Interoperability services

Name Description ELIXIR Node
ELIXIR Switzerland
ELIXIR UK
ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI

Our aim is to extend myFAIR Analysis into a cloud based service that can be executed using the advanced INDIGO PaaS services on-top of any ELIXIR Compute Platform cloud resource.  This approach will enable the advanced features provided by INDIGO to be made accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. The utility of this myFAIR cloud will be demonstrated using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA), and building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis.

Impact of the Study: 

  • Extend myFAIR Analysis into a cloud based service, executed using advanced INDIGO PaaS services on-top of any ECP cloud resource.
  • Enable INDIGO features to be accessible to the whole of ELIXIR by porting them on the standard ECP cloud resource. 
  • Demonstrate myFAIR cloud using existing validated test case scenarios (e.g. Mothur-SOP and/or EGA). 
  • Building towards providing myFAIR Analysis as a research service CLOUD (myFAIR CLOUD Analysis) supporting single/multi-user and single/multi-center for FAIR data management and analysis.
 ELIXIR Netherlands, ELIXIR Italy, EMBL-EBI

The scope of this task is to better align the Data and the Interoperability Platforms’ activities with the
Communities’ needs, via the creation of a FAIR Services Architecture Framework and the definition of
“interoperability stories” demonstrating impact, benefits and actions. Via this framework, the
Interoperability Platform aims to deliver:

  1. An expanded set of Recommended Interoperability Resources (RIRs), FAIRification services and strategies, also connected to the Core Data Resources (CDRs), Core Deposition Database (CDDs) and informed by the user communities more closely connected to the services, and supplied by the Nodes.
  2. A flow of products and best practice, and a series of experts able to answer interoperability queries and showcase exemplar solutions via applied use cases.
  3. A focus on and processes for putting ELIXIR’s FAIR house in order - with clear recommendations for our EIP flagship services ‘in action’; ensuring reuse of data and resources.
  4. A set of interoperability recommended licences, best practice cases, registries and products for interaction with other infrastructure and projects e.g. RDA, EOSC, highlighting EIP’s and ELIXIR’s activities
  5. Alignment with and support of, relevant emerging resources from ELIXIR-affiliated projects, which also support the flow of the data from instrument to services and deposition databases and data analysis workflows.
 EMBL-EBI, ELIXIR UK, ELIXIR Belgium, ELIXIR Greece, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway

A significant amount of work of the ELIXIR Interoperability Platform (EIP) is the dissemination of interoperability know-how, best practices, and use case examples, as well as the availability and applicability of resources for FAIR services in general and for interoperability in particular.

A systematic, sustainable approach to gathering and disseminating the collective knowledge of the Platform members and the outcomes of ELIXIR-related projects is needed, both internally to serve ELIXIR members and Nodes, and externally to researchers, infrastructure providers and projects that seek ELIXIR support.

The EIP Knowledge Hub is therefore proposed as a systematic approach to collate and disseminate knowledge, working in close partnership with the FAIR Services Architecture Framework to support and provide a dissemination forum for the outputs generated from Task 1.

The aim is to provide resources for both ELIXIR users and external researchers, and to act as a knowledge portal where researchers, ELIXIR communities, external projects and other RIs can find documentation on ELIXIR adopted services, resources, best practice and training materials.

Two major stakeholder communities with different knowledge dissemination routes will be addressed:

  1. Common practitioners, that is Data stewards, Developers and Researchers requiring knowledge of FAIR and interoperability best practice for Research Data management.
  2. Advanced practitioners in data stewardship and infrastructure and tool development that are developing ontologies, standards and FAIR services

To deliver the Knowledge Hub we will use the ELIXIR RDMkit and the FAIR CookBook as components of the knowledge dissemination platform thereby benefiting from their processes (using github as the delivery mechanism) and their community momentum. For advanced practitioners, we will engage communities and additional ELIXIR aligned projects who are creating content and have specific expertise. In both cases a significant focus is placed on community-driven content contribution.

The RDMkit, an output of ELIXIR CONVERGE, is a website-based toolkit designed to guide life scientists and data stewards in their efforts to better manage their research data. RDMkit comprises a set of RDM best practice guidelines, organised as web pages, that are reachable via a navigation structure of topics.

Each guideline page contains a description of the topic, including considerations, possible solutions, as well as a filtered view of a table of relevant tools and resources linked to entries in the ELIXIR Registries (bio.tools, FAIRsharing, TeSS). It also includes a hyperlink to the tool or resource homepage where available. The contents are generated and maintained by the ELIXIR community. The RDMKit’s underlying technical infrastructure has been established using GitHub and comprehensive community contribution and editorial processes have been put in place. A full discussion of the RDMkit is given in CONVERGE deliverable 3.1.

The GitHub-hosted FAIR CookBook is an output of the ELIXIR-driven FAIRplus project with contributions by ELIXIR Nodes, pharma and complements/connects the Pistoia Alliance's ‘FAIR ToolKit’.

The FAIRCookbook collates protocols organized according to the FAIR elements and a persona-based browsing. This includes how to FAIRify a number of exemplar datasets, putting the FAIR principles in practice. Recipes are contributed by ELIXIR members, pharmas and SMEs via collaborative ‘book-dash’ events.

Both the RDMkit and the FAIR Cookbook have been designed from the start for long term sustainability by the Nodes. The technical infrastructure is lightweight and off the shelf with a light hosting footprint (web and github). The editorial boards, of both resources, is made up of node representatives, as well as pharmas and SMEs.

The primary sustainability task is content managed, which is a distributed responsibility across all aspects of ELIXIR coordinated by the editorial boards. As with 99% of the ELIXIR resources, the RDMkit and the FAIR Cookbook will be sustained by the Node membership, including those participating in the current platforms and communities, and external partners. Responsibility for the RDMkit lies with the Node governance already in place.

 ELIXIR Norway, ELIXIR Netherlands, ELIXIR Belgium, ELIXIR UK, ELIXIR Portugal

This implementation study aims to understand the existing infrastructure, resources and protocols for human genome variation annotation and curation. Work focuses on processes that can be automated to support interpretation of high-throughput genome sequencing results. The outcome will be a report that describes the current status within ELIXIR member states, identified requirements and potential solutions. The report will be part of the ELIXIR Human Genomics and Translational Data Services strategy and roadmap.

This project coordinates with ELIXIR Data Platform on surveys regarding data archives and other resources. It also consults with Compute and Tools Platforms on potential models for resourcing, scaling and providing portable tools based on the identified requirements for running data analysis workflows. The aim is also to work in close collaboration with the ELIXIR Interoperability Platform to understand the future requirements on managing variation annotation and their interpretation.

