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

Lead Research Organisation: University of Manchester
Department Name: Computer Science

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.
 
Description The ISA 'Omics Data Sharing: the Investigation / Study / Assay (ISA) is an Infrastructure project (http://isa-tools.org). The ISA metadata tracking 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) general-purpose Tabular format, the ISA tools 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.

The project
- completed the core development of the ISA infrastructure:
Several new components of the modular ISA infrastructure have been delivered, others have been extended and new, enhanced versions have been released by the ISA Operational Team in Oxford.

The software components, meet the requirements of the Software Sustainability Institute. Several components have also been through and passed the User Acceptance Testing carried out by industrial users and collaborators at Janssen Research; Development in Belgium, The Novartis Institutes for BioMedical Research in USA, but also at the FDA's Center for Bioinformatics at the National Center for Toxicological Research in USA In addition, the ISA infrastructure as also been adopted by Eagle Genomics Ltd, a bioinformatics consulting company in Cambridge, UK, and they have signed a Memorandum of Understanding with the ISA Operational Team and the University of Oxford.

- set up a constellation of ISA networks - local environments for curating, aggregating and sharing multi-omics investigations. Another website (http://www.isacommons.org) has been set up to provide at a glance view of the community we have been working with and for, named the ISA Commons. These groups are the ISA user base. The majority of these groups are service providers running ISA-powered systems that are (i) local, institute-based, (ii) project, consortium-based, or (iii) global, international repositories.

- supported the 'integration' of reporting standards through continued consensus-building activities.
The ISA Operational Team has also developed the BioSharing prototype catalogue (http://biosharing.org), extending the work of the MIBBI portal (a predecessor of BioSharing), to map the landscape of community standards (minimum reporting requirements, terminologies and exchange formats), databases and policies. The initial work to collect the descriptions of key databases has been done in collaboration with Oxford University Press' NAR Database and DATABASE journals, and with the support of the International Society of Biocuration.
Launched in 2011, the BioSharing prototype catalogue has registered a total of approx 541 standards (66 minimum reporting requirements, 329 terminologies, 145 exchange formats), 18 data sharing policies, and 618 databases. The BioSharing website has 30,000 visitors, its twitter account approx 500 followers, and a growing community of 40 communities and prospective users groups (publishers, standard groups, service providers, data scientists associations and research consortia), including Nature Publishing Group, BioMedCentral, Genomics Standards Consortium, International Society of Biocuration, Proteomics Standards Initiative, Science Commons, Digital Curation Centre, DataCite, SEEK and the industry-driven Pistoia Alliance. Each of these groups serves hundreds to thousands of researchers in diverse life science domains and attests to the widespread interest.
BioSharing is part of several NIH BD2K Centres and is nominated as a service of the EU RI ELIXIR.
Exploitation Route Launched in 2011, the BioSharing prototype catalogue has registered a total of approx 541 standards (66 minimum reporting requirements, 329 terminologies, 145 exchange formats), 18 data sharing policies, and 618 databases. The BioSharing website has 30,000 visitors, its twitter account approx 500 followers, and a growing community of 40 communities and prospective users groups (publishers, standard groups, service providers, data scientists associations and research consortia), including Nature Publishing Group, BioMedCentral, Genomics Standards Consortium, International Society of Biocuration, Proteomics Standards Initiative, Science Commons, Digital Curation Centre, DataCite, SEEK and the industry-driven Pistoia Alliance. Each of these groups serves hundreds to thousands of researchers in diverse life science domains and attests to the widespread interest.

We know that the user bases of the groups within the ISA Commons range from hundreds to thousands of researchers in an increasingly diverse set of life, natural and biomedical sciences. However, providing an exact number of users for each ISA-powered instance is impossible. For example, the ISA-Tab compliant FAIRDOMHub Commons resource for Systems Biology projects serves over 50 EU projects and over 700 researchers; the ISA-enabled SEEK platform on which FAIRDOMHub is based is now deployed on 30 further sites. Similarly, the newly established public MetaboLights at EBI (fully powered by the ISA tools) is set to become the central repositories for all metabolomics-based datasets, also in the context of ELIXIR. Furthermore, emerging data publication platforms using ISA-Tab, such as GigaScience (by BioMedCentral and BGI) and Scientific Data (by Nature Publishing Group), are also set to contribute to the wider uptake of the format and of several of the software components. A first example is the agreement announced between Scientific Data and the Global Biodiversity Information Facility (GBIF) to help users of GBIF Integrated Publishing Toolkit submit data in ISA-Tab to the Nature Publishing Group platform. At this stage, we can safely estimate that collectively there are over 10,000 users, associated to the different ISA-powered instances; the number is expected to grow.
Sectors Agriculture, Food and Drink,Chemicals,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology
URL http://www.isa-tools.org/
 
Description The Manchester part of the project was very small - very modest PI support only - and was focused on (a) advising on and promoting the ISA approach; (b) the ISA Model; and (c) implementing ISA into other tools. Manchester exceeded well beyond their remit by incorporating ISA into the widely used SEEK4Science Systems Biology Model and Data Management platform (http://www.seek4science.org) - an infrastructure developed in other BBSRC grants (BB/G010218/1 and BB/1004637/1) to support SysBio projects - and the RightField (http://www.rightfield.org.uk) Microsoft Excel-based metadata management software, that is a sister to the ISA-Infrastructure Ontomaton and ISACollector software components. Consequently, the 1000 or so scientists that use a SEEK data and model management system built using the SEEK4Science platform / RightField are automatically using ISA model, methodology and infrastructure. The impact of ISA is profound. It is emerging as the de facto standard for organising life science experimental data, adopted by publishers (Nature Publishing Group Scientific Data, GigaScience etc) and international data archives (PRIDE, Metabolight etc.
First Year Of Impact 2007
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Economic
 
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 (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 EU FP7 ESFRI ISBE Infrastructure for Systems Biology Europe
Amount € 350,000 (EUR)
Funding ID 312455 
Organisation European Commission 
Department Seventh Framework Programme (FP7)
Sector Public
Country European Union (EU)
Start 08/2012 
End 09/2015
 
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
 
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 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 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 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 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 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 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 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 ISA Commons 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach International
Primary Audience Participants in your research or patient groups
Results and Impact The ISA Commons (www.isacommons,org) is a growing community that uses the ISA metadata tracking framework to facilitate standards-compliant collection, curation, management and reuse of datasets in an increasingly diverse set of life science domains. The ISA Commons represents more than 50 collaborators at over 30 scientific organizations around the globe with a growing ecosystem of public and internal resources that use the ISA-Tab file format, and/or is powered by one or more component of the ISA software suite. The ISA Commons includes groups at EBI, University of Manchester, Harvard, FDA-NCTR, BGI and The Novartis Institutes for BioMedical Research. Web site and international press release, jointly between Oxford and Harvard with BBSRC.

no actual impacts realised to date
Year(s) Of Engagement Activity 2012
URL http://www.isacommons,org
 
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 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 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/