The ELIXIR Recommended Interoperability Resources (RIRs) are tools and registries that have been selected by a panel of external reviewers and are identified as resources that facilitate the FAIR-supporting activities in scientific research, such as:
- Establishing connections between data (and other) resources
- Acquiring and exposing metadata of data (and other) resources
- Creating the infrastructure needed to build integratable data collections
- Using interoperability resources to support delivery of FAIR principles
ELIXIR Recommended Interoperability Resources
Updated December 2023
| Resource | Description |
|---|---|
| 3DBIONOTES API | A reusable platform-independent API call component for protein and gene metadata alignment, annotation, and integration across major bioinformatic data resources. |
| BioImage Informatics Index | A bioimaging resource (tool/workflow) finder based on biological questions, methods and tools with linked literature of the resource. |
| Bgee Knowledge Graph | The Bgee database through its SPARQL endpoint provides access to gene expression patterns in multiple animal species, which result from the integration and harmonisation of several data sources. |
| BridgeDb | A combination of a software framework and an API for mapping identifiers for related objects in life sciences. |
| Data Stewardship Wizard (DSW) | Data Stewardship Wizard (DSW) is a service for data management planning, i.e. preparing data management plans. |
| DisGeNET RDF API | An RDF SPARQL Endpoint for DisGeNET, a knowledge platform on human disease genes and variants. |
| European Galaxy Server | Galaxy is an interoperable open-source platform for scientific data analysis and sharing, covering diverse research fields such as *omics, machine learning, and climate science. |
| FAIR Cookbook | The FAIR Cookbook, a live, open, online, collaborative resource of hands-on recipes for “FAIR doers” in the Life Sciences. |
| FAIRsharing | A FAIR-supporting resource including a registry on data standards, repositories and policy, alongside informative and educational tools and services. |
| FAIRtracks | A set of JSON Schemas defining a draft minimal standard used to consolidate genomic track metadata from various sources, which can be queried by downstream clients through the TrackFind webtool/API. |
| g:Profiler | A gene-centric data integrator with web UI and API services. |
| Identifiers.org | Provider of persistent and compact identifiers for data objects in life sciences through a curated registry and associated resolver. |
| InterMine | Framework to integrate life sciences data based on an extensible data model, providing web interface and RESTful web services. |
| ISA Framework | The ISA (Investigation > Study > Assay) provides formats and tools to manage the experimental descriptions throughout the research life cycle, from collection, curation and deposition in public repositories, to analysis with existing tools and publication in data journals. |
| Jalview | Jalview is a Win/Mac/Linux/Web interactive graphical interface and command line tool for molecular sequence, alignment and 3D structure bioinformatics resource interoperability. |
| MOLGENIS | A flexible data integration platform to facilitate FAIR research data and accelerate scientific collaborations. |
| Omics Discovery Index (OmicsDI) | Provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics). |
| Ontology Lookup Service | Repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions through web UI or RESTFUL API. |
| OpenEBench | OpenEBench is a platform to evaluate life sciences tools from two points of view: Scientific performance through community-based benchmarking and Quality through an Observatory of Software Quality. |
| PLAZA | Provides an integrative resource for functional, evolutionary, and comparative genomics in plants. |
| RDMkit | The RDMkit is an open-source, online toolkit for researchers and data stewards, providing Research Data Management (RDM) best practices in line with the FAIR principles. |
The portfolio of ELIXIR Recommended Interoperability Resources will be regularly evaluated for quality assurance and quality control. Further resources will be included in future calls for RIR application as ELIXIR evolves, accommodating emerging technologies and changing scientific needs. Recommendations for use of RIRs should also be recognised as suggestions and not a mandate as we value emerging developments from our ELIXIR members based on upcoming ELIXIR use case requirements.