation Faculty of 1000
Department F1000 Research
Country United Kingdom 
Sector Private 
PI Contribution DataCite is a leading global non-profit organization, that provides persistent identifiers (DOIs) with a focus on research data. DataCite's portfolio of services provide the means to create, find, cite, connect, and use research. Based in my group, FAIRsharing is a curated, informative and educational resource on data and metadata standards, inter-related to repositories and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resources more findable, more widely adopted and cited. Both organizations aim to advance and enable FAIR research data. This joint effort between DataCite and FAIRsharing is set to improve, in collaboration with several leading publishers, the criteria used by journal publishers for the recommendation of research data repositories for the benefit of the broader research community. Our contribution has been to bring together publishers (Cambridge University Press, eLife, Elsevier, EMBO Press, F1000, Oxford University Press's GigaScience, PLOS, Springer Nature's Scientific Data, Taylor and Francis, Hindawi, and Wiley) that were part of the FAIRsharing network. We have also lead the discussion that has resulted in the proposed criteria, and written the article and run a survey to collect community feedback.
Collaborator Contribution Datacite has assisted with the discussion and dissemination of the work.
Impact Pre-print article: https://doi.org/10.17605/OSF.IO/N9QJ7 Blog post from a some of the participating publishers: - eLife https://elifesciences.org/inside-elife/7b9ba7ef/elife-latest-criteria-for-data-repository-selection - Elsevier https://www.elsevier.com/connect/share-your-thoughts-to-make-data-sharing-simpler-and-more-efficient?sf224886680=1&utm_campaign=MCRED_CMRE_DataElsevier&sf224890780=1 - F1000 https://blog.f1000.com/2019/11/29/data-repository-selection-criteria-that-matter-request-for-comments/ - GigaScience http://gigasciencejournal.com/blog/fairsharing-data-repository-selection/ - Hindawi https://about.hindawi.com/blog/data-repository-selection-criteria-that-matter-request-for-comments/ - Wiley https://www.wiley.com/network/researchers/latest-content/data-repository-selection-criteria-that-matter-we-want-to-hear-from-you - PLOS https://blogs.plos.org/plos/2019/11/request-for-comments-on-data-repository-selection-criteria-that-matter/ Taylor & Francis https://librarianresources.taylorandfrancis.com/data-repository-selection-criteria-that-matter/ - Cambridge University Press https://www.cambridge.org/core/blog/2019/12/10/openresearch-selecting-a-data-repository-criteria-that-matter - Springer Nature https://researchdata.springernature.com/users/69696-varsha-khodiyar/posts/57690-data-repository-selection-request-for-comments
Start Year 2019
 
Description FAIRsharing, Datacite and major scholarly publishers 
Organisation GigaScience
Country United Kingdom 
Sector Private 
PI Contribution DataCite is a leading global non-profit organization, that provides persistent identifiers (DOIs) with a focus on research data. DataCite's portfolio of services provide the means to create, find, cite, connect, and use research. Based in my group, FAIRsharing is a curated, informative and educational resource on data and metadata standards, inter-related to repositories and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resources more findable, more widely adopted and cited. Both organizations aim to advance and enable FAIR research data. This joint effort between DataCite and FAIRsharing is set to improve, in collaboration with several leading publishers, the criteria used by journal publishers for the recommendation of research data repositories for the benefit of the broader research community. Our contribution has been to bring together publishers (Cambridge University Press, eLife, Elsevier, EMBO Press, F1000, Oxford University Press's GigaScience, PLOS, Springer Nature's Scientific Data, Taylor and Francis, Hindawi, and Wiley) that were part of the FAIRsharing network. We have also lead the discussion that has resulted in the proposed criteria, and written the article and run a survey to collect community feedback.
Collaborator Contribution Datacite has assisted with the discussion and dissemination of the work.
Impact Pre-print article: https://doi.org/10.17605/OSF.IO/N9QJ7 Blog post from a some of the participating publishers: - eLife https://elifesciences.org/inside-elife/7b9ba7ef/elife-latest-criteria-for-data-repository-selection - Elsevier https://www.elsevier.com/connect/share-your-thoughts-to-make-data-sharing-simpler-and-more-efficient?sf224886680=1&utm_campaign=MCRED_CMRE_DataElsevier&sf224890780=1 - F1000 https://blog.f1000.com/2019/11/29/data-repository-selection-criteria-that-matter-request-for-comments/ - GigaScience http://gigasciencejournal.com/blog/fairsharing-data-repository-selection/ - Hindawi https://about.hindawi.com/blog/data-repository-selection-criteria-that-matter-request-for-comments/ - Wiley https://www.wiley.com/network/researchers/latest-content/data-repository-selection-criteria-that-matter-we-want-to-hear-from-you - PLOS https://blogs.plos.org/plos/2019/11/request-for-comments-on-data-repository-selection-criteria-that-matter/ Taylor & Francis https://librarianresources.taylorandfrancis.com/data-repository-selection-criteria-that-matter/ - Cambridge University Press https://www.cambridge.org/core/blog/2019/12/10/openresearch-selecting-a-data-repository-criteria-that-matter - Springer Nature https://researchdata.springernature.com/users/69696-varsha-khodiyar/posts/57690-data-repository-selection-request-for-comments
Start Year 2019
 
