'Omics Data Sharing: the Investigation / Study / Assay (ISA) Infrastructure

Lead Research Organisation: University of Oxford
Department Name: Oxford e-Research Centre

Abstract

There is a pressing and recognized need in the biological domain for improved data sharing and unified access to data from a wide range of sources. The use of 'omics technologies (such as genomics, metagenomics, transcriptomics, proteomics and metabolomics) is now wide-spread and the rate at which these technologies generate data is revolutionizing the scientific landscape. This massive influx of data brings both unprecedented scientific opportunities and a range of challenges that must be met if these data, and the public investment in science that they represent, are to be fully exploited. While there are many obstacles to overcome if we are to realize large-scale multi-omic data sharing at the community level, solutions are now possible due to the activities of a range of grass-roots standardisation projects including the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) project (http://mibbi.org/) and the Open Biological Ontologies (OBO) Foundry (http://obofoundry.org/). We propose to make more widely available our 'omics data sharing software based on the 'Investigation / Study / Assay' (ISA) concept (http://isatab.sf.net). The ISA concept allows the description of any 'Investigation' comprising one or more 'Studies' in which biological samples have been studied using one or more 'Assays' (technologies). The ISA concept is supported by the MIBBI community and has been used to structure a universal file format, ISA-Tab. The ISA-Tab file format leverages biologists' familiarity with, and trust of spreadsheet-based input and manipulation of information. Descriptive experimental information (metadata) captured in ISA-Tab format is made compliant with MIBBI-registered standards (for transcriptomics, MIAME; for proteomics, MIAPE; and for genomics, MIGS/MIMS) using pre-defined extensions. ISA-Tab can be configured to hold additional fields allowing users to comply with emerging standards as well. The availability of this universal file format has enabled the creation of a set of tools and a database to hold data sets captured in it. The current pilot-stage ISA Infrastructure provides a complete solution for managing multi-omic metadata at the community level. A core aspect of the design of the ISA Infrastructure is its integral use of OBO Foundry ontologies to describe investigations, rendering data descriptions unambiguous and computationally accessible. In the course of this proposed project, we will extend the current ISA Infrastructure implementation and work with identified research communities and their bioinformatic service providers to set up 'ISA Networks' in the UK and around the globe, covering a wide range of data types. These portals will serve as 'one-stop shops' for the aggregation and display of relevant datasets at the community level. The metadata captured will support searching and data discovery across organisms, technologies and data types. The shared use of minimum information standards, ontologies and a single file format will support exchange of data between communities and the transfer of data to and from public repositories. At the international level, we will work closely with the MIBBI and OBO Foundry communities to further unify MIBBI checklists and OBO Foundry ontologies to support descriptions of multi-omic investigations. The development of the ISA Infrastructure must be consensus-driven and is therefore best developed under the auspices of an international working group. We will therefore formalise the collaboration between ISA Networks and work within the data standardisation community to increase linkages between currently separated groups by launching the BioSharing Consortium (http://biosharing.org).

Technical Summary

Despite the many obvious benefits of data sharing, unification of our global, invaluable, and now vast, biological data stores has proven elusive. Associated concerns over the inaccessibility of data, leading both to lost opportunities for discovery and unnecessary duplication of effort, is driving a focus on 'omics data sharing. In 2009, major international groups of researchers held workshops to promote improved data sharing of pre- and post-publication resources. Funders are also concerned as evidenced by the publication of data policies aimed at improving stewardship of billions of pounds of hard won research data, especially in the field of 'omics research. Obstacles include the long-standing issue of a lack of software solutions for supporting data sharing that suits the needs of data submitters and users alike. To overcome these challenges we have designed and developed the ISA infrastructure, the first pilot-stage freely available software suite for curating, aggregating and sharing multi-omics investigations. In this project we will complete the software suite and help our wide range of collaborators to deploy several ISA Networks environments to: (i) assist in the reporting and local management of experimental metadata, (ii) empower their user communities to uptake community-defined MIBBI-registered checklists, OBO ontologies and the ISA-Tab format and (iii) facilitate submission of metadata to international public repositories. We will also continue our consensus-building standards activities, mapping/matching concepts in MIBBI to those in OBO Foundry ontologies and make sure all are can be captured in ISA-Tab format and manipulated/displayed in the ISA Infrastructure. Lastly, under the large BioSharing Consortium umbrella, we will formalize linkages between wide range of communities; including MIBBI, OBO Foundry and the ISA Networks, as well as journals, funders, industry, databases, biocurators, and next-generation technology providers.