This implementation study will also aim to support the coordination between ELIXIR Human Genomics and Translational Data use case and the relevant GA4GH technical work streams. The expected outcome is a better alignment of ELIXIR activities with those in the GA4GH and direct communication with relevant resources outside of ELIXIR such as ClinVar.

 ELIXIR Finland, EMBL-EBI, ELIXIR Switzerland, ELIXIR UK, ELIXIR Norway, ELIXIR Italy
ELIXIR Spain
ELIXIR Netherlands
ELIXIR France

This Implementation Study was designed to deliver Bioschemas.org specifications and demonstrators for the following content types:

  • Data repository
  • Dataset
  • Sample 
  • Protein annotations.

In addition there was support for the development of other content types like Phenotype and Beacons planned in other ELIXIR activities. The project provided support for the Bioschemas community, including meetings, hackathons, knowledge dissemination, and training in adoption of Bioschemas. The project is led by the ELIXIR Bioschemas working group.

This study is now completed, there are a number of links summarising the results of this work:

BioSchemas webinar (March 2016)

See the slides.

 ELIXIR Netherlands, ELIXIR UK, EMBL-EBI
ELIXIR UK, EMBL-EBI
ELIXIR UK

This Implementation Study plans to support the global scientific community by pioneering the community manager role in Bioschemas. Expected outcome includes a stable framework for the governance and role of this managerial task. This includes the global community outreach and interaction, and contribution to the technical planning of the tools supporting Bioschemas mark up and consumption.

 ELIXIR UK, ELIXIR France, ELIXIR Italy
ELIXIR Netherlands, ELIXIR UK, EMBL-EBI

The Bioschemas Travel grants aimed to encourage data providers to implement fully-compliant Bioschemas markup within their web resource.

The project consisted of a series of Travel grants which allowed Bioschemas experts to travel to another ELIXIR Nodes to give tutorials or implementation support to specific resources, or to implement Bioschemas tools and markup as part of a hacking project at the European Biohackathon (both 2018 and 2019). It also supported exchange of staff between ELIXIR Nodes for a specific period with the aim of delivering Bioschemas markup or tools.

EMBL-EBI, ELIXIR France, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Switzerland, ELIXIR UK

Bioschemas (http://bioschemas.org) is a community initiative which aims to improve data discoverability in the life sciences and provide better exposure of our data repositories, including the ELIXIR Core and Node Data Resources, to generic search engines, such as Google, and domain specific  repositories such as Identifiers.org, FAIRsharing.org, and DataMed. It does this by encouraging content providers in life sciences to use Schema.org markup to expose consistent structured data in their websites.

In March 2017 we started a pilot programme to build a Bioschemas community, define a first set of profiles for data repositories (catalogs), datasets, and specific data types, pilot markups for datasets primarily held by the EBI, and build a relationship with Schema.org. After an initial Implementation Study, we have succeeded in all these goals. The community momentum continues with:

This project aims to lift Bioschemas from “pilot” to “practice” and will:

  • Disseminate and Train: Develop training material; improve the Bioschemas website; make compliant datasets visible in ELIXIR registries.
  • Adopt: Topic specific workshops; Node-based workshops and inter-node staff exchange; strategic engagement with data platform Core Data Resources and implementation studies.
  • Sustain: Incorporation into Schema.org; and establish Bioschemas Community governance.
  • Impact: Highlight use cases, showcase impact stories and identify how to mitigate attrition.
 ELIXIR UK, EMBL-EBI, ELIXIR France, ELIXIR Belgium, ELIXIR Netherlands, ELIXIR Italy
ELIXIR France

The FAIRification process presents itself with specific commonly asked questions ranging from identification of the right ontologies/ schemas/ semantic web structures, mapping identifiers and cross referencing, retrospective data curation, and prospective sustainable FAIR process curation.

This Capacity Building task proposes to build the knowledge dissemination infrastructure to answer these challenges with scalability by compiling tools and training materials, and consolidated them to a centralised Knowledge hub online portal that is equipped with the feedback and feedforward communication channels between the Interoperability Platform and the users of all levels.

Aim: To improve content and ELIXIR Interoperability Platform (EIP) service registry organisation for public and internal communications on the EIP Knowledgehub, to transition to an EIP enhanced online Knowledge Portal, and to provide a sustainable knowledge-sharing mechanism through training and outreach.

 ELIXIR UK, ELIXIR Norway, ELIXIR Portugal, ELIXIR Italy, ELIXIR Sweden, ELIXIR Netherlands, ELIXIR Estonia, ELIXIR Finland, ELIXIR Belgium, ELIXIR France, ELIXIR Czech Republic
ELIXIR Italy
ELIXIR Netherlands

The aim of this Implementation Study is to determine the requirements for validation with ELIXIR partners, to build prototype open validation services for archetype archival databases and knowledge bases, in particular:

  • Content validation according to minimum information checklists.
  • Syntactic format validation according to a standard format in conjunction with the GA4GH file formats team as part of the Large Scale Genomics Workstream.
  • Syntactic format validation for Phenotyping data.
  • Semantic validation according to a publicly available ontology.
 ELIXIR Belgium, ELIXIR France, EMBL-EBI, ELIXIR UK
ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Ireland, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI
ELIXIR Italy
ELIXIR Belgium
ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Ireland, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI
ELIXIR Germany, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Spain, ELIXIR UK
ELIXIR Denmark
ELIXIR UK
ELIXIR UK
ELIXIR UK

The Interoperability Platform aims to help people and machines discover, access, integrate and analyse biological data. The Platform has created an ecosystem of products and information and is now maturing into a sustainable framework to address challenges involving identifiers, discoverability, ontologies, metadata, and vocabularies, as well as APIs and workflows.

The FAIR-enabling activities of the Interoperability Platform have strengthened the recognition of Research Data Management (RDM) as a discipline in its own right, which has led to the creation of the ELIXIR RDM Community. This Community will be instrumental in this new phase of the Platform, in order to share, co-create, and reuse resources, tools and services to achieve greater real-world impact.

The Interoperability Platform's vision now covers three themes (designated “The 3 Ps”): mature Products that enable FAIRification and responsible RDM, specific Processes that use (or need) Products, and broader Practices that enable a user to succeed.

  • Products: the goal is to provide a comprehensive and context-aware collection of FAIR-enabling and RDM-supportive products, within the broader context of the European Open Science Cloud (EOSC) framework.
  • Processes: we aim to develop a common framework for the application of the Products to support FAIRification of data and services across ELIXIR Nodes, Communities, and projects, while also aligning with EOSC and global partners.
  • Practices: we will enable users to convert knowledge gathered into actionable content, including guidance materials based on the interoperability stories. These should empower users to navigate and successfully utilise the resources within the portfolio. 