Description FAIRsharing, Datacite and major scholarly publishers 
Organisation Hindawi
Country Egypt 
Sector Private 
PI Contribution DataCite is a leading global non-profit organization, that provides persistent identifiers (DOIs) with a focus on research data. DataCite's portfolio of services provide the means to create, find, cite, connect, and use research. Based in my group, FAIRsharing is a curated, informative and educational resource on data and metadata standards, inter-related to repositories and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resources more findable, more widely adopted and cited. Both organizations aim to advance and enable FAIR research data. This joint effort between DataCite and FAIRsharing is set to improve, in collaboration with several leading publishers, the criteria used by journal publishers for the recommendation of research data repositories for the benefit of the broader research community. Our contribution has been to bring together publishers (Cambridge University Press, eLife, Elsevier, EMBO Press, F1000, Oxford University Press's GigaScience, PLOS, Springer Nature's Scientific Data, Taylor and Francis, Hindawi, and Wiley) that were part of the FAIRsharing network. We have also lead the discussion that has resulted in the proposed criteria, and written the article and run a survey to collect community feedback.
Collaborator Contribution Datacite has assisted with the discussion and dissemination of the work.
Impact Pre-print article: https://doi.org/10.17605/OSF.IO/N9QJ7 Blog post from a some of the participating publishers: - eLife https://elifesciences.org/inside-elife/7b9ba7ef/elife-latest-criteria-for-data-repository-selection - Elsevier https://www.elsevier.com/connect/share-your-thoughts-to-make-data-sharing-simpler-and-more-efficient?sf224886680=1&utm_campaign=MCRED_CMRE_DataElsevier&sf224890780=1 - F1000 https://blog.f1000.com/2019/11/29/data-repository-selection-criteria-that-matter-request-for-comments/ - GigaScience http://gigasciencejournal.com/blog/fairsharing-data-repository-selection/ - Hindawi https://about.hindawi.com/blog/data-repository-selection-criteria-that-matter-request-for-comments/ - Wiley https://www.wiley.com/network/researchers/latest-content/data-repository-selection-criteria-that-matter-we-want-to-hear-from-you - PLOS https://blogs.plos.org/plos/2019/11/request-for-comments-on-data-repository-selection-criteria-that-matter/ Taylor & Francis https://librarianresources.taylorandfrancis.com/data-repository-selection-criteria-that-matter/ - Cambridge University Press https://www.cambridge.org/core/blog/2019/12/10/openresearch-selecting-a-data-repository-criteria-that-matter - Springer Nature https://researchdata.springernature.com/users/69696-varsha-khodiyar/posts/57690-data-repository-selection-request-for-comments
Start Year 2019
 