Planned Impact

See lead organisation form.

Publications

10 25 50

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Amann RI (2019) Consent insufficient for data release-Response. in Science (New York, N.Y.)

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Amann RI (2019) Toward unrestricted use of public genomic data. in Science (New York, N.Y.)

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Ashrafian H (2021) Metabolomics: The Stethoscope for the Twenty-First Century. in Medical principles and practice : international journal of the Kuwait University, Health Science Centre

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Baker NA (2013) Standardizing data. in Nature nanotechnology

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Bandrowski A (2016) The Ontology for Biomedical Investigations. in PloS one

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Batista D (2022) Machine actionable metadata models in Scientific Data

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Brandizi M (2012) graph2tab, a library to convert experimental workflow graphs into tabular formats. in Bioinformatics (Oxford, England)

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Brinkman RR (2010) Modeling biomedical experimental processes with OBI. in Journal of biomedical semantics

 
Description We have developed better ways to help users to:
o Collect and curate, following standards: describe the experimental steps using community-defined minimum reporting requirements and ontologies, where possible.
o Store and browse, locally or publicly: create your own repository to search and browse the experimental description and associated data, hosted openly or privately.
o Submit to public repositories: when required, reformat experiments for submission to supported public repositories (such as those at EBI) or directly export to those already using ISA formats (as as MetaboLights).
o Analyse with existing tools: upload experimental descriptions and associated data to a growing number of well-known analysis systems that ISA formats connect with.
o Release, reason and nanopublish: explore and reason over your experiments, open them to the linked data universe, or publish nano-statements of your discoveries.
o Publish data alongside your article: directly export your experiments to a new generation of data journals that are accepting submissions in ISA formats; this latest work is being enhanced by the new Datascriptor component
Exploitation Route A growing numbers of researchers, as well as (i) local, institute- based (in academia and industry), (ii) project, consortium-based, and (iii) global, international repositories, already use the tools: http://isacommons.org
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Pharmaceuticals and Medical Biotechnology,Other

URL http://www.isa-tools.org
 
Description We have and are still helping researchers to better manage their datasets at the source: http://isacommons.org A measure of the usage and community impact of the ISA framework is the number and the calibre of the (public and internal) resources powered by one or more component of the ISA framework; these encompass: (i) local, institute- based (in academia and industry), (ii) project, consortium-based, as well as (iii) global, international repositories listed. Exemplars are: the ISA-powered system of biology and space-related datasets by the National Aeronautics and Space Administration (NASA, USA)'s GeneLab team, and the ISA-Tab-Nano extension created by the Nanotechnology Group of the US NIH National Cancer Informatics Program for their community; this extension is now a formal standard.
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Pharmaceuticals and Medical Biotechnology,Other
Impact Types Policy & public services

 
Description Advised NPG Scientific Data journal on its data policy
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
Impact Increase in data publication and sharing via public, community-approved repositories
URL http://www.nature.com/sdata/data-policies
 
Description Advised Springer Nature on the data policy
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
URL http://www.springernature.com/gp/group/data-policy/
 
Description Co-authored a review commissioned by the NIH Big Data to Knowledge Initiative on policies and framework to support open data and interoperability standards
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
URL https://figshare.com/articles/New_draft_item/3795816/2
 
Description Co-authored a review commissioned by the Wellcome Trust focusing on interoperability standards for digital research outputs
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
URL https://figshare.com/articles/Review_Interoperability_standards/4055496
 
Description FAIRsharing, FAIR Cookbook and ISA resources are core to ELIXIR data management services
Geographic Reach Europe 
Policy Influence Type Influenced training of practitioners or researchers
URL https://elixir-europe.org/sites/default/files/documents/annual-report-2020.pdf
 
Description IMI Data Management and Standardization
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
URL https://www.etriks.org/standards-starter-pack/
 
