ELIXIR Implementation Study

3D-Bioinfo Community Implementation study

The structural Bioinformatics Community (3D-BioInfo) has the mission to better integrate protein structure-based data and tools across Europe, and to improve standardisation through better ontologies and agreed benchmarking. The ties with the structural biology research communities in Europe will be strengthened and dedicated training and outreach efforts will be taken. Four major topics form the basis of this study:

  • WP1: Infrastructure for FAIR structural and functional annotations
  • WP2: Standards and workflows for annotating and characterising biologically meaningful 3D structures of macromolecular assemblies
  • WP3: Biomacromolecule-ligand interactions
  • WP4: Tools to build and analyse Nucleic Acid structures: interoperability and FAIR data

Fourteen ELIXIR Nodes are involved in this study: ELIXIR UK, ELIXIR Czech, EMBL-EBI, ELIXIR Belgium (Shoshana Wodak, Wim Vranken), ELIXIR Swiss, ELIXIR Spain, ELIXIR the Netherlands, ELIXIR France, ELIXIR Israel, ELIXIR Germany, ELIXIR Denmark, ELIXIR Italy, ELIXIR Sweden and ELIXIR Slovenia.

Timing of the study 1/06/2020 – 31/05/2022

1/6/2020 - 31/5/2022

Exploiting Bioschemas Markup to Support ELIXIR Communities

Bioschemas leverages Schema.org, a widely implemented community effort supported by the main search engines to provide a way to add semantic markup to webpages. By enriching webpages with Bioschemas annotation, independently published content can be harvested and used by other resources without the need for APIs. As such, Bioschemas has the potential to boost Open and FAIR science.

This study aims to make data more discoverable for ELIXIR communities by exploiting Bioschemas markup deployed by data providers on their web resources. Four communities will be focussed on: Rare Diseases, Plant Sciences, Toxicology, and Intrinsically Disordered Proteins to apply Bioschemas to their resources in order to support search/index, resources markup for tools, metadata exchange and auto-curation. A roadmap, training and best practice examples will be provided for other communities.

The study is a joint effort of ELIXIR UK (Alasdair Gray, Carole Goble, Nick Juty), ELIXIR Belgium (Frederik Coppens, Bert Droebeke), ELIXIR France (Cyril Pommier, Marc Hanauer, Raphael Flores), ELIXIR the Netherlands (Marco Roos, Rajaram Kaliyaperumai), ELIXIR Portugal (Celia Miguel, Ines Chaves, Daniel Faria), ELIXIR Italy (Silvio Tosatto, Ivan Micetic, Damiano Piovesan), ELIXIR Hungary (Zsuzsanna Doszatanyi), ELIXIR Germany (Toby Gibson) and the ELIXIR hub (Sira Sarntivijai).

Timing of the study 1/01/2020 – 31/12/2021

1/1/2020 - 31/12/2021

Federated Human Data

Many countries in Europe have nascent personalised medicine programmes indicating a shift in human genomics from a predominantly research-driven activity to one funded through healthcare. This is evidenced by the declaration of many European countries to sequence and share transnationally at least 1 million genomes by 2022. As healthcare is subject to national laws, genetic data generated in this way is not likely to be shared as widely as research data. The ELIXIR Federated Human Data Community envisions to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders.

Current study will coordinate the delivery of FAIR compliant metadata standards, interfaces, and reference implementation to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-Phenome Archive (EGA). This includes a structured roadmap for ELIXIR Nodes to join the EGA federated network by providing the necessary technical, logistical, and training coordination across the network.

The study builds on earlier work in the ELIXIR-EXCELERATE, CORBEL and Tryggve projects. It is led by the European Genome-Phenome Archive (EGA, EMBL-EBI) to ensure alignment with the policies, legal agreements, and governance model for establishing the Federated EGA. Seventeen national ELIXIR Nodes are involved in this study among which ELIXIR Belgium (Yves Moreau).