Description FAIRsharing, Datacite and major scholarly publishers 
Organisation Springer Nature
Country Germany 
Sector Private 
PI Contribution DataCite is a leading global non-profit organization, that provides persistent identifiers (DOIs) with a focus on research data. DataCite's portfolio of services provide the means to create, find, cite, connect, and use research. Based in my group, FAIRsharing is a curated, informative and educational resource on data and metadata standards, inter-related to repositories and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resources more findable, more widely adopted and cited. Both organizations aim to advance and enable FAIR research data. This joint effort between DataCite and FAIRsharing is set to improve, in collaboration with several leading publishers, the criteria used by journal publishers for the recommendation of research data repositories for the benefit of the broader research community. Our contribution has been to bring together publishers (Cambridge University Press, eLife, Elsevier, EMBO Press, F1000, Oxford University Press's GigaScience, PLOS, Springer Nature's Scientific Data, Taylor and Francis, Hindawi, and Wiley) that were part of the FAIRsharing network. We have also lead the discussion that has resulted in the proposed criteria, and written the article and run a survey to collect community feedback.
Collaborator Contribution Datacite has assisted with the discussion and dissemination of the work.
Impact Pre-print article: https://doi.org/10.17605/OSF.IO/N9QJ7 Blog post from a some of the participating publishers: - eLife https://elifesciences.org/inside-elife/7b9ba7ef/elife-latest-criteria-for-data-repository-selection - Elsevier https://www.elsevier.com/connect/share-your-thoughts-to-make-data-sharing-simpler-and-more-efficient?sf224886680=1&utm_campaign=MCRED_CMRE_DataElsevier&sf224890780=1 - F1000 https://blog.f1000.com/2019/11/29/data-repository-selection-criteria-that-matter-request-for-comments/ - GigaScience http://gigasciencejournal.com/blog/fairsharing-data-repository-selection/ - Hindawi https://about.hindawi.com/blog/data-repository-selection-criteria-that-matter-request-for-comments/ - Wiley https://www.wiley.com/network/researchers/latest-content/data-repository-selection-criteria-that-matter-we-want-to-hear-from-you - PLOS https://blogs.plos.org/plos/2019/11/request-for-comments-on-data-repository-selection-criteria-that-matter/ Taylor & Francis https://librarianresources.taylorandfrancis.com/data-repository-selection-criteria-that-matter/ - Cambridge University Press https://www.cambridge.org/core/blog/2019/12/10/openresearch-selecting-a-data-repository-criteria-that-matter - Springer Nature https://researchdata.springernature.com/users/69696-varsha-khodiyar/posts/57690-data-repository-selection-request-for-comments
Start Year 2019
 
Description FAIRsharing, Datacite and major scholarly publishers 
Organisation Taylor & Francis Group
Country United Kingdom 
Sector Private 
PI Contribution DataCite is a leading global non-profit organization, that provides persistent identifiers (DOIs) with a focus on research data. DataCite's portfolio of services provide the means to create, find, cite, connect, and use research. Based in my group, FAIRsharing is a curated, informative and educational resource on data and metadata standards, inter-related to repositories and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resources more findable, more widely adopted and cited. Both organizations aim to advance and enable FAIR research data. This joint effort between DataCite and FAIRsharing is set to improve, in collaboration with several leading publishers, the criteria used by journal publishers for the recommendation of research data repositories for the benefit of the broader research community. Our contribution has been to bring together publishers (Cambridge University Press, eLife, Elsevier, EMBO Press, F1000, Oxford University Press's GigaScience, PLOS, Springer Nature's Scientific Data, Taylor and Francis, Hindawi, and Wiley) that were part of the FAIRsharing network. We have also lead the discussion that has resulted in the proposed criteria, and written the article and run a survey to collect community feedback.
Collaborator Contribution Datacite has assisted with the discussion and dissemination of the work.
Impact Pre-print article: https://doi.org/10.17605/OSF.IO/N9QJ7 Blog post from a some of the participating publishers: - eLife https://elifesciences.org/inside-elife/7b9ba7ef/elife-latest-criteria-for-data-repository-selection - Elsevier https://www.elsevier.com/connect/share-your-thoughts-to-make-data-sharing-simpler-and-more-efficient?sf224886680=1&utm_campaign=MCRED_CMRE_DataElsevier&sf224890780=1 - F1000 https://blog.f1000.com/2019/11/29/data-repository-selection-criteria-that-matter-request-for-comments/ - GigaScience http://gigasciencejournal.com/blog/fairsharing-data-repository-selection/ - Hindawi https://about.hindawi.com/blog/data-repository-selection-criteria-that-matter-request-for-comments/ - Wiley https://www.wiley.com/network/researchers/latest-content/data-repository-selection-criteria-that-matter-we-want-to-hear-from-you - PLOS https://blogs.plos.org/plos/2019/11/request-for-comments-on-data-repository-selection-criteria-that-matter/ Taylor & Francis https://librarianresources.taylorandfrancis.com/data-repository-selection-criteria-that-matter/ - Cambridge University Press https://www.cambridge.org/core/blog/2019/12/10/openresearch-selecting-a-data-repository-criteria-that-matter - Springer Nature https://researchdata.springernature.com/users/69696-varsha-khodiyar/posts/57690-data-repository-selection-request-for-comments
Start Year 2019
 