Description (PrecisionTox) - Toward Precision Toxicology: New Approach Methodologies for Chemical Safety
Amount € 19,305,584 (EUR)
Funding ID 965406 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 02/2021 
End 01/2026
 
Description AgroServ
Amount € 15,000,000 (EUR)
Funding ID 101058020 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 09/2022 
End 08/2027
 
Description COpenPlantOmics (COPO): a Collaborative Bioinformatics Plant Science Platform
Amount £1,000,000 (GBP)
Funding ID BB/L024101/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2015 
End 12/2018
 
Description Common Fund Data Ecosystem https://nih-cfde.org
Amount £7,000,000 (GBP)
Funding ID 3OT3OD025459-01S3 
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 03/2019 
End 12/2020
 
Description EC - PHC-32-2014 - MultiMot
Amount € 100,000 (EUR)
Funding ID H2020-EU.3.1, 634107 
Organisation European Commission 
Department Horizon 2020
Sector Public
Country European Union (EU)
Start 08/2015 
End 07/2018
 
Description EC H2020 - INFRADEV-3-2015 - ELIXIR EXCELERATE
Amount € 240,000 (EUR)
Organisation European Commission 
Department Horizon 2020
Sector Public
Country European Union (EU)
Start 09/2015 
End 08/2019
 
Description EINFRA-2015-1 - PhenoMeNal
Amount € 600,000 (EUR)
Funding ID H2020-EU.1.4.1.3, 654241 
Organisation European Commission 
Department Horizon 2020
Sector Public
Country European Union (EU)
Start 09/2015 
End 08/2018
 
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 IMPRiND
Amount € 4,000,000 (EUR)
Funding ID IMI 116060 
Organisation European Commission 
Department Innovative Medicines Initiative (IMI)
Sector Public
Country Belgium
Start 01/2017 
End 12/2021
 
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 NIH Big Data to Knowledge Initiative - CEDAR
Amount $400,000 (USD)
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 07/2014 
End 06/2018
 
Description NIH Big Data to Knowledge Initiative - bioCADDIE
Amount $450,000 (USD)
Funding ID 1U24AI117966-0 
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 10/2014 
End 09/2017
 
Description NIH Data Commons: Cloud agnostic architecture to safely access, reuse indexed FAIR objects
Amount £51,200 (GBP)
Funding ID 1OT3OD025462-01 
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 10/2017 
End 09/2018
 
Description NIH Data Commons: Development and implementation plan for community supported FAIR guidelines and metrics
Amount £67,265 (GBP)
Funding ID 1OT3OD025467-01 
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 10/2017 
End 09/2018
 
Description NIH Data Commons: Facilitation center
Amount £61,385 (GBP)
Funding ID 1OT3OD025459-01 
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 10/2017 
End 09/2018
 
Description Sharing of metabolomics data and their analyses as Galaxy workflows through a UK-China collaboration
Amount £30,500 (GBP)
Funding ID BB/M027635/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2015 
End 10/2018
 
Description eTRIKS
Amount € 400,000 (EUR)
Funding ID IMI 115446 
Organisation European Commission 
Department Innovative Medicines Initiative (IMI)
Sector Public
Country Belgium
Start 07/2014 
End 06/2017
 
Title BioSharing 
Description Registry of standards and databases linked to data policies by funders and journals. 
Type Of Material Improvements to research infrastructure 
Year Produced 2011 
Provided To Others? Yes  
Impact Launched in 2011, the BioSharing portal (https://biosharing.org) of interrelated standards, databases, and policies has 53,741 users and is a resource of the ELIXIR UK Node and the ELIXIR Interoperability Platform. Endorsed by a community of 68 organizations, including publishers (embedded in the data policies of 600 Springer Nature's journals, also PloS, EMBO press, BMJ, F1000Research, BioMedCentral, Oxford University Press, Wellcome Trust Open Research), standardization groups, and research data management support initiatives and libraries (such as those at JISC, Stanford, Cambridge and the Oxford Universities). 
URL http://biosharing.org/
 