Lead partners: University of Oxford (UK), EMBL-EBI, Maastricht University (The Netherlands)

This WP aims to:

  • Facilitate communication and collaboration among Platform members by chairing monthly coordination calls.
  • Coordinate the scientific agenda for the annual Platform face-to-face meeting.
  • Oversee the implementation of the Platform Work Plan to ensure objectives are met within the designated time frame.
  • Provide reporting and progress updates to ELIXIR governance bodies and stakeholders, where necessary, to foster transparency and accountability.
  • Regularly review Platform strategy to identify areas for improvement and propose necessary adjustments for enhanced efficiency and effectiveness.
  • Establish communication channels with other ELIXIR Platforms to ensure alignment and knowledge sharing.
  • Participate in joint-platform activities to leverage collective expertise and resources.
  • Actively engage with external partners and organisations to seek collaboration and resource-sharing opportunities to enhance Platform capabilities and impact.
  • Where appropriate, pursue additional avenues of funding and support, including industry engagement, to boost sustainability.
  • Contribute to the broader impact of the Platform, by aligning with the ELIXIR Programme and other Research Infrastructures and initiatives, such as EOSC.
  • Communicate Platform activities by engaging with ELIXIR Communities and research communities in general.
  • Represent the Platform in external contexts and strategic partnerships.
  • Coordinate and contribute to drafting and finalisation of Platform Work Plan for remainder of 2024-2028 Programme.

Lead partners: University of Luxembourg (Luxembourg)

This WP aims to:

  • Align and coordinate the development of the RDMkit and FAIR Cookbook;
  • Map out the landscape of FAIR-enabling products, including services and standards, within ELIXIR.

Activity 1: Coordination of the RDMkit and FAIR Cookbook in the wider context of the RDM ecosystem

The aim of this activity is to formalise the coordination between the RDMkit and FAIR Cookbook to:

  1. help their developers with growth, synchronisation and sustainability of the resources;
  2. better serve the ELIXIR and wider user community with complementary and comprehensive coverage; and
  3. engage efficiently with the RDM and other ELIXIR Communities, as well as external collaborators.

Specifically, in this Activity we will bring together their respective editorial boards to:

  • Define an aligned strategic vision across the two resources;
  • Further develop the technical and operational alignments currently in place;
  • Identify gaps/new content from a range of avenues, including outcomes from WP2 Activity 2, WP3 and 4, as well as ELIXIR Communities and Focus Groups;
  • Coordinate the addition of new content in alignment with the resources' remits and the shared strategic vision;
  • Continue to ensure cross-links between the two resources, and to others such as FAIRsharing, DSW, and bio.tools;
  • Organise focus groups, joint hackathons, and contentathons to add guidelines and recipes on topics of strategic relevance to ELIXIR RDM and other Communities.

Activity 2: Establish portfolio of endorsed FAIR-enabling services and standards

The aim of this activity is to formalise and endorse a portfolio of services and standards that support and enable FAIRness. We will leverage activities from WP3 and WP4, as well as review the impact of the RIRs, to identify revisions and improvements required for this process.

Specifically, we will:

  • Survey and analyse the landscape of FAIR-enabling services and standards used across the ELIXIR RDM and other Communities and Nodes;
  • Identify core services and standards, as well as gaps in the ELIXIR portfolio, working closely with WP3 and informed by the 'interoperability stories';
  • Review and update the RIRs procedures, categorisation, and evaluation criteria for services, based on experiences to date (does RIR serve its purpose?);
  • Create ‘live’ representations of standards and their profiles in FAIRsharing, to track their status and maximise their use by data resources;
  • Formalise the ELIXIR portfolio and how it is disseminated to the user, enhancing relevant pages of the ELIXIR website.

Lead partners: SIB (Switzerland), Uppsala University (Sweden)

This WP aims to:

  • Define the components of a common framework for interoperability that will support FAIRification of data and services across ELIXIR Nodes, Communities and Projects and promote alignment with EOSC and ELIXIR’s global partners
  • Curate a comprehensive and well-organised library of interoperability case studies and use cases that will serve as input to initiatives across ELIXIR Platforms, and as examples including lessons learned to a wide range of stakeholders across ELIXIR

This work package will identify, assess, refine and test processes, resources and best practices in FAIR data management. It will consolidate them into a common FAIRification framework. Ultimately, this framework will be used as a reference to which FAIR implementations across ELIXIR Nodes, Communities and Projects can be realigned.

The common FAIRification framework will describe the requirements, recommendations, processes and resources that drive successful FAIR implementations to deliver the objectives of the ELIXIR Interoperability Platform. The work will be organised under two activities:

  1. defining the common FAIRification framework
  2. collecting a comprehensive library of 'Interoperability stories' that illustrate how the framework manifests in use cases across ELIXIR

Activity 1: Converge communities around the use of a common FAIRification framework

Data stewards across ELIXIR routinely define new, ad hoc approaches and workflows in an attempt to create FAIR data, despite the existing resources supporting interoperability. Activity 1 will establish a common framework that will enable ELIXIR data stewards to approach FAIRification of data and services with a systematic and scalable process.

The work will initially build and improve on the FAIR in action FAIRification framework and supporting initiatives such as the FAIR Dataset Maturity model, FAIRification goal development, and FAIR Cookbook in alignment with the EIP FAIR Services architecture Framework.

This work will formalise a practical framework for FAIRification tasks, based on feedback from work in WP2 (landscaping) and guided by the ‘interoperability stories’ in WP3, Activity 2. This framework will be validated practically and refined over the course of the work plan through the proposed series of BYOD workshops.

Plan of work:

  • Analyse a selection of FAIRification and interoperability frameworks that are well-documented and familiar to the WP contributors, to create an initial list of requirements and a first minimal draft framework.
  • Define a minimal reporting structure for the workshop events to collect experiences to guide the future revisions and validation of the framework.
  • Iteratively select/define use cases to focus on for each of the workshops, to maximise the utility of the framework and demonstrate its efficacy across EIP stakeholders—arranging the workshops in coordination with Activity 2.
  • Define a candidate release of the framework and call for EIP members to review and provide feedback for final revisions and validation.
  • Finalise the framework and alignment with Activity 2.

Activity 2: Collect a comprehensive library of 'Interoperability stories' from across ELIXIR

This activity will extend the number of stories that represent the stakeholders of the EIP, and adopt a common structure to support the development of the common FAIRification framework of Activity 1.

The work will begin by analysing the current collection of ‘interoperability stories’ to identify recurring concepts and use cases of relevance to the framework of Activity 1, and to define an initial list of gaps with regards to the types of tools and use cases covered.

The work will involve soliciting new and more detailed ‘interoperability stories’ by reaching out to ELIXIR Projects, Nodes and Communities and a selection of relevant EOSC initiatives and other external partners to request and support their contributions.

