ELIXIR Communities

ELIXIR Communities bring together experts from across ELIXIR Nodes and partner organisations to develop standards, services and training within specific life science domains. They are ELIXIR’s means to capture the needs of a particular research community and translate them into formal requirements that drive the work of the ELIXIR Platforms. This close collaboration ensures that the services developed by the ELIXIR Platforms serve the needs of their research communities.

ELIXIR recognises three different types of communities: those focused on a specific research field (e.g. Rare Diseases), those dealing with specific technology (e.g. Proteomics) and those providing specialist user support (e.g. Galaxy). In 2019, there were eleven ELIXIR Communities, including three Communities grouped under the Human Data Communities umbrella (p. 34).

The ELIXIR Communities have diverse interests ranging from scientific research domains to specific technical experimental or computational platforms. They also range in emphasis from pure technical development to community building. They nevertheless share some common goals: participating in and driving the development of data and metadata standards, often in collaboration with global partners; driving the uptake of standards, for example by designing federated data networks linked by common APIs; the design, evaluation and containerization of workflows, making use of openly available tools, that the research community can use to execute routine, large volume tasks; and ensuring that data held by and shared by ELIXIR Node partners conform as much as possible to the FAIR Principles.

The ELIXIR Communities also play a critical role in facilitating collaboration with other biomedical research infrastructures, as in many cases members of ELIXIR Communities from ELIXIR Nodes have close links with the national Nodes of other research infrastructures. On the other hand, members of ELIXIR Communities have the opportunity to engage in and drive global standardisation efforts via ELIXIR.

COMMUNITIES Intrinsically Proteins

Galaxy

Disordered Plant Science

Metabolomics

Microbial Biotechnology 3DBioInfo

Marine Metagenomics

Human Data

Human Copy Number Variations Proteomics

Rare Diseases

The Plant Sciences Community played a major role in the development and dissemination of two standards: MIAPPE (Minimum Information About a Plant Phenotyping Experiment) and BrAPI (Breeding API). These two standards provide the framework for describing and accessing plant phenotype data from a distributed network of repositories.

Building on top of these standards, the Community developed and released FAIDARE, the ELIXIR plant data search service 1 which provides search access to data from seven ELIXIR Nodes plus one database from USA.

In addition, MIAPPE and BrAPI played an important role in documenting and advertising plant genome submissions to EMBL-EBI databases, including genome update challenges via two Implementation Studies 2 .

The Marine Metagenomics Community completed its ELIXIR-EXCELERATE activities in 2019. These resulted in the expansion of pipelines to increase the scope of analysis, updating tools and the analysis pipeline to meet the demands of the Community.

The Community also generated benchmark datasets evaluating amplicon analyses across a range of biomes and developed six different marine shotgun metagenomics datasets. The analysis pipelines were described in the Common Workflow Language to enable reproducibility, facilitate comparisons and enhance development agility. The pipelines were deployed in a cloud environment to increase compute capacity. To allow federated searches across different programmatic interfaces, the Community also generated examples for all the resources involved.

The Galaxy Community has two roles: developing the Galaxy infrastructure, and building and widening the Galaxy community in Europe. Technical developments included integration of ELIXIR AAI into Galaxy, establishing a network of remote servers across Europe to process jobs from usegalaxy.eu, and establishing a network of CVMFS (CernVM File System) mirrors that enables distribution of reference data across Galaxy instances. They also supported the expansion of the network of usegalaxy.* servers in Europe.

In 2019 the Community started a new implementation study focussed on meeting the needs of other ELIXIR Communities (metabolomics, metagenomics, structural bioinformatics, plants and proteomics) The Proteomics Community focuses on standardising and evolving infrastructure for proteomics data. The Community continued work on their Implementation Study ”Crowd-sourcing the annotation of public proteomics datasets to improve data reusability” and started a new Implementation Study “Comparison, benchmarking and dissemination of proteomics data analysis pipelines”.

To further develop the proteomics infrastructure, the Community held a meeting on Proteomic Privacy to discuss the risk of re-identification in clinical proteomics data and their implications for proteomics data management.

It also started work towards adopting the Beacon technology for proteomics data.

The Metabolomics Community concentrates on technical progress in improving the analysis and utility of metabolomics data. In its Implementation Study on “Metabolite Identification” it is developing an optimised Galaxy pipeline for metabolite identification including some tool development and mechanisms for import and export of workflows between infrastructures.

In 2019, the Metabolomics Community was awarded a new Implementation Study to improve the technology underlying fluxomics analysis using metabolomics data. It comprises of cataloguing and developing tools for fluxomics analysis to develop a standardized fluxomics workflow and standards for isotopic tracer data deposition.

In addition to these five well-established Communities ELIXIR approved the establishment of another three Communities in 2019.

The Microbial Biotechnology Community will develop a formal framework for microbial biotechnology to manage and manipulate strains, samples, knowledge, data and metadata.

The Intrinsically Disordered Proteins (IDP) Community will support the development of standards, tools and resources to accelerate the identification, analysis and functional characterisation of IDPs.

The 3DBioInfo Community will focus on structural bioinformatics and will provide methods and tools to analyse, predict, archive and validate the threedimensional structure data of biomacromolecules such as proteins, RNA and DNA.

These Communities will start their work in 2020 with the award of dedicated Implementation Studies.