ELIXIR Service Bundles for Rare Diseases

The ELIXIR Rare Diseases Service Bundles are aimed at users and consumers of bioinformatic tools, services, and training materials.

These Service Bundles provide Use Case focussed user journeys through the suite of tools and services that can be used in rare diseases research. Members of the ELIXIR Rare Diseases Community have generated these Service Bundles and they are continuously updated. For any questions please contact Gary Saunders at the ELIXIR Hub (gary.saunders@elixir-europe.org).

Assessing Molecular Pathogenicity for Rare Diseases

Use this Service Bundle to
Identify supporting evidence to define genotype-phenotype relationships.
Predict the impact of genetic variations on protein structure and function.
Characterise the molecular mechanisms underlying rare diseases.

The ELIXIR Service Bundle "Assessing Molecular Pathogenicity for Rare Diseases" (AMP4RD) aims to define the procedures and guidelines for the annotation and interpretation of genetic variants in the human genome. Our initiative aims to implement an integrated infrastructure for characterizing the relationship between genotype and phenotype both from the clinical and research perspectives, and  deliver computing workflows and tools for the annotation and interpretation of genetic variants.

Link(s):
Coordinators:
David Salgado (ELIXIR-FR), Emidio Capriotti (ELIXIR-IT)
Contact(s):
  • david.salgado@univ-amu.fr
  • emidio.capriotti@unibo.it
Nodes involved:
ELIXIR France, ELIXIR Italy, ELIXIR Spain, EMBL-EBI

Systems Biology Service Bundles for Rare Diseases

Use this Service Bundle to
Create and curate rare disease pathways.
Extract variant-gene associations and information about functional information.
Analyse lists of differentially expressed genes in pathways and networks.

The analysis workflows in the systems biology Service Bundle for rare diseases cover a variety of tasks that are demanded for rare disease data analysis.  For example, it is possible to collect biomedical expert knowledge, e.g. from published papers, databases etc., and make the results machine readable for pathway and network analysis and to link it with information from other databases.

The Service Bundles were developed together and within the European Joint Programme on Rare Diseases (EJP-RD). For each of the tasks a concept map was published, we expect these to be extended and new maps to be added in the future.

Link(s):
Coordinators:
Friederike Ehrhart (ELIXIR-NL)
Contact(s):
  • friederike.ehrhart@maastrichtuniversity.nl
  • chris.evelo@maastrichtuniversity.nl
Nodes involved:
ELIXIR Netherlands

ELIXIR Trainground for Rare Diseases

Use this Service Bundle to
Bring together a cloud (tools, pipelines and services), repository for learning materials, interactive online teaching features, and user management with ELIXIR AAI through a single-access point.

The ELIXIR Trainground for Rare Diseases Service Bundle is intended as a non-commercial alternative to cloud learning management systems (LMS) that are used for training in the field of genomic analysis. Our platform, the ELIXIR-SI eLearning Platform (EeLP), brings together a cloud (tools, pipelines and services), repository for learning materials, interactive online teaching features, and user management with ELIXIR AAI through a single-access point.

Coordinators:
Lennart Johansson (ELIXIR-NL), Marko Vidak (ELIXIR-SI)
Contact(s):
  • l.johansson@umcg.nl
  • marko.vidak@mf.uni-lj.si
  • elixir@mf.uni-lj.si
Nodes involved:
ELIXIR Netherlands, ELIXIR Slovenia