The structure and content will be refined as the framework evolves and the work will shift focus towards consolidating the stories into a library of case studies and use cases, and soliciting feedback to ensure that the library can be used as input to future initiatives and stakeholders across ELIXIR.

Plan of work:

  • Identify recurring concepts and use cases of relevance to the framework of Activity 1 in EIP’s current collection of ‘interoperability stories’, and define a list of gaps in the tools and use cases covered.
  • Define a minimal common reporting structure for the workshop events, to facilitate contributions of new and more detailed ‘interoperability stories’, and to assess their utility for EIP stakeholders.
  • Identify opportunities to improve the structure of the library, to support the workshops and to avoid overlaps with existing resources (such as in the RDMkit / FAIR Cookbook), arranging the workshops in coordination with Activity 1.
  • Define a candidate release of the library and proposed path to integrating the ‘interoperability stories’ in RDMkit, FAIR Cookbook and the wider RDM ecosystem, followed by a call for EIP members to review and provide feedback for revision and validation.
  • Design and open a call for contributions of 'interoperability stories’ from ELIXIR Projects, Nodes and Communities and a selection of relevant EOSC initiatives and other external partners.
  • Finalise the library and alignment with Activity 1 and extract a summary of the FAIR enabling technologies in use while highlighting emerging tools and use cases.

This WP aims to:

  • Evaluate and draw attention to issues of interoperability (positive or negative) that occur during data analysis or integration of different types of data, and also in relation to data and compute models.
  • Conduct a use case-driven inventory of individual steps and complete workflows, and the resources supporting these processes, to identify any missing components.
  • Evaluate resources with training materials for their content and links among these resources (think TeSS, Galaxy, WorkflowHub) and between them and bio.tools.
  • Assess both the content of training materials provided by resources such as TeSS, Galaxy and WorkflowHub, and the connections between those same resources and to others such as bio.tools.

Activity 1: Engage RDM and analysis experts to identify services, tools, workflows, and their usage, using data from deposition databases and example FAIR data

This activity will evaluate the interoperability approaches, workflows and tools used for data analysis, integration and reuse. By doing so, we aim to enhance the reusability of datasets and metadata that are being shared in selected (OMICS) deposition databases. To achieve this, we plan to establish connections between these deposited datasets and various other types of data using interoperable tools and workflows. This will also help identify existing methods we can better support and promote across ELIXIR and beyond. To accomplish this, we will:

  • Identify and select deposited datasets in ELIXIR deposition databases (specifically using OmicsDI, BioSamples, Biostudies in the process and then ArrayExpress, ENA, PRIDE, Metabolights and possibly EGA for the actual datasets) and evaluate their reusability.
  • Choose a number of example data reuse approaches to examine, and potentially improve their data requirements. Examples mentioned, but not yet chosen, were disease maps (used in many communities), ordinary differential equation based physiological kinetic models (as used in toxicology and systems biology communities), and whole genome metabolic maps (used in microbiome, food and nutrition, metabolomics). Collate use cases (stories) from Activity 2 WP3 that are relevant to different ELIXIR communities based on these approaches
  • Utilise the workflows collected from Activity 2 WP3 to link and integrate the chosen datasets.
  • Identify interoperability resources relevant during data reuse and for combining identical, related, or hierarchically related entities. Examples are ontology lookup and mapping (e.g. OLS, BioPortal, OxO, Zooma), database identifier resolution (e.g. identifiers.org and BridgeDb), chemical structure resolution and (sub)structure mapping (e.g. CDK, ontologies), executable transformations and models (e.g. Omnipy, conversions to and from SBML and to LaTeX), the whole set of sequence similarity tools (e.g. CleanUp). Evaluate relevant standards (e.g. SSSOM, SBML).
  • Evaluate the interoperability of the deposited datasets.
  • Evaluate a mechanism for post-deposition enrichment of annotation of data in the deposition databases, and an associated validation procedure.
  • Create a list of recommendations for dataset requirements, to ensure successful interoperability when reusing datasets. These recommendations may be generic and applicable to multiple workflows or specific to a particular interoperability task. Creation of FAIRsharing ELIXIR Community Champions to ensure enriched ELIXIR content and highlight recommendations of FAIR-enabling ELIXIR resources in WP2 and help with the profile of resources using FAIR data.

Activity 2: Outreach, dissemination and training

Based on the use cases of Activity 1, make an inventory of existing training material for workflows, molecular data analysis procedures and tutorials for analytical and interoperable tools relevant for data reuse and integration.

We will especially focus on interoperability resources that support finding relations and mappings needed during data reuse in the fields also covered in Activity 1 (i.e. text to ontologies, ontological terms mappings, database identifiers and their resolvability, chemical structure relationships, hierarchical relationships (e.g. SNPs to genes to processes or gene expression to proteins to tissue localization). Our work plan will be:

  • Decide on the best places to make these available (e.g. TeSS, Galaxy, FAIRsharing and/or WorkflowHub).
  • Improve training material metadata via ontology terms (e.g. from EDAM) and explore the interlinking between the different training resources (e.g. by using Bioschemas). Wherever possible, provide approaches for the reuse of these training materials and explore mechanisms for assessing their validity over time.
  • Work with the bio.tools and FAIRsharing platforms on better, ideally automated, links between training material and the involved tools, aiming at reducing annotation needs and increasing findability. Whenever possible, use the same technology approach for providing links among the actual training repositories.
  • Identify specific gaps in existing training material on data reuse, aligned to the findings of the other Activities in the Interoperability Platform. Work with the Training Platform and engage relevant ELIXIR Communities to fill them. Generate guidelines of good data reuse practices, so they can be included in existing and upcoming materials.
 ELIXIR Belgium, ELIXIR Switzerland, ELIXIR Czech Republic, ELIXIR Germany, EMBL-EBI, ELIXIR Spain, ELIXIR UK, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Sweden, ELIXIR Slovenia
ELIXIR UK

This document sets out the formal position of ELIXIR Europe on good data management practice in the life sciences and the practical implementation of FAIR Data Management principles by ELIXIR Nodes. It represents the collective recommendation of the 21 ELIXIR Nodes on how to implement FAIR​ ​in​ ​life​ ​sciences.  

The principles set out in this document will guide ELIXIR’s engagement in the European Open Science Cloud. The principles also signal our commitment to the First EOSC Summit Declaration. They provide specific recommendations for implementing FAIR and by building capacity and empowering our national Nodes, ELIXIR achieves the coordinated action requested in the EOSC Declaration.
ELIXIR Germany, ELIXIR UK
ELIXIR UK
ELIXIR UK
ELIXIR UK
ELIXIR Belgium, ELIXIR France, ELIXIR UK, EMBL-EBI
ELIXIR Norway, ELIXIR Spain, EMBL-EBI
ELIXIR UK
ELIXIR UK, EMBL-EBI
ELIXIR Belgium, ELIXIR UK
ELIXIR Netherlands
ELIXIR Belgium, ELIXIR Germany, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Portugal, ELIXIR Spain, ELIXIR Sweden, ELIXIR UK

The Marine Metagenomics Community has adopted the use of the Common Workflow Language (CWL) as an interoperable way to describe their analysis pipelines. One of the most complex and fully developed CWL workflows implements the EBI metagenomics analysis pipeline.

