Delivering ELIXIR-UK

Lead Research Organisation: University of Oxford
Department Name: Physiology Anatomy and Genetics

Abstract

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

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

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

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

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

Technical Summary

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

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

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

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

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

Planned Impact

For Academic Impact please see 'Academic Beneficiaries'.

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

Publications

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Related Projects

Project Reference Relationship Related To Start End Award Value
BB/L005069/1 02/06/2014 31/12/2015 £1,031,385
BB/L005069/2 Transfer BB/L005069/1 01/01/2016 31/05/2018 £547,648
 
Description ELIXIR UK set out to assess the current state of training in the UK that helps biological science researchers make use of the large, high-throughput datasets that are now being produced by modern laboratory methods such as next generation sequencing technologies. To do this, we have set up working parties to look at several different fields of life science research - with the purpose of surveying current training availability, gaps and training needs; and to develop a strategy to address the training needs of life scientists across academia and industry - both in the UK and wider into Europe.

To date, our sector-specific working groups have undertaken surveys and consultations - delivering comment, review and opinion on training provision and need. We have seen that there are training requirements due to emerging technical or funding priority areas, some arising due to novel opportunities across the boundaries of traditional scientific disciplines, or where there is a systematic gap in basic education/training which is becoming acute due to modern data-analysis requirements (specifically training in statistics).

ELIXIR UK is making results of this process available to the wider community, whilst developing a training development strategy focussed on 5 strategically important, priority training areas, in: Structural Bioinformatics, Clinical Genomics, Advanced Scientific Skills, Metabolomics, and Applied Genomics.

The next stages of the project will build on this ground work - supporting activities of our sector working groups and building capability and training specifically in our strategic priority areas. Continual liaison with Industry is key as well as with other stakeholders, both at national level and across the wider pan-European ELIXIR community.
Exploitation Route By making our survey and consultation results publically-available, and in making our processes, aims, objectives and working practices transparent; the wider community - both within the UK and across the pan-European ELIXIR partners - will be able to reflect on their own training needs and provision.

ELIXIR UK will be focussed on transitioning from identified gaps in training towards a comprehensive and current training portfolio available to the UK life science community, by using our network of subject experts to plug training gaps.

As we engage with local academic and industry partners, national stakeholders and European collaborators, we will be developing not only training materials to address the needs/gaps we have highlighted - but also metrics and guidelines, examples of best practice, and providing frameworks for working together that will enable widespread development and adoption of related training and approaches wherever needed.

By providing technical platforms and infrastructure to support the training effort, along with advice, expertise and resources to develop and support trainers we will build a wider community participating in training for the future - based on the principles and ethos of that developed by ELIXIR and ELIXIR UK.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

URL http://www.elixir-uk.org
 
Description When the aims of ELIXIR UK are realised - in terms of developing a comprehensive training provision and infrastructure in the UK, linked to the wider community in Europe - significant benefits be seen through the facilitation of better data access, use and research impact in the life science field. Although we are a not at a point in the project to see this yet - we are already beginning to see benefits arising from our collaborative and community-focussed approach. Many different institutes, funding bodies, professional societies, companies and industry bodies are reviewing training and skills gaps. As we work with those different groups we are finding areas of mutual interest/benefit, opportunities for collaboration - and also opportunities to reduce duplication of effort - and this sharing approach is leveraging greater value from the different investments (both financial and time) each of these groups represents. Openness and sharing of training and skills-related data, knowledge and expertise is beginning to change the post-doctoral training landscape, particularly with the industry we engage with starting to view training as part of the pre-competitive workspace. As we foster community and bring these traditionally separate groups together in thinking and planning for future development in training provision, we begin to have the opportunity to impact on earlier skills development, influencing higher education curricula at pre and post-graduate - to doctoral level. This will have much further reach and impact on training gaps in the future and bring sustainability to the efforts of producing a more skilled life science base in modern (and future) data-driven biology.
First Year Of Impact 2014
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
Impact Types Cultural,Economic,Policy & public services

 
Description FAIRsharing is one of the elements mentioned in the "Framework for Discipline-specific Research Data Management" report by Science Europe.
Geographic Reach Europe 
Policy Influence Type Influenced training of practitioners or researchers
URL https://www.scienceeurope.org/wp-content/uploads/2018/01/SE_Guidance_Document_RDMPs.pdf
 