Description FAIRsharing, Datacite and major scholarly publishers 
Organisation University of California, Los Angeles (UCLA)
Department PLOS Medicine Journal
Country United States 
Sector Academic/University 
PI Contribution DataCite is a leading global non-profit organization, that provides persistent identifiers (DOIs) with a focus on research data. DataCite's portfolio of services provide the means to create, find, cite, connect, and use research. Based in my group, FAIRsharing is a curated, informative and educational resource on data and metadata standards, inter-related to repositories and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resources more findable, more widely adopted and cited. Both organizations aim to advance and enable FAIR research data. This joint effort between DataCite and FAIRsharing is set to improve, in collaboration with several leading publishers, the criteria used by journal publishers for the recommendation of research data repositories for the benefit of the broader research community. Our contribution has been to bring together publishers (Cambridge University Press, eLife, Elsevier, EMBO Press, F1000, Oxford University Press's GigaScience, PLOS, Springer Nature's Scientific Data, Taylor and Francis, Hindawi, and Wiley) that were part of the FAIRsharing network. We have also lead the discussion that has resulted in the proposed criteria, and written the article and run a survey to collect community feedback.
Collaborator Contribution Datacite has assisted with the discussion and dissemination of the work.
Impact Pre-print article: https://doi.org/10.17605/OSF.IO/N9QJ7 Blog post from a some of the participating publishers: - eLife https://elifesciences.org/inside-elife/7b9ba7ef/elife-latest-criteria-for-data-repository-selection - Elsevier https://www.elsevier.com/connect/share-your-thoughts-to-make-data-sharing-simpler-and-more-efficient?sf224886680=1&utm_campaign=MCRED_CMRE_DataElsevier&sf224890780=1 - F1000 https://blog.f1000.com/2019/11/29/data-repository-selection-criteria-that-matter-request-for-comments/ - GigaScience http://gigasciencejournal.com/blog/fairsharing-data-repository-selection/ - Hindawi https://about.hindawi.com/blog/data-repository-selection-criteria-that-matter-request-for-comments/ - Wiley https://www.wiley.com/network/researchers/latest-content/data-repository-selection-criteria-that-matter-we-want-to-hear-from-you - PLOS https://blogs.plos.org/plos/2019/11/request-for-comments-on-data-repository-selection-criteria-that-matter/ Taylor & Francis https://librarianresources.taylorandfrancis.com/data-repository-selection-criteria-that-matter/ - Cambridge University Press https://www.cambridge.org/core/blog/2019/12/10/openresearch-selecting-a-data-repository-criteria-that-matter - Springer Nature https://researchdata.springernature.com/users/69696-varsha-khodiyar/posts/57690-data-repository-selection-request-for-comments
Start Year 2019
 