In coordination with MG-RAST, a US based metagenomics analysis pipeline, there are now two different large-scale metagenomics CWL workflows. Each uses a different CWL execution framework (namely Toil and AWE) and are run on different compute infrastructures. During the course of the coming year, the Marine Use Case expects META-pipe (the ELIXIR-NO, marine specific metagenomics pipeline) and other metagenomics related tools (e.g. ITS1 analysis from ELIXIR-IT) to adopt CWL. These additional tools can be used as alternatives for pre­existing tools or extend the functionality of the current workflows.

This Implementation Study aims to:

  1. demonstrate the benefits of using CWL by combining different workflows components to make new workflows;
  2. extend the current CWL workflows to enable greater reuse;
  3. enhance the execution frameworks to improve both deployment and scalability;
  4. deploy a single CWL workflow on different ELIXIR cloud environments to enable parallel processing and reproducibility.

To provide an exemplar to both the ELIXIR and the broader scientific communities, we will work through a community case study and ensure that the data, analysis and results conform to a bona fide Research Object (RO), ensuring that they comply with FAIR principles. We will develop appropriate training materials for two key target audiences - producers of (workflows and ROs) and consumers.

This study is closely linked with the work of the Bioschemas Community.

 ELIXIR France, ELIXIR UK, EMBL-EBI, ELIXIR Finland
ELIXIR Finland, ELIXIR Spain, ELIXIR UK, EMBL-EBI

This project aims to make data more discoverable for ELIXIR communities by exploiting Bioschemas markup deployed by data providers on their web resources.
Objectives:

  • Enable each community’s repositories and tools to exploit and benefit from Bioschemas markup;
  • Demonstrate the benefits of Bioschemas to community data providers and their applications; 
  • Provide a roadmap, training and best practice examples for other communities to encourage deployment of Bioschemas markup within ELIXIR communities;
  • Steer the development of the Bioschemas community by extending Schema.org and encouraging tool development. 
 ELIXIR UK, ELIXIR Belgium, ELIXIR France, ELIXIR Netherlands, ELIXIR Portugal, ELIXIR Italy, ELIXIR Hungary, ELIXIR Germany

The ELIXIR Interoperability Platform (EIP) has been established to deal with the challenge of delivering FAIR (Findable, Accessible, Interoperable, Reusable) data: to make available the services needed to make data FAIR, to work with FAIR data and to enable its actual reuse.

The FAIR Service Architecture Task (EIP Task 1) workplan proposes a solution that answers to the challenge that spans the different levels of complexity and variety of life science data types; across the datasets, data catalogues, data tools and services; across the multitude of biological disciplines and organisational boundaries and, at the European Open Science Cloud level, across disciplines and to support e-Infrastructure services. The adoption of standards, services and stewardship best practice by data providers will provide scientists with the tools they need to do research efficiently.

Aim: To maximise value and benefit by integrating data from disparate resources across disciplines and borders by developing the FAIR service infrastructure that incorporates tools that are fit-for-purpose.

The Interoperability Platform aims to provide Services, Standards and Expertise in order to maximise the value and benefit by integrating data from disparate resources across disciplines and borders, and align with activities in other platforms. We work with the extended ELIXIR community to deliver a sustainable portfolio of FAIR Recommended Interoperability Resources (RIRs) including those embedded within national data management practices and Node service delivery plans (SDPs), and to provide the infrastructure that will aid the discovery, exploration, interoperability and reuse of scientific data.

 ELIXIR UK, EMBL-EBI, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Sweden, ELIXIR Italy, ELIXIR Germany

FAIRDOM, based on the SEEK platform by the group of Carole Goble and the group of Wolfgang Müller, is used by multiple Nodes in ELIXIR as data management platform.

Through a joint event organised in June 2019 in Ghent we have initiated adoption and capacity building in the Belgian Node. Within the ELIXIR-CONVERGE project FAIRDOM is put forward as a component of the data management toolkit. We have regular teleconferences where people from Belgium, Germany, Norway and UK discuss developments and future directions of FAIRDOM. The different Nodes have different expertises and focus areas, which are well aligned and complementary.

The development of FAIRDOM initiated in the UK and Germany. In the UK this platform will be the basis for the workflow registry (EOSC-Life WP2). Integration with other platforms, such as Galaxy and Jupyter Notebooks, is one of the focus areas for the German Node. These aspects are of interest for all Nodes involved.

In Norway the platform has been integrated with the NeLS infrastructure, this is very much of interest for the Belgian Node, where a national/regional infrastructure is being planned. Within the Belgian national project, we will be focussing on the integration of metadata schemas for life sciences data into the platform. This will enable users to capture all required metadata to submit data to the recommended Deposition Databases. Also community engagement is an important topic, lead by the UK Node.

The aim of the staff exchange project is to:

  • kickstart the integration of submission capabilities into Deposition Databases into FAIRDOM. This will facilitate submission of FAIR data for end-users
  • expedite integration of FAIRDOM with the underlying storage platform in Belgium, based on the experience in the Norwegian Node
  • further develop pipelines and workflows for research projects and data analysis in FAIRDOM, based on the experience of the ELIXIR UK Node
  • to better understand how FAIRDOM is currently used by researchers in the UK, Norway and Germany, and identify the features that must be improved
  • discuss and identify specific features that need to be implemented in FAIRDOM in order to improve the user interface
 ELIXIR Belgium, ELIXIR UK, ELIXIR Norway, ELIXIR Germany

We propose to advance the application of FAIR principles to metadata for human genomic tracks by developing recommendations for metadata as well as algorithmic tools, to apply the recommendations to tracks from selected hubs associated with the Ensembl TrackHub Registry, to implement a track search service that integrates metadata from different track hubs, and to test the implementation with selected track-oriented analytical tools. The recommendations will form a basis for developing a standard for metadata on genomic tracks.

Currently ChIP-seq, RNAseq, variant, and epigenetic tracks lack standardisation. This Study  will generate a set of published recommendations that will result in a published minimum standard for such tracks. This will be applied to Ensembl TrackHub tracks and GSuite HyperBrowser (NO).