Description FAIRsharing is one of the resources recommended by the EU EOSC "Turning FAIR into Reality" report.
Geographic Reach Europe 
Policy Influence Type Influenced training of practitioners or researchers
 
Description FAIRsharing is one of the resources recommended by the UK Jisc "FAIR in Practice report".
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
 
Description Input on skills needs for the development of the Association of the BioPharmaceutical Industry skills report (ELIXIR UK cited)
Geographic Reach National 
Policy Influence Type Participation in a national consultation
URL http://www.abpi.org.uk/our-work/library/industry/Documents/Skills_Gap_Industry.pdf
 
Description Input on skills needs for the development of the Science Industry Partnership strategy (ELIXIR UK cited)
Geographic Reach National 
Policy Influence Type Participation in a national consultation
URL http://www.scienceindustrypartnership.com/skills-strategy/
 
Description Input to Welsh Genomic Medicine Task Force - Developing a strategy for genomic and precision medicine in Wales
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
 
Description Support and input to the development of the European Metabolomics Training Coordination Group
Geographic Reach Europe 
Policy Influence Type Participation in a advisory committee
Impact EmTraG's mission is to harmonise metabolomics training across Europe in order to improve its scientific coverage, geographical reach, quality and impact, thereby empowering the next generation of analytical, computational and applied metabolomics scientists.
URL http://www.emtrag.eu/
 
Description BBSRC STARS
Amount £27,989 (GBP)
Funding ID BB/P022766/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start  
 
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-EOSC - EOSC-Life
Amount £23,745,978 (GBP)
Funding ID 824087 
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 03/2019 
End 02/2023
 
Description FAIRplus
Amount £3,996,150 (GBP)
Funding ID 802750 
Organisation European Commission 
Department Innovative Medicines Initiative (IMI)
Sector Public
Country Belgium
Start 01/2019 
End 01/2022
 
Description Horizon 2020 (INFRADEV3) award
Amount £502,372 (GBP)
Organisation European Commission 
Department Horizon 2020
Sector Public
Country European Union (EU)
Start 09/2015 
End 08/2019
 
Description ISA-InterMine: accelerating and rewarding data sharing
Amount £1,174,660 (GBP)
Funding ID 208381/A/17/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2018 
End 07/2021
 
Description The FAIRsharing service: supporting the research life-cycle
Amount £742,702 (GBP)
Funding ID 212930/Z/18/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2019 
End 07/2023
 
Title Continued improvements to the ISA toolkit 
Description Started in 2003 and first released in 2007, the ISA tools have been developed over time by the Oxford team and collaborators or directly contributed by partnering contributors, via the ISA Commons collaborative community. Short description of the developments and achievements of the resource over the last year: • Awarded Wellcome Trust funds (2018-2021), as collaborative project with the University of Cambridge's InterMine team to link the two resources and reward researchers for annotating and publish FAIR data; also, ISA is embedded in two ELIXIR Implementation Studies, on a Plant-focused data validation and on metabolomics. • With the uptake of ISA-Galaxy tools (https://github.com/ISA-tools/isatools-galaxy) and integration with the Galaxy Framework, ISA has struck a major milestone by showcasing how prospective data management can be done, demonstrating a full deposition workflow to Metabolights and creating training material (10.7490/f1000research.1115757.1). • Jupyter notebooks (https://github.com/ISA-tools/dtp-isa-exercises) have been developed as teaching material to showcase the use of ISA-API in various context to undergraduate and postgraduate courses on data readiness. 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? Yes  
Impact Community use and impact is tracked via the ISA Commons, which currently has over 40 international groups, projects, and organizations that use and contribute to the development of components of the ISA metadata tracking framework. Therefore, we can say that the ISA user base ranges from hundreds to thousands of researchers from increasingly diverse domains (ranging from -omics, cell-based research, biomedical nanotechnology, plant phenotyping, toxicology, biodiversity, metagenomics, stem cell research, system biology, neuroscience, microbial science and immunology), and goes beyond researchers, curators, others resource developers and service providers, to also include journals. For example, ISA is used by the University of Oxford' GigaScience and underpins Springer Nature's Scientific Data data journal, supporting intelligent data sharing and credit; ISA is used to describe the experiment and to provide browse and search functionality for Scientific Data's content (http://scientificdata.isa-explorer.org). The ISA framework is currently embedded in a number of UK, EC and NIH and pharma funded infrastructure and research projects; here are exemplars from the ELIXIR UK Node and other Nodes: o EMBL-EBI MetaboLights' new web-based submission relies on ISA-JSON format to build web component and on the ISA-API to validate, convert experiments represented in ISA objects. o BBSRC-funded COPO infrastructure relies on the ISA API, ISA-JSON serialization and on the ISA configurations to support plant-based experiment molecular profiling experiments; it also used the ISAconverter to deposit to the ENA database. o ELIXIR-UK Node partners, University of Birmingham and Imperial College London use ISA Galaxy Tools, ISA-API and ISA validator - as part of their work in the UK Phenome Centre - to collect data prospectively but also organise public deposition to repositories. o ELIXIR Plant Community's MIAPPE standards and BrAPI rely on availability of ISA parsers and validation tools in the context of data validation programs. 
URL http://isa-tools.org
 
