Marine Metagenomics services

Name Description ELIXIR Node

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 Norway

ELIXIR is about integration of diverse resources including tools, training materials and technical services. Within EXCELERATE, ELIXIR is building portals to collate information on tools and data services (bio.tools), training events and material (TeSS, WP11 e-learning environment), compute resources (WP4 technical service registry) and cross-linked policy, standards and databases (FAIRsharing, WP4). A focus of EXCELERATE is to set up these portals such that they can interoperate.

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and FAIRsharing to find standards and databases. At the moment these ELIXIR portals provide a useful, but fragmented service.  Ideally, linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. In this implementation study, we want to achieve the first step and link TeSS and bio.tools via most prevalent bioinformatics workflows and lay the foundation to later incorporate other ELIXIR platforms, such as the compute resources, to provide an even more useful service for the researcher.

The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.

 ELIXIR UK, ELIXIR Estonia, ELIXIR Belgium, ELIXIR Denmark, ELIXIR Switzerland, EMBL-EBI, ELIXIR Norway, ELIXIR France
EMBL-EBI

The objective is to develop and deploy an “ELIXIR Contextual Data Clearinghouse (clearinghouse)” for extending, correcting and improving publicly available annotations on records in sample and sequencing data resources.

Contextual data is fundamental for FAIR data in ELIXIR. So far, little attention has been paid to connect and exchange curated contextual data to improve the quality of primary and secondary and data resources within the metagenomics domain. In this proposal, we will build a “clearinghouse” to allow seamless exchange of contextual data between ELIXIR data resources.

The project will strengthen the collaborations between these ELIXIR resources, build synergies to improve the quality and impact of the content and, not least, build more sustainable data resources. The proposed project will be an excellent showcase on how the outcomes of the EXCELERATE Marine Metagenomics Use Case, together with established and new ELIXIR data resources, can improve the quality and impact of publicly available data, especially towards the marine domain.

 ELIXIR Norway, EMBL-EBI, ELIXIR Germany, 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

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

Comparison of environmental sequences to reference sets from curated marker loci provides a mainstay for taxonomic analysis of microbial communities. Microbial eukaryotic sequencing requires many distinct reference sets to cover diversity adequately. Those producing reference sets follow different curation workflows, but share the need to provide their data onwards to a common set of tools and services, such as EMG, Megan, MetaPIPE and BioMaS.

There are multiple inefficiencies:

  • reference set providers must build services to sustain and feed their data to consumer tools and services
  • consumers must import reference sets from several sources with different formats.

Led by the ITSoneDB team, who provide the leading fungi and other eukaryotes ITS1 reference set, we will develop a new data type within ENA that will capture systematically these reference sets and serve them to dependent resources, eliminating inefficiencies, leveraging this core ELIXIR resource and building sustainability into reference set generation workflows.

Currently, taxonomic analysis of microbial communities relies on multiple dispersed reference data sets.  The impact of this study will be that ENA will be enriched with a new structured data type to accommodate these taxonomic reference datasets, beginning with ITS1 from rRNA, from the ITSoneDB team.  

By enhancing the connectivity and coordination between the various reference datasets and ENA a stable system to systematically capture their data and serve them to the consumer services from one place will be made available. This will increase both the sustainability and exposure of the data and facilitate/promote their use and re-use.

 ELIXIR Italy, EMBL-EBI

Marine genomics and metagenomics is still in its infancy, but is a rapidly expanding area of life science research. This study started in 2014 and has been instrumental in certain developments. 

To prevent the large-scale implementation of such studies from being disruptive (where the data production is faster than the speed users are able to analyze and interpret it) there is an urgent need to establish dedicated data management e-infrastructure and bioinformatics pipelines specialized for marine research.  

This project, involving ELIXIR Norway, EMBL-EBI and other partners from the ELIXIR Nodes, aimed to harmonize existing pipelines, either through improve established components or developing new in order to establish long-term sustainable service platforms. More recently, this work has led the announcement of a Marine Metagenomics Community including a dedicated website with details of meetings, workshops and other activities. 

The project outcomes have been published: Marine metagenomics – towards a domain specific set of sustainable services. The study is now complete, the end report is available here.

Webinar summarising the outcomes

(rec. June 2015) 

 ELIXIR Norway, EMBL-EBI
ELIXIR Finland
EMBL-EBI, ELIXIR Norway