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 Continued improvements to the ISA toolkit: the new graphql interface and RDF representation of ISA. 
Description The open source ISA framework and tools help to manage an increasingly diverse set of life science, environmental and biomedical experiments that employing one or a combination of technologies. 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 two new components, graphql interface to query ISA documents and a RDF representation of ISA in obo, sdo or wikidata (as part of the Wellcome Trust award, 2018-2021), a collaborative project with the University of Cambridge's InterMine team. 
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 50 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. 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://github.com/ISA-tools/isa-api
 
Title ISA Toolkit new API 
Description ISA-API v0.14.2 is released, with the new features and fixes: graphql, json-ld/rdf, sql, IO optimization 
Type Of Material Improvements to research infrastructure 
Year Produced 2023 
Provided To Others? Yes  
Impact Better use of the ISA tools by orther developers. 
URL https://github.com/ISA-tools/isa-api/releases/tag/v0.14.2
 
Title ISA tools 
Description Tools to collect, annotate, store, share and publish datasets 
Type Of Material Improvements to research infrastructure 
Year Produced 2010 
Provided To Others? Yes  
Impact Running since 2007, the open source metadata reporting ISA software suite has a user base ranging from hundreds to thousands of users from diverse domains (http://isa-tools.org), and is a resource of the ELIXIR UK Node. Currently it is embedded in 27 public resources (institute-based, project/consortium-based or global repositories, including some based at EBI, in USA, Japan, China and Australia), supports two data-driven journals (Springer Nature Scientific Data, Oxford University Press GigaScience), and complements 9 internal data platforms (also at the FDA National Centre for Toxicological Resources and Janssen R&D)- http://www.isacommons.org. The extension of the ISA metadata representation format for nanotechnology applications became a formal ASTM standard in 2013. 
URL http://www.isa-tools.org
 
Title MIAPPE specification and tools 
Description Minimum Information About a Plant Phenotyping Experiment is an open, community driven project to harmonize data from plant phenotyping experiments. MIAPPE specification comprises both a conceptual checklist of metadata required to adequately describe a plant phenotyping experiment, and software to validate, store and disseminate MIAPPE-compliant data. 
Type Of Material Improvements to research infrastructure 
Year Produced 2017 
Provided To Others? Yes  
Impact MIAPPE is a logical standard - but there are specific implementations of tools designed to support its use and application, for example, in the ISA-tools framework. We are working with the developers of the Plant Breeding API (BRAPI) to ensure the compliance of BRAPI with the MIAPPE standard, and to coordinate future developments. 
URL http://www.miappe.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 BioInvestigation Index 
Description Database for storing and searching experimental metadata, one of the ISA tools components 
Type Of Material Database/Collection of data 
Year Produced 2010 
Provided To Others? Yes  
Impact There are several public, project-based and institutionally based databases that are powered by the BioInvestigation Index; these include the EBI MetaboLigths repositories and many others listed at: http://isacommons.org/ 
URL http://www.isa-tools.org/tools.html
 
Title Supporting data for "ISA API: An open platform for interoperable life science experimental metadata" 
Description The Investigation/Study/Assay (ISA) Metadata Framework is an established and widely used set of open-source community specifications and software tools for enabling discovery, exchange and publication of metadata from experiments in the life sciences. The original ISA software suite provided a set of user-facing Java tools for creating and manipulating the information structured in ISA-Tab - a now widely used tabular format. To make the ISA framework more accessible to machines and enable programmatic manipulation of experiment metadata, a JSON serialization ISA-JSON was developed. In this work, we present the ISA API, a Python library for the creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats by using a common data model engineered as Python object classes. We describe the ISA API feature set, early adopters and its growing user community. The ISA API provides users with rich programmatic metadata handling functionality to support automation, a common interface and an interoperable medium between the two ISA formats, as well as with other life science data formats required for depositing data in public databases. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Community use and impact is tracked via the ISA Commons, which currently has over 50 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. 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 http://gigadb.org/dataset/100907
 
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 ELIXIR Plant Use Case 
Organisation ELIXIR
Department ELIXIR UK
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution My team has contributed ISA-related work to the ELIXIR Plant Science use case, work and report.
Collaborator Contribution We have gained more visibility for the ISA work and COPO activities.
Impact ISA is used by the BRAPI and there is an ISA implementation of the MIAPPE specification.
Start Year 2016
 