 ELIXIR Norway, EMBL-EBI, ELIXIR Spain

The FAIR (Findable, Accessible, Interoperable and Reusable) principles aim to maximize the discovery and reusability of digital resources. While the principles have enjoyed rapid uptake across communities (ELIXIR, G20, EOSC, H2020, NIH), the implementation details remain unclear.

Recently, we developed a prototype software infrastructure and a set of metrics to assess the FAIRness of digital resources (http://fairmetrics.org/). In this ELIXIR Implementation Study we will put these into practice for the ELIXIR community by starting to FAIRify ELIXIR Core Data Resources ArrayExpress, ENA, PDBe, PRIDE, CatH, CHEMBL, ChEBI, UNIPROT, HPA, INTERPRO, MINT, and STRING-db.

Our study will first establish effective guidelines for implementation, then involve hands-on FAIRification workshops, in which FAIRness will be assessed before and after the work done. Our work will raise awareness around what it takes to be FAIR, and to help drive interoperability between core ELIXIR resources and with efforts outside of ELIXIR.

 ELIXIR Netherlands, ELIXIR UK, EMBL-EBI, ELIXIR Italy, ELIXIR Sweden
ELIXIR UK

This Study's work will address the following themes:

  1. Optimal CNV detection pipelines for research and diagnostics: to release a set of sensitive and reliable pipelines, optimized and validated to detect CNV from various high throughput datasets. These pipelines will be available either through the ELIXIR compute nodes and/or as stand-alone solutions.
  2. Definition of reference datasets: to provide open reference datasets of fully validated somatic and germline CNVs representing a wide range of samples types and experimental technologies.
  3. Improvement of community formats for CNV exchange: to improve the VCF format and identify other nomenclatures and widely used formats in other communities (in alignment with GA4GH and the ELIXIR Interoperability Platform)
  4. Enabling CNV data discovery in diagnostic and phenotypic context: The hCNV Community will work towards enabling the ELIXIR Beacon Project for the envisioned patient discovery, through the support of extended clinical descriptions including enabling and testing of relevant annotation standards (e.g. HPO, NCIt and additional ontologies).
  5. Functional annotation of CNVs
  6. Combinatorial approaches to CNV interpretation
  7. Identification of landmark genes in regions of interest
  8. FAIRification of hCNV databases and datasets: The FAIR principles (Findable, Accessible, Interoperable, Reusable) will be applied to those systems to demonstrate the feasibility and utility of distributed CNV databases in order to allow interoperability (including resource and data discovery).
  9. Dissemination:
    1. Training materials
    2. Train actors, patients and the general public
    3. Capacity Building training events across certain ELIXIR Nodes
 ELIXIR France, ELIXIR Switzerland, ELIXIR Germany, EMBL-EBI, ELIXIR Spain, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Hungary, ELIXIR Slovenia, ELIXIR UK

Recent progress in sequencing technologies has produced several large scale genotyping data sets for crops. The insights afforded by this data have been published in high profile scientific articles, but the underlying raw genotype data and the associated sample and population metadata have not been routinely submitted to appropriate archives.

The aim of this implementation study, led by the ELIXIR Plant Community and in coordination with the ELIXIR Interoperability Platform and Data Platform, is to provide this wealth of data according to FAIR principles. It will ensure an interoperable link with the phenotypic data that is stored in distributed institutional repositories which is crucial for excelerated crop breeding.

We propose to create a sustainable toolbox to submit data to the ELIXIR Deposition Database “European Variation Archive” (EVA) and enrich the data with interoperable metadata regarding plant data standards like “Multi-Crop Passport Descriptor” (MCPD) and “Minimum Information About a Plant Phenotyping Experiment” (MIAPPE).

 ELIXIR France, ELIXIR Germany, ELIXIR Belgium, ELIXIR Netherlands, EMBL-EBI
ELIXIR Germany
ELIXIR Italy
ELIXIR UK, EMBL-EBI

This Implementation Study has established Identifiers.org as a stable ELIXIR system for uniform identifier resolution to major bioinformatics resources (with a focus on ELIXIR reference resources). The upgraded Identifiers.org API supports interoperability and identifier resolution for ELIXIR services, national programmes and external users.

This approach will ensure that all stored reference links will always point to the right data source. It helps developers of bioinformatics tools and database providers using interconnected networks of cross-referenced systems, and avoids broken links or 'dead ends' that can compromise the whole network. 

This study has now finished, the end report is available here. The establishment of Identifiers.org and N2T.net was announced in May 2018. 

Publications

Webinar summarising the outcomes

This study is associated with a number of ELIXIR Platforms, Communities and Projects: 

 EMBL-EBI
ELIXIR France, ELIXIR Germany, ELIXIR Hungary, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI

This project will increase interoperability between four ELIXIR resources (CATH, SWISS-MODEL, InterPro and PDBe), three of which are Core Resources, by building APIs that facilitate the import and export of data between them.

The ultimate goal is to improve provision of 3D-Models for protein domain sequences via CATH, SWISS-MODEL and InterPro. Less than 10% of known sequences have experimentally characterised 3D structural information and yet this data is often essential for understanding the protein’s molecular function and biological role and for determining whether residue mutations could damage the protein and lead to disease. So this integration is very timely as it will enhance links between sequence and structure data.

APIs will be built using well-established protocols and as well as promoting interoperability, and therefore sustainability, we will expand the data in each resource to ensure they serve a wider community of biologists.

 ELIXIR UK, ELIXIR Switzerland, EMBL-EBI

This project will increase interoperability between four ELIXIR resources (CATH, SWISS-MODEL, InterPro and PDBe), three of which are Core Resources, by building APIs that facilitate the import and export of data between them.

The ultimate goal is to improve provision of 3D-Models for protein domain sequences via CATH, SWISS-MODEL and InterPro. Less than 10% of known sequences have experimentally characterised 3D structural information and yet this data is often essential for understanding the protein’s molecular function and biological role and for determining whether residue mutations could damage the protein and lead to disease. So this integration is very timely as it will enhance links between sequence and structure data.

APIs will be built using well-established protocols and as well as promoting interoperability, and therefore sustainability, we will expand the data in each resource to ensure they serve a wider community of biologists.