Description FAIRsharing, Datacite and major scholarly publishers 
Organisation Wiley
Country United States 
Sector Private 
PI Contribution DataCite is a leading global non-profit organization, that provides persistent identifiers (DOIs) with a focus on research data. DataCite's portfolio of services provide the means to create, find, cite, connect, and use research. Based in my group, FAIRsharing is a curated, informative and educational resource on data and metadata standards, inter-related to repositories and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resources more findable, more widely adopted and cited. Both organizations aim to advance and enable FAIR research data. This joint effort between DataCite and FAIRsharing is set to improve, in collaboration with several leading publishers, the criteria used by journal publishers for the recommendation of research data repositories for the benefit of the broader research community. Our contribution has been to bring together publishers (Cambridge University Press, eLife, Elsevier, EMBO Press, F1000, Oxford University Press's GigaScience, PLOS, Springer Nature's Scientific Data, Taylor and Francis, Hindawi, and Wiley) that were part of the FAIRsharing network. We have also lead the discussion that has resulted in the proposed criteria, and written the article and run a survey to collect community feedback.
Collaborator Contribution Datacite has assisted with the discussion and dissemination of the work.
Impact Pre-print article: https://doi.org/10.17605/OSF.IO/N9QJ7 Blog post from a some of the participating publishers: - eLife https://elifesciences.org/inside-elife/7b9ba7ef/elife-latest-criteria-for-data-repository-selection - Elsevier https://www.elsevier.com/connect/share-your-thoughts-to-make-data-sharing-simpler-and-more-efficient?sf224886680=1&utm_campaign=MCRED_CMRE_DataElsevier&sf224890780=1 - F1000 https://blog.f1000.com/2019/11/29/data-repository-selection-criteria-that-matter-request-for-comments/ - GigaScience http://gigasciencejournal.com/blog/fairsharing-data-repository-selection/ - Hindawi https://about.hindawi.com/blog/data-repository-selection-criteria-that-matter-request-for-comments/ - Wiley https://www.wiley.com/network/researchers/latest-content/data-repository-selection-criteria-that-matter-we-want-to-hear-from-you - PLOS https://blogs.plos.org/plos/2019/11/request-for-comments-on-data-repository-selection-criteria-that-matter/ Taylor & Francis https://librarianresources.taylorandfrancis.com/data-repository-selection-criteria-that-matter/ - Cambridge University Press https://www.cambridge.org/core/blog/2019/12/10/openresearch-selecting-a-data-repository-criteria-that-matter - Springer Nature https://researchdata.springernature.com/users/69696-varsha-khodiyar/posts/57690-data-repository-selection-request-for-comments
Start Year 2019
 
Description FAIRsharing, Datacite and major scholarly publishers 
Organisation eLife
Sector Charity/Non Profit 
PI Contribution DataCite is a leading global non-profit organization, that provides persistent identifiers (DOIs) with a focus on research data. DataCite's portfolio of services provide the means to create, find, cite, connect, and use research. Based in my group, FAIRsharing is a curated, informative and educational resource on data and metadata standards, inter-related to repositories and data policies. FAIRsharing guides consumers to discover, select and use these resources with confidence, and producers to make their resources more findable, more widely adopted and cited. Both organizations aim to advance and enable FAIR research data. This joint effort between DataCite and FAIRsharing is set to improve, in collaboration with several leading publishers, the criteria used by journal publishers for the recommendation of research data repositories for the benefit of the broader research community. Our contribution has been to bring together publishers (Cambridge University Press, eLife, Elsevier, EMBO Press, F1000, Oxford University Press's GigaScience, PLOS, Springer Nature's Scientific Data, Taylor and Francis, Hindawi, and Wiley) that were part of the FAIRsharing network. We have also lead the discussion that has resulted in the proposed criteria, and written the article and run a survey to collect community feedback.
Collaborator Contribution Datacite has assisted with the discussion and dissemination of the work.
Impact Pre-print article: https://doi.org/10.17605/OSF.IO/N9QJ7 Blog post from a some of the participating publishers: - eLife https://elifesciences.org/inside-elife/7b9ba7ef/elife-latest-criteria-for-data-repository-selection - Elsevier https://www.elsevier.com/connect/share-your-thoughts-to-make-data-sharing-simpler-and-more-efficient?sf224886680=1&utm_campaign=MCRED_CMRE_DataElsevier&sf224890780=1 - F1000 https://blog.f1000.com/2019/11/29/data-repository-selection-criteria-that-matter-request-for-comments/ - GigaScience http://gigasciencejournal.com/blog/fairsharing-data-repository-selection/ - Hindawi https://about.hindawi.com/blog/data-repository-selection-criteria-that-matter-request-for-comments/ - Wiley https://www.wiley.com/network/researchers/latest-content/data-repository-selection-criteria-that-matter-we-want-to-hear-from-you - PLOS https://blogs.plos.org/plos/2019/11/request-for-comments-on-data-repository-selection-criteria-that-matter/ Taylor & Francis https://librarianresources.taylorandfrancis.com/data-repository-selection-criteria-that-matter/ - Cambridge University Press https://www.cambridge.org/core/blog/2019/12/10/openresearch-selecting-a-data-repository-criteria-that-matter - Springer Nature https://researchdata.springernature.com/users/69696-varsha-khodiyar/posts/57690-data-repository-selection-request-for-comments
Start Year 2019
 