1/6/2019 - 31/12/2021

Exploration work about the use of Beacons for proteomics data

While the existing Beacon network permits the discovery of genomic variants, the expression of these variants on the functional level depends on a wide range of factors. Adding information on variants on the proteome level will help to filter and to prioritize variants of functional relevance. The presence of genomic variants on the proteome level implies that clinical proteomics data is highly likely to be identifiable and thus specially protected under the EU GDPR guidelines.

The goals of this study are to 1) develop rules and best-practice guidelines for dealing with this type of data and align these efforts with the genomics community, 2) generate a list of potential use cases, 3) assemble a prototypical cloud-enabled pipeline for the extraction of proteomic variants, and 4) build a prototype Beacon implementation that integrates the extracted protein-level variants using existing local analysis pipelines in ELIXIR Belgium and ELIXIR Germany, and use it as a “proof of concept” to integrate proteomics data into the Beacon network.

The study is a joint effort of EMBL-EBI (Juan Antonio Vizcaíno), ELIXIR Belgium (Lennart Martens) and ELIXIR Germany (Oliver Kohlbacher).

1/11/2018 - 30/9/2019

Standardizing the fluxomics workflows

This Metabolomics Community-led study focusses on the standardization of fluxomics workflows. The study is led by ELIXIR Greece and ELIXIR Spain and supported by EMBL-EBI and 11 other national ELIXIR Nodes, among which ELIXIR Belgium (Bart Ghesquire).

The study aims at 1) establishing standards for isotopic labelling data deposition, a major fluxomics input, and accordingly extending Metabolights -  the reference database for quantitative metabolomics datasets, 2) establishing interoperability among largely-used fluxomic tools, building upon the PhenoMeNal fluxomic tool inventory, 3) extending BioSchemas to metabolic reactions and their dynamics, using the metabolic reaction database Rhea for metabolic model reconstruction, 4) containerizing the fluxomic workflow for use in cloud-based environment, and 5) standardizing the fluxomics training.

1/6/2019 - 31/5/2021

Interoperability Services for the Cloud

FAIRification for large-scale life sciences research requires FAIRification of all aspects: data, tools, training and hardware infrastructure. Cloud computing has emerged a key infrastructure that calls for interoperability of software to facilitate data retrieval and processes that are dispersed across multiple sites. The European Open Science Cloud (EOSC) programme is established in realisation of the large-scale cloud-based data integration. The ELIXIR Interoperability platform mission aligns with the EOSC terms of standardised best practices of implementation, and support of interoperability tools in the cloud.

This study will establish the need for cloud deployed instances of individual Recommended Interoperability Resources (RIRs) through consultation with ELIXIR Communities and established use cases. Cost benefit analyses will be performed for each RIR and the landscape and extent of the current cloud-enabled interoperability resources will be evaluated.

This project is part of the ELIXIR Interoperability platform tasks for the 2019-2023 Scientific programme. The study is a joint effort of EMBL-EBI (Helen Parkinson), ELIXIR Belgium (Frederik Coppens) and ELIXIR Norway (Sveinung Gundersen).

1/6/2019 - 31/12/2021

Packaging, containerisation & deployment

Software containers are a key element in the frame of Open Science & Open Source which is strongly supported and advocated by ELIXIR. Software containers guarantee data provenance when described as part of scientific workflows and are an important element towards reproducibility. This study is divided into three work-packages that complement each other:

  • WP1: Maintain and improve biocontainers infrastructure
  • WP2: Developing an integrated “Tools platform Ecosystem”
  • WP3: Fostering and evolving community participation and community workflows,

and aims to provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. This implies integrating data repositories, tools and training material. The provided workflows and tools will be curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

This project is part of the ELIXIR Tools platform tasks for the 2019-2023 Scientific programme. Eight ELIXIR Nodes are involved: ELIXIR Spain (Salvador Capella, Josep Gelpi), ELIXIR Germany (Bjorn Gruning), EMBL-EBI (Yasset Perz-Riverol), ELIXIR Belgium (Frederik Coppens), ELIXIR Denmark (Piotr Chmura, Jon Ison), ELIXIR France (Herve Menager, Olivier Sallou), ELIXIR Italy (Giacomo Tartari) and ELIXIR Norway (Matus Kalas, Abdulrahman Azab, Kjetil Klepper, Kjell Petersen).  