Description ELIXIR Plant Use Case 
Organisation ELIXIR
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution My team has contributed ISA-related work to the ELIXIR Plant Science use case, work and report.
Collaborator Contribution We have gained more visibility for the ISA work and COPO activities.
Impact ISA is used by the BRAPI and there is an ISA implementation of the MIAPPE specification.
Start Year 2016
 
Description ELIXIR UK Node 
Organisation Earlham Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description ELIXIR UK Node 
Organisation Heriot-Watt University
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description ELIXIR UK Node 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description ELIXIR UK Node 
Organisation Newcastle University
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description ELIXIR UK Node 
Organisation Rothamsted Research
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description ELIXIR UK Node 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description ELIXIR UK Node 
Organisation University of Birmingham
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description ELIXIR UK Node 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description ELIXIR UK Node 
Organisation University of Dundee
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description ELIXIR UK Node 
Organisation University of Edinburgh
Department Edinburgh Genomics
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description ELIXIR UK Node 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description ELIXIR UK Node 
Organisation University of Liverpool
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description ELIXIR UK Node 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description ELIXIR UK Node 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution Help create the ELIXIR UK Node
Collaborator Contribution Contribute to the creation of the ELIXIR UK Node
Impact Creation of a virtual entity that represents UK strengths in bioinformatics and provides a route for UK bioinformatics resources to participate in, and benefit from, ELIXIR. The Node is currently being formalized.
Start Year 2012
 
Description Hanna Cwiek - 2 month visit : MIAPPE and ISA 
Organisation Polish Academy of Sciences
Department Institute of Plant Genetics
Country Poland 
Sector Academic/University 
PI Contribution Members of my team, namely Philippe Rocca-Serra and Alejandra Gonzalez-Beltran has assisted Hanna in her ISA-related work.
Collaborator Contribution Dr Hanna Cwiek from the Poznan Institute of Genetic Research in Poland (in Pawel Krajewski's team) visited my team to work on ISA and MIAPPE, helping to refine ISA tools relevant to plant science and COPO activities.
Impact Possible paper on the work done
Start Year 2017
 
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 Model and Serialization 
Description The original ISA-Tab specification was published as a Release Candidate document in 2008, documenting the initial work that forms the ISA framework, with a further update in 2009. Since then, we have done work on a new serialization in JSON, ISA-JSON, and abstracted out the data model from both the tabular and JSON formats. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact Serialisations implemented by several ISA components; the documentation also helps other users to implement ISA formats. 
URL http://isa-tools.org/2016/10/release-of-the-isa-specs/
 
Title ISA Python API 
Description The ISA API aims to provide software developers with a set of tools to help you easily and quickly build your own ISA objects, validate, and convert between serializations of ISA-formatted datasets and other formats/schemas (e.g. SRA schemas). The ISA API is published on PyPI as the isatools package. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact The vision for the ISA API is to provide a programming library that will become the core for all software tooling that supports the ISA framework. It enables the import of various data formats into an implementation of the ISA Abstract Model as Python objects, and export of ISA content from Python objects back to different serialization formats. 
URL http://isa-tools.org/2017/01/isa-api-milestone/
 
Title ISA software suite (built iteratively, component by component) 
Description The open source ISA framework and tools help to manage an increasingly diverse set of life science, environmental and biomedical experiments that employing one or a combination of technologies. Built around the 'Investigation' (the project context), 'Study' (a unit of research) and 'Assay' (analytical measurement) data model and serializations (tabular, JSON and RDF), the ISA framework helps you to provide rich description of the experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) so that the resulting data and discoveries are reproducible and reusable. 
Type Of Technology Software 
Year Produced 2010 
Open Source License? Yes  
Impact Growing number of users, as listed at http://isacommons.org; but also of co-developers have and are contributing to the collaborative enhancements. 
URL http://isa-tools.org/
 