 ELIXIR UK, ELIXIR Switzerland, EMBL-EBI

The implementation study project plan of ELIXIR Italy consists of six activities that aim to boost the cooperation with existing ELIXIR activities and are expected to deepen the interaction between ELIXIR-IIB, the Joint Research Unit embodying the Italian Node, and ELIXIR. The partners involved have already established contacts with other ELIXIR Nodes and the relevant ELIXIR Platforms and Services in order to ensure an advantageous outcome for all the involved parties. The goal of the proposed activities is to create and/or reinforce collaborations based on concrete measures. With this implementation study the Italian ELIXIR Node will achieve greater integration within ELIXIR service infrastructures and data interoperability policies. The topics of the selected activities and an additional coordination task are summarized below:

  1. Integration in ELIXIR Bioschemas activities.
  2. Integration in ELIXIR Data Curation activities.
  3. Integration in ELIXIR Galaxy activities through a project on practical feasibility of creating and running large-scale Galaxy-based variant calling pipelines on microservice infrastructures.
  4. Integration in ELIXIR Human Data activities through Beacons.
  5. Integration in ELIXIR Marine Metagenomics activities through a web-service supporting ITS1-based survey of marine communities.
  6. Integration in ELIXIR Rare Diseases activities.
  7. Coordination of the Italian ELIXIR Node Implementation study project.
 ELIXIR Italy

The implementation study project plan of ELIXIR Italy consists of six activities that aim to boost the cooperation with existing ELIXIR activities and are expected to deepen the interaction between ELIXIR-IIB, the Joint Research Unit embodying the Italian Node, and ELIXIR. The partners involved have already established contacts with other ELIXIR Nodes and the relevant ELIXIR Platforms and Services in order to ensure an advantageous outcome for all the involved parties. The goal of the proposed activities is to create and/or reinforce collaborations based on concrete measures. With this implementation study the Italian ELIXIR Node will achieve greater integration within ELIXIR service infrastructures and data interoperability policies. The topics of the selected activities and an additional coordination task are summarized below:

  1. Integration in ELIXIR Bioschemas activities.
  2. Integration in ELIXIR Data Curation activities.
  3. Integration in ELIXIR Galaxy activities through a project on practical feasibility of creating and running large-scale Galaxy-based variant calling pipelines on microservice infrastructures.
  4. Integration in ELIXIR Human Data activities through Beacons.
  5. Integration in ELIXIR Marine Metagenomics activities through a web-service supporting ITS1-based survey of marine communities.
  6. Integration in ELIXIR Rare Diseases activities.
  7. Coordination of the Italian ELIXIR Node Implementation study project.
 ELIXIR Italy

Intrinsically disordered proteins (IDPs), characterized by high conformational variability, cover almost a third of the residues in Eukaryotic proteomes. As major players in cellular regulation, IDPs are involved in numerous diseases.

Specialized IDP databases provide a starting point for analysis, yet their integration into core databases remains very limited. Here, we propose to start integrating IDP information into ELIXIR Core Data Resources.

This will be achieved with a three pronged approach:

  1. Integration of an expanded version of MobiDB-lite into UniProtKB and PDBe including links back to MobiDB via the InterPro infrastructure.
  2. Creation of a minimal information about IDP experiments (MIADE) standard and data interchange format will help ensure interoperability between databases with manually curated IDP data.
  3. Sustainability of curated IDP data will be enhanced by creating PubDisProt, a new deposition resource for linking curated literature and protein identifiers across databases.
 ELIXIR Italy, EMBL-EBI, ELIXIR Switzerland, ELIXIR Hungary, ELIXIR Ireland

InterMine is an ELIXIR recommended interoperability resource, and Institut Pasteur is a non-profit biomedical research foundation and part of ELIXIR France, with a strong focus on infectious diseases.

The Institut Pasteur has played a major role in the sequencing of a number of bacteria involved in such diseases, and the publication of their genomes. A number of these are currently available in databases based on older proprietary technology stacks (http://genolist.pasteur.fr/). We propose to enable a member from the Institut to visit Cambridge, where the InterMine team is based, for 10 working days, to learn how to load data from a legacy database into a new InterMine instance.

Expected Impact: “Digital preservation” is a term for the concrete, proactive steps required to keep data and database systems readable and useable - so preventing the so-called “digital dark age” phenomenon.

One preventative measure recommended by Smit et al is to transform data, refreshing it by moving it to current easily-readable formats (Smit, Van Der Hoeven, and Giaretta 2011). By using InterMine to reserve these data, researchers will be able to take advantage of a database system which explicitly strives to be FAIR and has existing documentation, flexible advanced queries, API client libraries in six languages, tutorials, and a common interface that already is utilised by dozens of existing databases (registry.intermine.org).

 ELIXIR UK, ELIXIR France

InterMine, an ELIXIR Recommended Interoperability Resource (RIR), is an open source data warehouse used around the world. It allows biologists and bioinformaticians easily to query integrated biological data, providing a common interface to biological data resources.

CNR-Istituto di Tecnologie Biomediche (CNR-ITB) is an institute of the Italian National Research Council (CNR) expert in applying omics technologies to understand human diseases with a strong expertise in bioinformatics. One of the main research topics in the Bari branch is the analysis of differential microRNA (miRNA) expression derived from small-RNA sequencing and assessment of the impact on downstream genes in various pathologies like neurological disorders and cancers.

We propose a member of CNR-ITB to visit the InterMine group for 10 days, in order to collaborate with InterMine staff to create a database that integrates expression data and data from miRBase, miRecords, TarBase, MiRTarBase, GENCODE and Ensembl.

At the moment all the public data necessary for miRNA expression analysis and interpretation has to be collected manually from each related resource for each particular analysis, and imported to local databases in CNR-ITB Bari servers. In addition, researchers from CNR-ITB Bari produce their own data (typically NGS data) that they would like to integrate with these existing public resources, thus allowing integrative querying and enabling re-use of the data. Such analysis will facilitate the identification of miRNAs as new potential biomarkers for disease onset and/or progression.

 ELIXIR UK, ELIXIR Italy

FAIRification for a large-scale life science research requires FAIRifying of all aspects: data, tools, standards, training, and hardware infrastructure. Cloud computing has emerged as a key infrastructure that calls for interoperability of softwares to facilitate data retrieval and processes that are dispersed across multiple sites.

The European Open Science Cloud (EOSC) programme (​https://www.eosc-portal.eu/​) is established in realisation of the large-scale cloud-based data integration. The Interoperability Platform mission aligns with EOSC terms of standardised best practices of implementation, and support of Interoperability tools in the Cloud.

The EIP Task 4 (Interoperability Services for the Cloud) identifies the requirements of the FAIR Service Infrastructure that will also fit the Cloud computing environment. EOSC EDMI compliant and the support for inter-catalogue metadata exchange and EOSC e-Infrastructure services will be explored for deployment in contingency to EOSC-Life discussion.

Aim: To establish the need for cloud deployed instances of individual RIRs (Recommended Interoperability Resources) through consultation with ELIXIR Communities and through established use cases; perform cost benefit analysis for each such RIR and evaluate the landscape and extent of the current cloud-enabled interoperability resources.

The landscape survey of service and gap analysis of cloud and non-cloud Interoperability services will identify the ​‘glue’​ activities needed to facilitate or support those existing services (process improvements for robustness, or to improve their cooperativity, etc).