Description ISA Commons 
Organisation ISA Commons
Sector Charity/Non Profit 
PI Contribution We have helped many users, service providers and other developers to implement one or more components of the ISA software suite at their site to fit their data needs.
Collaborator Contribution They have helped us to refine the ISA software suite, filling gaps and tuning it for certain data types.
Impact The ISA Commons is a growing ecosystem of institute-based (e.g. USA NASA GeneLab Data Repository) and global repositories (e.g. EMBL-EBI MetaboLights), as well as data-driven journals (e.g. Springer Nature Scientific Data) that use the ISA formats, and/or are powered by one or more component of the ISA software suite. But also grass-root standards groups that leverage on the ISA data model and formats. The sustainability and maintenance of the ISA data model, formats, and tools, is guided by the ISA Working Group.
Start Year 2010
 
Title Datascriptor 
Description From structured dataset to data article. Leveraging our experience and links with the communities, we are now designing an open-source web-based tool - part of an ecosystem of existing annotation and authoring systems - to help researchers to use community standards to describe their (meta)data at the source, and capitalize on their effort to accelerate the creation of a data article. The user will be guided to provide (semi)structured descriptions of the experimental design, and of the post-processed data, to generate, respectively, the Methods and a set of statements to populate the Results section of a manuscript. Datascriptor will work: (i) as a stand-alone tool - for anyone to use - implementing generic metadata models, such as W3C Data Catalog vocabulary; and (ii) as a component of the ISA Tools - for its user communities - implementing the ISA metadata model. To output short sentences from the (semi)structured input, we will evaluate a mixed data-to-text approach using template-based and neural-based (i.e. machine learning) methods. To further enrich the content of the manuscript, Datascriptor will connect to existing authoring systems, including Substance, Texture, Stenci.la and Manuscripts, and export the result in JATS format. Our plans also include an export as a DAR file and in LaTeX format. 
Type Of Technology Webtool/Application 
Year Produced 2019 
Open Source License? Yes  
Impact Work has just started, but to ensure continued impact in the stakeholder community, the Datascriptor User Advisory Board includes a core group of existing collaborators: Thomas Lemberger (EMBO Press), Scott Edmunds (GigaScience), Holly Murray ( F1000), Varsha Khodiyar (Springer Nature). 
 
Title ISA-API Python library 
Description Project name: ISA-API Project home page: http://github.com/ISA-tools/isa-api Operating system(s): Platform independent Programming language: Python 3 Other requirements: None License: CPAL-1.0 ISA-API, a Python library that supports the creation, editing, parsing, and validatiation of both ISA-Tab and ISA-JSON formats, using a common data model implemented as native Python objects. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact This provides users with a common interface and interoperable medium between the two ISA formats, as well as conversion to a set of other formats required for depositing data in public databases. 
 