Title 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
 
Description Connecting GOBLET and ELIXIR 
Organisation Global Organisation for Bioinformatics Learning, Education & Training
Country Netherlands 
Sector Public 
PI Contribution ELIXIR-UK brokered the formal partnership between ELIXIR (www.elixir-europe.org) and GOBLET (mygoblet.org/) to coordinate training and the training community across the European Life Sciences.
Collaborator Contribution ELIXIR-UK brokered the formal partnership between ELIXIR (www.elixir-europe.org) and GOBLET (mygoblet.org/) to coordinate training and the training community across the European Life Sciences.
Impact Training workshops e.g. https://www.elixir-europe.org/events/elixir-ukgoblet-training-workshop
Start Year 2015
 
Description Development of training in Genomic Medicine for Wales 
Organisation Bangor University
Department North Wales Organistion for Randomised Trials in Health
Country United Kingdom 
Sector Academic/University 
PI Contribution Dr Larcombe (ELIXIR UK training coordinator) has been working with Bangor University to develop an MSc programme in Genomic Medicine to support workforce development in Wales following the recent (2016) involvement of Wales with the 100,000 genomes project. Having had consultation input to the developing Welsh Assembly Government Genomics Task Force strategy, " A strategy for genomic and precision medicine in Wales", this partnership has begun to implement plans to offer an MSc programme for Wales similar to that offered through Health Education England for NHS and clinical-related staff in England
Collaborator Contribution Bangor University has committed School and College-level staff to the development of the MSc programme internally, as well as incorporating development of the NHS workforce in Wales in genomic technologies into their development strategy. The University is currently working towards validation of the course and once this is done, will actively handle recruitment of the first cohort - and the majority of the delivery of the course material.
Impact There are no outputs yet - the MSc programme is currently under validation at Bangor University with the intention of a September 2017 intake.
Start Year 2016
 
Description ELIXIR Interoperability Platform and FAIRsharing 
Organisation ELIXIR
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution FAIRsharing is part of the ELIXIR Recommended Interoperability Resources (RIRs) to facilitate interoperability and reusability of life science data and support the principles of FAIR data management.
Collaborator Contribution The ELIXIR Recommended Interoperability Resources have been selected by external panel of reviewers, based on the selection criteria published in the Call for RIR application, which measure how they facilitate scientific research and how they improve FAIRness of life science data.
Impact FAIRsharing is and will continue to be used by and further linked to other ELIXIR registries and services.
Start Year 2018
 
Description ELIXIR Interoperability Platform and ISA 
Organisation ELIXIR
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution ISA is part of the ELIXIR Recommended Interoperability Resources (RIRs) to facilitate interoperability and reusability of life science data and support the principles of FAIR data management.
Collaborator Contribution The ELIXIR Recommended Interoperability Resources have been selected by external panel of reviewers, based on the selection criteria published in the Call for RIR application, which measure how they facilitate scientific research and how they improve FAIRness of life science data.
Impact ISA is and will continue to be used by and further developed with ELIXIR communities, especially with Plant and Metabolomics use cases.
Start Year 2018
 