Title ISA tooling for the metabolomics community 
Description A new set of ISA software tools have been developed out of the EU H2020 PhenoMeNal: Large-Scale Computing for Medical Metabolomics project (http://phenomenal-h2020.eu/home). The ISA team has been contributing to the project since 2015, and has been collaborating on the development of user-facing, cloud-based data management and processing infrastructure in the project. The PhenoMeNal software includes a new set of ISA-related Galaxy workflow tools, as well as native support for the ISA-Tab format in Galaxy. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact The tools work with the EBI MetaboLights database as well as with ISA-Tab studies uploaded directly into the Galaxy platform, and builds on the Python ISA-API. The Metabolights' use of ISA-API: Python-based REST service relying on the ISA-API https://github.com/EBI-Metabolights/MtblsWS-Py 
URL http://isa-tools.org/2018/03/isa-galaxy-developed-for-metabolomics/
 
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 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 CUDDEL closing workshop/hackathon, EBI 
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 Closing workshop of the CUDDEL grant, following up on issues outstanding from the 2017 Hong Kong workshop; discussion to explore the feasibility of making a follow up BBSRC Partnering application in the future.
Year(s) Of Engagement Activity 2018
URL https://github.com/ISA-tools/cuddel-mzml2isa-enhance
 
Description Data Sharing Hackathon - Hong Kong 
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 first ISA hackathon - Bring Your Own Data Party, hold at the BGI-GigaScience office in Hong Kong delivered a new ISA-Tab viewing component for web browsers, and the conversion of Metabolights ISA-Tab content to RDF and 5 experiments, accounting for nearly 750 samples worth of data being generated. On top of boosting the data in Metabolights and GigaScience's GigaDB, some of these outputs are currently being written up as Data Note articles and peer reviewed by the GigaScience editorial team. The work also led to sharing and refining curation guidelines. Finally, efforts to deliver an API supporting the programmatic creation of ISA-Tab documents were started.
Year(s) Of Engagement Activity 2014
URL http://gigasciencejournal.com/blog/aint-no-party-like-a-bring-your-own-data-party
 
Description Data Sharing Hackathon - Oxford 
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 Hack-the-Spec event, named "ISA as a FAIR research object" was hold in Oxford, with representatives from The Genome Analysis Centre (now Earlham), the EBI, Leiden, Manchester and Birmingham universities and the Hong Kong based BGI-funded GigaScience journal team. The work focused around: evolving ISA to enable FAIR (Findable, Accessible, Interoperable, Reusable) research objects; fixing ambiguities, missing structures and elements in ISA 1.0; enabling integration of standard identification schemes such as ORCID; redefining the spec to define the 'core' ISA elements and separating out domain specific 'extensions'; and specifying conventions, mechanisms, and best practices for developing extensions to this new 'ISA core'.
Year(s) Of Engagement Activity 2015
URL http://isa-tools.org/2015/07/investigation-study-assay-hacks-coffee-cakes
 
Description Data discovery - NIH workshop 
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 Prof. Sansone co-organized and chaired this NIH event to explore current capabilities, gaps and opportunities for global data search across the data ecosystem.
Year(s) Of Engagement Activity 2022
URL https://web.cvent.com/event/9eec8239-babb-4beb-a0fe-45945e00bc4e/websitePage:645d57e4-75eb-4769-b2c0...
 
Description Datascriptor hackathon - eLife Innovation Sprint 
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 Hackathon on the Datascriptor prototype, part of the ISA toolkit. Datascriptor aims to taking the pain out of beginning to write papers, making it easy to automatically generate the parts of a paper that can be easily scaffolded and incentivising reproducible papers by ensuring the scaffolds include well-structured data and metadata. During the online event the prototype was fleshed out by user testing with hands-on use cases.
Year(s) Of Engagement Activity 2020
URL https://sprint.elifesciences.org/data-paper-skeleton-tools-for-life-sciences/
 
Description ELIXIR-UK All Hands meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Showcasing latest work on FAIRsharing and and presentation by Dr. Rocca-Serra of the FAIR Cookbook, as well as discussing how to best connect with other UK resources and those from other Nodes.
Year(s) Of Engagement Activity 2021
URL https://elixir-europe.org/events/elixir-all-hands-2021
 
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 and FAIRsharing - Euroscience Open Forum 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Overview of FAIR and FAIRsharing, with focus on work done with and for publishers; followed by a panel and Q&A session on data sharing and its impact on scientific careers and their evaluation.
Year(s) Of Engagement Activity 2020
URL https://www.esof.eu/en/programme/programme-event-list-all-events/event-information/scientific-data-s...
 