Description Alan Turing - The Turing Way Book; London 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Turing Way is an online handbook - and global community - dedicated to fostering gold-standard reproducible research. It's a cultural movement with the potential to transform data science. A book dash is a one day collaborative event where selected contributors are invited to work with others to add to and improve the Turing Way book. I wrote a section on FAIR and FAIRsharing and my experience in research data management. My contribution is also featured in ATI's Impact Story on "Changing the culture of data science".
Year(s) Of Engagement Activity 2019
URL https://www.turing.ac.uk/research/impact-stories/changing-culture-data-science
 
Description Biohackathon; ELIXIR, Paris 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The team participated to several tracks, especially working on ISA for plant and metabolomics community, as well as for use in Galaxy, and the bioschema work. The work carried our continue to embed ISA and FAIRsharing into ELIXIR-driven infrastructure and activities.
Year(s) Of Engagement Activity 2018
URL https://www.elixir-europe.org/events/biohackathon-2018-paris
 
Description ELIXIR-UK AllHands meeting, Birmingham 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Showcasing latest work on FAIRsharing and ISA, as well as discussing how to best connect with other UK resources and those from other Nodes.
Year(s) Of Engagement Activity 2018
URL https://elixiruknode.org/event/elixir-uk-all-hands-2018/
 
Description FAIR Funder Implementation Vision; video 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact The 'FAIR made easy' is an animation that depicts the vision of the seven steps of the FAIR Funding. This vision was developed over time and after a series of meetings, bringing together several service providers to demonstrate a joint plan to bring the FAIR Funding cycle to life in a sustainable and scalable manner. Our FAIRsharing and ISA are part of this vision, as elements of the FAIR-enabling ecosystem.
Year(s) Of Engagement Activity 2019
URL https://www.go-fair.org/today/FAIR-funder/
 
Description FAIR in a nutshell; Harnessing FAIR Data event, London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Raised awareness in and around FAIR principles and practices, as well as participated at a panel discussion that highlighted the importance as well as the challenges around implementing FAIR data.
Year(s) Of Engagement Activity 2019
URL https://www.ses.ac.uk/event/harnessing-fair-data/
 
Description FAIR, ISA and FAIRsharing; MAQC Society, Riva del Garda 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The MAQC Society communicates, promotes, and advances reproducible science principles and quality control for analysis of the massive data generated from the existing and emerging technologies in solving biological, health, and medical problems. My talk and discussion that followed introduced the audience to the FAIR Principles, the ecosystem of tools and resources.
Year(s) Of Engagement Activity 2019
URL https://maqc2019.fbk.eu/
 
Description FAIR, ISA and FAIRsharing; Pharmas, San Antonio 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact The FDA-organized session focused on communicating, promoting, and advancing reproducible science principles and quality control for data generated from the existing and emerging technologies in solving biological, health, and medical problems. My talk and discussion that followed introduced the audience to the FAIR Principles, the ecosystem of tools and resources.
Year(s) Of Engagement Activity 2019
URL https://www.aaps.org/pharmsci
 
Description FAIRsharing Chemical Data; IUPAC workshop, Amsterdam 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Introducing FAIRsharing to a new audience and engaging with databases and standards creators in the chemistry domain.
Year(s) Of Engagement Activity 2018
URL https://iupac.org/event/supporting-fair-exchange-chemical-data-standards-development/
 
Description FAIRsharing and terms4FAIRskills at EOSC; Budapest 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This is the annual event where "Where the EOSC makers & shakers meet". I was invited to expert panels to give an introduction on the FAIRsharing growing update and the terms4FAIRskills initiative.
Year(s) Of Engagement Activity 2019
URL https://www.eoscsecretariat.eu/eosc-symposium
 
Description FAIRsharing; BOSC conference, Portland 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Introducing FAIRsharing to a new audience of databases and standards developers
Year(s) Of Engagement Activity 2018
URL https://gccbosc2018.sched.com/event/FEX7/b21-fairsharing-working-with-the-community-to-map-the-lands...
 