Description Established collaboration between ELIXIR(-UK) and Big-Data-To-Knowledge (BD2K) Training Consortium 
Organisation National Institutes of Health (NIH)
Department Big Data to Knowledge (BD2K)
Country United States 
Sector Public 
PI Contribution Involved in the establishment of a collaboration between ELIXIR and the USA Big-Data-To-Knowledge (BD2K) Training Consortium
Collaborator Contribution Involved in the establishment of a collaboration between ELIXIR and the USA Big-Data-To-Knowledge (BD2K) Training Consortium
Impact None as yet
Start Year 2015
 
Description Partnership with the Metabolomics Society on training needs 
Organisation The Metabolomics Society
Country United States 
Sector Charity/Non Profit 
PI Contribution We conducted an international survey to determine the training needs of the metabolomics community.
Collaborator Contribution The survey was conducted in association with the international Metabolomics Society (http://metabolomicssociety.org/). The Metabolomics Society was established to promote the growth of this relatively new scientific field, of which training early-career scientists and scientists who have not applied metabolomics previously is a core objective. ELIXIR-UK is the BBSRC/MRC/NERC funded UK node within the ELIXIR infrastructure in the European Union and focuses on bioinformatics training provision in partnership with other European ELIXIR Nodes. ELIXIR-UK has prioritized 5 critical areas of UK training need. Metabolomics is one of those priorities and this collaborative effort will be key to engaging the community and addressing the emerging skills gap. Our international survey had the objectives to determine the training courses currently available, areas where training is required and the delivery mechanisms preferred by the community. The results and recommendations were recently summarised in the journal Metabolomics and all results are available on the Metabolomics Society website (http://metabolomicssociety.org/publications/training-needs-in-metabolomics).
Impact The Birmingham National Metabolomics Training Centre. The launch of the centre and the survey results were additionally published in MetaboNews here: http://www.metabonews.ca/Dec2015/MetaboNews_Dec2015.htm#spotlight
Start Year 2015
 
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. 
 
Title TESS - ELIXIR Training Portal 
Description TeSS is ELIXIR's Training e-Support System, developed by ELIXIR-UK, for disseminating, discovering and packaging training resources, primarily by aggregating information from ELIXIR nodes, but also from various 3rd-party content providers. The team is based in Manchester and Oxford: Niall Beard (TeSS manager, University of Manchester); Milo Thurston (TeSS developer, Oxford e-Research Centre); Finn Bacall (TeSS developer, University of Manchester); Terri Atwood (TeSS co-investigator, University of Manchester); Carole Goble (TeSS co-investigator, University of Manchester); Susanna-Assunta Sansone (TeSS co-investigator, University of Oxford). 
Type Of Technology Webtool/Application 
Year Produced 2016 
Open Source License? Yes  
Impact New technologies are generating huge amounts of life-science data, which scientists need to transform into new discoveries. However, few researchers have all the right skills to take advantage of this sudden data bonanza. ELIXIR-UK is responding to this challenge by coordinating European initiatives to training research scientists in computing, statistics and bioinformatics. By plugging the skills gap, ELIXIR-UK aims to strengthen life sciences across Europe and set the agenda for future training needs. 
URL https://tess.elixir-europe.org/
 
Title The Statistics Training Signposting (StaTS) project portal 
Description The StaTS project portal has been produced to further the aims of the StaTS working group in widening access to, and improving availability of, introductory training and support in statistics for life scientists. This website includes statistics online support, linked resources from other projects such as ELIXIR TeSS - and will develop to become the online portal and resource for training materials developed as part of the BBSRC STARS award for face-to-face StaTS-related courses delivered by Cambridge University 
Type Of Technology Webtool/Application 
Year Produced 2016 
Impact The full functionality and promotion of this resource will coincide with the implementation of STARS-funded courses in 2017. 
URL http://www.statschoices.org.uk
 
Description BioSchemas workshop at ELIXIR-UK All-hands meeting, Birmingham (UK), October 2015 
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 Community Workshop kicked-off a new initiative to create a system for sharing information about events, traninig materials, people and organisations across all domains of life sciences.

This system will be based on a common format for describing life science events, training materials, organisation and people, using schema.org, an initiative to promote and maintain schemas for structured data on the internet.