This task will deliver a needs assessment and best-practice guidelines for cloud deployed services for the service consumers from ELIXIR Communities and use cases (in collaboration with the FAIR Service Architecture in Task 1 and Compute Platform). Where indicated, documentation of designing of a transition plan for cloud deployment of prioritised services identified in the needs assessment, and for new services appearing throughout the Programme will be provided, this is a critical task for the FAIR SA Task (Task 1).

 EMBL-EBI, ELIXIR Norway, ELIXIR Belgium

The FAIR Principles lay out the generalisable framework that can be applied to a wide range of data integration supporting exercises: software development, hardware implementation, best-practice guidelines, or data management planning.

FAIRification (to make ​something FAIR) requires different activities at execution in each domain. The Interoperability Platform Task 2 (Interoperability with a Purpose) proposes studies that showcase the EIP support in each area by demonstrating both community-driven implementation in a specific use case, and node-capacity building implementation of establishing user’s framework (first mile/last mile) network at Nodes.

Aim: To deliver demonstrable and improved level of usage support for FAIR data by key interoperability resources and services at the National Nodes and within Use Case Communities, while promoting global collaboration of FAIR service implementation network.

 ELIXIR Netherlands, ELIXIR Belgium, ELIXIR Norway, EMBL-EBI, ELIXIR Spain, ELIXIR Italy, ELIXIR Portugal, ELIXIR UK, ELIXIR France, ELIXIR Czech Republic

This implementation study is designed to

  1. Further identify communities of curators within ELIXIR, with the aim to reach out to those who may not initially identify with this role;
  2. Review and map the type of curation work being done, for which databases across ELIXIR, and in which life science/health domains;
  3. Identify the tools they are currently using for curation tasks;
  4. Assess the capacity requirements for new curators and training provision available;
  5. Produce an initial map of biocurators, manually curated knowledgebases and data repositories, curation tools / resources covering a range of topics and domains;  this will ensure that these resources are added to FAIRsharing as appropriate, providing an interoperable community resource mapping the landscape of biocuration and biological databases across Europe and the ELIXIR Nodes;
  6. Link training for biocuration resources to training available in TeSS and identify gaps in training provision.

The outcomes of this study have been published in F1000Research and were presented in a webinar.

Part of this work has been presented in the ISB Biocuration 2019 meeting (Cambridge, UK, April 2019):

  1. Holinski A, Burke M, Morgan S, Palagi P and McQuilton P.  Mapping the landscape of biocuration – where are the biocurators and what do they need? F1000Research2019, 8:735 (slides)
  2. McQuilton P.  FAIRsharing.org – mapping the landscape of databases, standards and policies (describing, linking and assessing their FAIRness) F1000Research2019, 8:712 (slides) 
  3. Palagi PM, McQuilton P and Beard N. TeSS: the ELIXIR training portal. F1000Research2019, 8:709 (slides) 

and also in the ELIXIR All-Hands Meeting 2019 (Lisbon, Portugal, June 2019):

  1. Holinski A, Burke M, Morgan S, Palagi P and McQuilton P. Mapping the landscape of biocuration – where are the biocurators and what do they need? F1000Research2019, 8:1519 (slides)

This work is carried out in collaboration with 

 ELIXIR UK, ELIXIR Switzerland, EMBL-EBI, ELIXIR Luxembourg, ELIXIR Slovenia

This implementation study is designed to

  1. Further identify communities of curators within ELIXIR, with the aim to reach out to those who may not initially identify with this role;
  2. Review and map the type of curation work being done, for which databases across ELIXIR, and in which life science/health domains;
  3. Identify the tools they are currently using for curation tasks;
  4. Assess the capacity requirements for new curators and training provision available;
  5. Produce an initial map of biocurators, manually curated knowledgebases and data repositories, curation tools / resources covering a range of topics and domains;  this will ensure that these resources are added to FAIRsharing as appropriate, providing an interoperable community resource mapping the landscape of biocuration and biological databases across Europe and the ELIXIR Nodes;
  6. Link training for biocuration resources to training available in TeSS and identify gaps in training provision.

The outcomes of this study have been published in F1000Research and were presented in a webinar.

Part of this work has been presented in the ISB Biocuration 2019 meeting (Cambridge, UK, April 2019):

  1. Holinski A, Burke M, Morgan S, Palagi P and McQuilton P.  Mapping the landscape of biocuration – where are the biocurators and what do they need? F1000Research2019, 8:735 (slides)
  2. McQuilton P.  FAIRsharing.org – mapping the landscape of databases, standards and policies (describing, linking and assessing their FAIRness) F1000Research2019, 8:712 (slides) 
  3. Palagi PM, McQuilton P and Beard N. TeSS: the ELIXIR training portal. F1000Research2019, 8:709 (slides) 

and also in the ELIXIR All-Hands Meeting 2019 (Lisbon, Portugal, June 2019):

  1. Holinski A, Burke M, Morgan S, Palagi P and McQuilton P. Mapping the landscape of biocuration – where are the biocurators and what do they need? F1000Research2019, 8:1519 (slides)

This work is carried out in collaboration with 

 ELIXIR UK, ELIXIR Switzerland, EMBL-EBI, ELIXIR Luxembourg, ELIXIR Slovenia

Metabolomics aims to provide novel insights into the biochemical reactions of organisms by characterising the presence and concentrations of low molecular weight compounds from biological samples. The primary analytical tools for such high-throughput data collection are mass spectrometry (MS), often preceded by chromatographic or electrophoretic separation technologies, and nuclear magnetic resonance spectroscopy (NMR).

These technologies produce relatively large and complex data sets that require bioinformaticians, cheminformaticians, biostatisticians, data scientists and computer scientists. Together they develop and apply a wide range of algorithms, software tools, repositories and computational resources to process, analyse, report and store the data and metadata.

Increasingly, insights from genomics, epigenomics, transcriptomics, proteomics/protein interactomics and metabolomics are combined, to gain insights into the dynamics of biological processes. Metabolomics activities are well represented within Europe and ELIXIR nodes. Metabolite identification is the area that the community believes will have maximal impact of computational metabolomics and metabolomics data management and will benefit most from interactions with the existing five ELIXIR platforms and where progress will contribute most to other ELIXIR communities.

The progress through this integrative Implementation Study will benefit industry and academia alike as metabolite identification is one of the major bottlenecks in metabolomics and resolving this challenge requires a community effort.

 ELIXIR Netherlands, EMBL-EBI, ELIXIR France, ELIXIR UK, ELIXIR Germany, ELIXIR Spain, ELIXIR Sweden, ELIXIR Italy, ELIXIR Estonia, ELIXIR Switzerland, ELIXIR Belgium
ELIXIR Netherlands
ELIXIR UK
ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Sweden