Description FAIRsharing; ELIXIR AllHands 2018, Berlin. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Helped to shape the role of FAIRsharing in the context of other ELIXIR FAIR-supporting resources.
Year(s) Of Engagement Activity 2018
URL https://www.elixir-europe.org/events/elixir-all-hands-2018
 
Description FAIRsharing; GO-FAIR meeting, Leiden. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Create a critical mass around FAIRsharing, discussed and launched an Implementation Network around making Standards, Repositories, and Policies FAIR, named FAIR StRePo: https://www.go-fair.org/implementation-networks/overview/fair-strepo
Year(s) Of Engagement Activity 2019
URL https://www.go-fair.org/implementation-networks/overview/
 
Description Fostering a FAIR research culture; Porto 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The workshop explored examples where successes have been realised and consider if these are extensible to other domains. This work will feed into recommendations being developed by the EU EOSC-funded FAIRsFAIR project (https://www.fairsfair.eu) to help improve FAIR policy and practice. I gave examples of what has and what has not worked in the life science community.
Year(s) Of Engagement Activity 2019
URL https://www.opensciencefair.eu/
 
Description My role in the FAIR ecosystem 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was nominated as one of the European Group of FAIR Champions (EGFC), which is a group of scientific experts and "doers" in the field of FAIR data. My role is to be an ambassador of FAIR by sharing FAIR implementation stories, enhancing synergies, contributing to training activities and webinars, and doing an effective cross fertilization with other communities, towards a broader engagement on FAIR. This short video is an example of my activity as an EGFC.
Year(s) Of Engagement Activity 2019
URL https://www.fairsfair.eu/videos
 
Description Poster presentation: ISAcreate and Galaxy; Galaxy conference, Portland 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact ISA-Tab format is now used by Galaxy tools; the discussion helped ensuring the uptake continue
Year(s) Of Engagement Activity 2018
URL https://gccbosc2018.sched.com/event/FEWs/g26-isacreate-a-galaxy-tool-for-prospective-data-management...
 
Description RDA FAIRsharing WG - overview of the work; IDW, Gaborone 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Overview and discussion of the RDA-Force FAIRsharing WG activities, especially the recommendations, to guide the users and producers of standards, databases and repositories on how to best select and describe these resources; and to guide funders and publishers on how to recommend them in data policies.
Year(s) Of Engagement Activity 2018
URL https://rd-alliance.org/group/fairsharing-registry-connecting-data-policies-standards-databases-wg/o...
 
Description RDA FAIRsharing WG - overview of the work; RDA, Berlin 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Overview and discussion of the RDA-Force FAIRsharing WG activities, especially the recommendations, to guide the users and producers of standards, databases and repositories on how to best select and describe these resources; and to guide funders and publishers on how to recommend them in data policies.
Year(s) Of Engagement Activity 2018
URL https://rd-alliance.org/group/fairsharing-registry-connecting-data-policies-standards-databases-wg/o...
 
Description RDA FAIRsharing WG; Helsinki 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Overview and discussion of the RDA-Force FAIRsharing WG activities, especially the recommendations, to guide the users and producers of standards, databases and repositories on how to best select and describe these resources; and to guide funders and publishers on how to recommend them in data policies.
Year(s) Of Engagement Activity 2019
URL https://rd-alliance.org/group/fairsharing-registry-connecting-data-policies-standards-databases-wg/o...
 
Description RDA FAIRsharing WG; Philadelphia 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Overview and discussion of the RDA-Force FAIRsharing WG activities, especially the recommendations, to guide the users and producers of standards, databases and repositories on how to best select and describe these resources; and to guide funders and publishers on how to recommend them in data policies.
Year(s) Of Engagement Activity 2019
URL https://rd-alliance.org/group/fairsharing-registry-connecting-data-policies-standards-databases-wg/o...
 
Description The layered cake of FAIR coordination: how many is too many? Blog post 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact With two colleagues I wrote a blog post to elaborate on the discussioin that followed a workshop on FAIR practices and efforts at the Open Science FAIR event. The blog has trigged lots of discussion and positive comments around the need to reduce the number of coordination activities. Coordination is also a necessary evil, but to be effective, a coordination effort has to be realistic and targeted at the right level.
Year(s) Of Engagement Activity 2019
URL http://blogs.nature.com/scientificdata/2019/10/22/the-layered-cake/