The project is a collaboration between ELIXIR, Pistoia Alliance, GOBLET and BioSharing, and is open to anyone interested.
Year(s) Of Engagement Activity 2015
 
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 Biosoftware description using bio.tools and schema.org; NETTAB, Rome (IT), October 2016 
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 Workshop to discuss the development and implementation of bioschemas to describe software
Year(s) Of Engagement Activity 2016
 
Description ELIXIR BioSchemas Implementation study kick-off meeting, Hinxton (UK), March 2017 
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 ELIXIR Bioschemas project has 4 stages: planning, agreement, adoption and implementation. The topic of this first meeting is planning. Below you can find a preliminary list of objectives. Feel free to comment. We will reshape and improve the agenda within the next weeks so your feedback is very welcome.

Understand the objectives and the outcomes of the project and subprojects
Get an update of existing activities and related work
Agree on the requirements for each subproject
Define and assign responsibilities
Discuss how we will deliver expected outcomes
Discuss interdependencies within the project
Define the relationship among proposed data types
If necessary reshape proposal based on the outcome of this meeting
Year(s) Of Engagement Activity 2017
 
Description ELIXIR Training coordination meeting including software demo for TeSS; NETTAB Rome October 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Engaged in discussions on future plans for the ELIXIR Training Platform and presented the TeSS training platform
Year(s) Of Engagement Activity 2016
URL https://drive.google.com/file/d/0B-QlUcsdljZgVmlYbmhzZHpveUk/view
 
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 in a nutshell; Harnessing FAIR Data event, London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Raised awareness in and around FAIR principles and practices, as well as participated at a panel discussion that highlighted the importance as well as the challenges around implementing FAIR data.
Year(s) Of Engagement Activity 2019
URL https://www.ses.ac.uk/event/harnessing-fair-data/
 
Description FAIRsharing Chemical Data; IUPAC workshop, Amsterdam 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Introducing FAIRsharing to a new audience and engaging with databases and standards creators in the chemistry domain.
Year(s) Of Engagement Activity 2018
URL https://iupac.org/event/supporting-fair-exchange-chemical-data-standards-development/
 
Description FAIRsharing; BOSC conference, Portland 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Introducing FAIRsharing to a new audience of databases and standards developers
Year(s) Of Engagement Activity 2018
URL https://gccbosc2018.sched.com/event/FEX7/b21-fairsharing-working-with-the-community-to-map-the-lands...
 
Description FAIRsharing; ELIXIR AllHands 2018, Berlin. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Helped to shape the role of FAIRsharing in the context of other ELIXIR FAIR-supporting resources.
Year(s) Of Engagement Activity 2018
URL https://www.elixir-europe.org/events/elixir-all-hands-2018
 
Description FAIRsharing; GO-FAIR meeting, Leiden. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Create a critical mass around FAIRsharing, discussed and launched an Implementation Network around making Standards, Repositories, and Policies FAIR, named FAIR StRePo: https://www.go-fair.org/implementation-networks/overview/fair-strepo
Year(s) Of Engagement Activity 2019
URL https://www.go-fair.org/implementation-networks/overview/
 
Description 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 Poster presentation, ECCB 2016, The Hague: Bioschemas: structured data for life science using schema.org 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation, "Bioschemas: structured data for life science using schema.org", to disseminate information about the Bioschemas initiative to the wider bioinformatics and computational biology research community, at ISMB 2016, 8-12 July, Florida (US).
Year(s) Of Engagement Activity 2016
URL https://f1000research.com/posters/5-2296
 
Description Poster presentation, ECCB 2016, The Hague: TeSS - The Life Science Training Portal 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation, "TeSS - The Life Science Training Portal", to disseminate latest progress with TeSS to the wider bioinformatics and computational biology research community, at ECCB 2016, 3-7 September, The Hague (NL).
Year(s) Of Engagement Activity 2016
URL https://f1000research.com/posters/7-250
 
Description Poster presentation, ELIXIR AllHands 2016, Barcelona: ELIXIR-UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation, "ELIXIR-UK", to inform the ELIXIR community about the work of ELIXIR-UK, at ELIXIR AllHands 2016, 8-9 March, Barcelona (ES).
Year(s) Of Engagement Activity 2016
URL https://f1000research.com/posters/5-346
 
