Expertise building on Galaxy Administration, Pulsar, and CernVM File System

UseGalaxy.eu (https://usegalay.eu) is the main European Galaxy public instance, providing more than 2000 tools belonging to different bioinformatics research fields. Tens of smaller scale Galaxy instances are also available across Europe, while ELIXIR-IT is launching its first own Galaxy on-demand cloud service at the ReCaS Cloud and GARR Cloud facilities.

Indexing and search support for single-cell cytometry data repositories

Single-cell flow and mass cytometry has become a widely used method for biological research in developmental biology, immunology, clinical oncology, and various other areas. In recent years, a multitude of algorithms for analyzing the collected samples has emerged; allowing vast simplifications and speed-ups in processing large samples and sample sets. Various research efforts (including clinical data collection and e.g. International mouse phenotyping consortium (IMPC)) have collected hundreds of thousands of annotated samples.

Unification of alternative forms of chemical entities with collaborative effort

The ELIXIR Core Data Resource ChEBI is a dictionary of molecular entities and, currently, is able to handle all possible forms of a given chemical structure (E.g. neutral, tautomeric, protonated, isotopic, zwitterionic forms). Each form is assigned its own unique ChEBI identifier, which enables inter-relations within ChEBI via the ontology. 

Enabling FAIR plant phenotyping data submission through the Breeding API

Over the past four years, the ELIXIR Plant Sciences Community has been making large strides towards enabling FAIR plant phenotyping data: the ELIXIR plant data search service FAIDARE (https://urgi.versailles.inra.fr/faidare/) addresses findability by integrating the various BrAPI (https://brapi.org) end-points of ELIXIR Nodes, which address accessibility and ensure compliance with the MIAPPE metadata standard (https://www.miappe.org/) and therefore interoperability.