1/6/2019 - 31/12/2021

FONDUE: FAIRification of plant genotyping data and its linking to phenotyping using ELIXIR platforms

Recent progress in sequencing technologies has produced several large scale data sets for crops. The insights gained 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 is to provide this wealth of data according to FAIR principles ensuring an interoperable link with the phenotypic data that is stored in distributed institutional repositories which is crucial for accelerated crop breeding. A sustainable toolbox will be created to submit data to the ELIXIR deposition database “European Variation Archive” (EVA) and to enrich the data with interoperable metadata regarding plant data standards like “Multi-Crop Passport Descriptor” (MCPD) and “Minimal Information About a Plant Phenotyping Experiment (MIAPPE).

The study is a joint effort of ELIXIR France (Cyril Pommier, Anne-Francoise Adam-Blondon, Nacer Mohellibi, Manuel Ruiz), ELIXIR Germany (Uwe Scholz, Heidrun Gundlach, Klaus F.X. Mayer), ELIXIR the Netherlands (Richard Finkers), ELIXIR Belgium (Frederik Coppens, Bert Droesbeke) and EMBL-EBI (Cristina Yenyxe, Gonzalez Garcia, Melanie Courtot, Bruno Contreras-Moreira, Marc Rosello).

1/6/2019 - 31/5/2021

Deploying reproducible containers and workflows across cloud environments

This Strategic Implementation study around Container Orchestration aims to coordinate the ELIXIR Platforms (Compute & Tools) expertise within the Nodes, related projects and resources to establish ELIXIR-wide standards, protocols and processes for the orchestration of containerised applications provided by ELIXIR Communities.

The study will be approached in  4 workpackages: WP1) Leveraging EOSC-Life workflows infrastructure, WP2) ELIXIR infrastructure for orchestrating containers and workflows, WP3) Coordinating ELIXIR data discovery and transfer services, WP4) Community-led use cases. ELIXIR Belgium co-leads WP 3 and contributes to WP2.

Thirteen ELIXIR nodes and the ELIXIR Hub are involved in this study: Spain, Finland, Germany, France, Denmark, Belgium (Frederik Coppens), Sweden, Italy, Czech, the Netherlands, UK, Switzerland, EMBL-EBI.

1/6/2019 - 31/5/2021

Expanding the Galaxy: (meeting) the needs of ELIXIR Communities

As data analysis is common place in life sciences, we need to establish scalable ways to develop and share analysis workflows and train researchers to make use of them. The latter entails an end-to-end approach from access to data over selection and proper usage of the appropriate workflow and deploying this on available (cloud) resources.

As the ELIXIR Communities bring together domain experts, this is an ideal way to identify and develop standard workflows for commonly used analysis in specific domains. Since summer 2016, the Galaxy training network has been collecting and further developing training material for analysis and administration of Galaxy in a collaborative way (https://training.galaxyproject.org).

This project has three main goals: 1) Expand the portfolio of Community workflows including training material to describe them, 2) Facilitate access to data in Core Data Resources and Deposition Databases, 3) Improve the user experience of the Galaxy platform.

The study is a joint effort of ELIXIR France (Gildas le Gorguille, Erwan Corre), ELIXIR UK (Ralf Weber, Philippe Rocca-Serra, Christine Orengo), ELIXIR-NL (Michael Van Vliet, Saskia Hiltemann, Leon Mei, Peter Horvatovich, Anton Feenstra), ELIXIR Germany (Bjorn Gruning, Berenice Batut, Christophe Steinbeck, Oliver Kolhbacher), ELIXIR Spain (Salvador Capella, Oswaldo Trelles), ELIXIR Portugal (Daniel Faria, Ricardo Leite, Ana Portugal Melo), ELIXIR Norway (Erik Hjerde, Nils-Peder Willassen), EMBL-EBI (Henning Hermjakob), ELIXIR Greece (Irene Liampa), ELIXIR Italy (Marco Tangaro, Manuela Helmer-Citterich), ELIXIR Czech (Martin Hubalek), ELIXIR Belgium (Frederik Coppens).

1/6/2019 - 31/5/2021