Description Poster presentation, ELIXIR AllHands 2016, Barcelona: TeSS - Training Portal 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation, "TeSS - Training Portal", to disseminate latest progress with TeSS to the ELIXIR community, at ELIXIR AllHands 2016, 8-9 March, Barcelona (ES).
Year(s) Of Engagement Activity 2016
 
Description Poster presentation, ISMB 2016, Florida: TeSS - Training Portal 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation, "TeSS - Training Portal", to disseminate information about TeSS to the wider bioinformatics and computational biology research community, at ISMB 2016, 8-12 July, Florida (US).
Year(s) Of Engagement Activity 2016
URL https://f1000research.com/posters/5-1762
 
Description Poster presentation, ISMB/ECCB 2015, Dublin: ELIXIR-UK TeSS Training Portal 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation, "ELIXIR-UK TeSS Training Portal", to disseminate latest progress with TeSS to the wider bioinformatics and computational biology research community, at ISMB 2015, 10-14 July, Dublin (IE).
Year(s) Of Engagement Activity 2015
URL https://f1000research.com/posters/4-518
 
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 Presentation at ELIXIR 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 Presentation on progress of the TeSS Training e-Support System
Year(s) Of Engagement Activity 2016
URL https://www.elixir-europe.org/events/elixir-all-hands-2016
 
Description RDA FAIRsharing WG - overview of the work; IDW, Gaborone 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Overview and discussion of the RDA-Force FAIRsharing WG activities, especially the recommendations, to guide the users and producers of standards, databases and repositories on how to best select and describe these resources; and to guide funders and publishers on how to recommend them in data policies.
Year(s) Of Engagement Activity 2018
URL https://rd-alliance.org/group/fairsharing-registry-connecting-data-policies-standards-databases-wg/o...
 
Description RDA FAIRsharing WG - overview of the work; RDA, Berlin 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Overview and discussion of the RDA-Force FAIRsharing WG activities, especially the recommendations, to guide the users and producers of standards, databases and repositories on how to best select and describe these resources; and to guide funders and publishers on how to recommend them in data policies.
Year(s) Of Engagement Activity 2018
URL https://rd-alliance.org/group/fairsharing-registry-connecting-data-policies-standards-databases-wg/o...
 
Description TeSS - The Life Science Training Portal 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presenting the TeSS training portal at the international ECCB (European Conference on Computational Biology) conference, The Hague (NL), September 2016;
Year(s) Of Engagement Activity 2016
URL https://f1000research.com/posters/5-1762
 
Description TeSS Presentation at ELIXIR-UK All hands meeting, Rothamsted (UK), November 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation of the TeSS training platform to other participants in ELIXIR-UK
Year(s) Of Engagement Activity 2016
 
Description TeSS: ELIXIR Training Portal for Life Sciences 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presented at ISMB (Intelligent Systems for Molecular Biology) conference in Orlando (USA), July 2016

TeSS (life sciences training portal, https://tess.elixir-uk.org) aggregates links to disparate training events and materials, scattered across ELIXIR Nodes and other training portals, and makes them centrally discoverable.

Aggregation is effected automatically, via custom-built scripts that scrape training metadata descriptors (title, description, prerequisites, goals, categories, keywords, contributors, audience, etc.) from participating websites. This task is made difficult by the lack of consistency in training pages' structures and lack of agreement on training metadata descriptors.

In the past year, we helped initiate the BioSchemas Working Group, which aims to reach consensus among life-science communities in defining metadata standards for describing training resources. BioSchemas are extending specifications from Schema.org, reusing existing metadata standards. This is in line with Google and other major search engines, which already utilise Schema.org's schemas for search optimisation.

We have also started to actively promote the use of 'bioschemas' among content providers. A first follower was GOBLET, whose training portal has embedded the new BioSchemas-proposed mark-up within their training pages. Ultimately, our goal is for all content providers to adhere to the agreed schemas, making the job of search engines more efficient, and scrapers redundant.

Our next immediate task is to increase the content from ELIXIR Nodes, and to further promote take-up of the evolving 'bioschemas'. At the same time, to make further efficiency gains and broaden the scope of the resource, we are partnering with the emerging US BD2K's Training Coordination Centre, which has a similar remit to that of TeSS, sharing expertise, training resources and technical know-how.
Year(s) Of Engagement Activity 2016
URL https://www.iscb.org/cms_addon/conferences/ismb2016/posterlist.php
 
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