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 ISA presentation to GARnet workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact David Johnson - in my team - gave a presentation on "Data Infrastructures to Foster Data Reuse" at a workshop on Integrating Large Data into Plant Science: From Big Data to Discovery hosted by GARnet (the UK network for Arabidopsis researchers) and Egenis (the Exeter Centre for the Study of the Life Sciences). The workshop was held at Dartington Hall in Devon, South West England, and was well attended by researchers from the plant and biological science community worldwide as well as representatives from industry from organisations such as Syngenta.
Year(s) Of Engagement Activity 2016
URL http://isa-tools.org/2016/07/plant-science-takes-a-focus-on-isa/
 
Description Metabolomics Data Sharing Hackathon - Hong Kong 
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 hackathon focussed on the computational pipelines and tools processing and analysing that metabolimics data was hold at the BGI GigaScience office in Hong Kong, with the EBI, the Universities of Birmingham, Manchester and Oxford, the Sainsbury Laboratory and the Genome Analysis Centre (now Earlham), and guests from Australia. This hackathon extends on the recently completed BBSRC award (BB/J020265/1) to the University of Oxford and BGI/GigaScience that kicked off the work around data sharing in metabolomics and omics, delivering two ISA-related events: the first in Hong Kong, 2014, and the second in Oxford, 2015.
Year(s) Of Engagement Activity 2017
URL http://gigasciencejournal.com/blog/cuddeling-up-to-metabolomics-in-hong-kong
 
Description Metadata and data standards, ISA and FAIRsharing - MAQC Society, Shanghai 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Plenary presentation on metadata and data standards, and FAIR principles from theory to practice with overview of exemplar activities. The use of FAIR to enable meaningful and intelligent data sharing and reuse is a hot topic of great interest to all stakeholders.
Year(s) Of Engagement Activity 2018
URL https://www.pmgenomics.ca/maqcsociety/meeting_feb_2018
 
Description Metadata for machine: the work of ISA and FAIRsharing; GO-FAIR workshop, Leiden 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Our team showcased our preliminary work done to make machine-actionable metadata from standards in FAIRsharing that can be used as templated for ISA and other annotation tools. The creation of machine-actionable metadata from standards is key to enable FAIR data and is a hot topic.
Year(s) Of Engagement Activity 2018
URL https://www.go-fair.org/resources/go-fair-workshop-series/metadata-for-machines-workshops/
 
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 NERC DataTree 
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 Undergraduate students
Results and Impact Video to introduce the basic concepts of the FAIR principles, FAIR data management and FAIRsharing. The target audience for Data Tree is NERC funded PhD students and early career researchers, however, Data Tree will be an openly available resource.
Year(s) Of Engagement Activity 2017
URL https://datatree.org.uk/
 
Description NLM Curation at Scale 
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 To foster discussion on the critical need for increased curation speed, scale, and reliability
Year(s) Of Engagement Activity 2022
URL https://www.nlm.nih.gov/curationworkshop2022/agenda.html
 
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; 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 Short introduction to data readiness and FAIR data to lay audience 
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 Media (as a channel to the public)
Results and Impact A 1.30 min video to present my group's work on data readiness to a lay audience.
Year(s) Of Engagement Activity 2019
URL https://www.research.ox.ac.uk/Article/2019-01-22-video-making-data-reusable
 
Description The ELIXIR Plant Use Case - BRAPI meeting 
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 Ensure the use of ISA formats in the BRAPI API, which is part of the ELIXIR Plant Use Case, and that will connect plant -related ELIXIR Node repositories. This will benefit the ISA-compliant COPO infrastructure, which is also part of the ELIXIR UK Node.
Year(s) Of Engagement Activity 2017
URL https://www.elixir-europe.org/use-cases/plant-sciences
 
Description The FAIR movement - Oxford Open Data Week 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact An update to the Oxford staff and students on developments in the UK, EU and internationally on FAIR-related activities and projects, as part of the Oxford Open Data Week.
Year(s) Of Engagement Activity 2020
URL https://talks.ox.ac.uk/talks/id/12039464-4d00-4951-bf42-2a8e0f185fa7/