The ELIXIR Recommended Interoperability Resources (RIRs) are tools and registries that have been selected by a panel of external reviewers. These resources build a network of foundational components underlying the ELIXIR Interoperability FAIR Service Framework (see the Interoperability Platform page). The RIRs are identified as resources that facilitate the FAIR-supporting activities in scientific research, such as:
- Establish connections between data (and other) resources
- Acquire and expose metadata of data (and other) resources
- Create the infrastructure needed to build integratable data collections
- Use interoperability resources to support delivery of FAIR principles
See the slide presentation by Prof Carole Goble for more details.
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 (next one to be announced in November 2021) 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.
ELIXIR Recommended Interoperability Resources list
|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.|
|BridgeDb||A combination of a software framework and an API for mapping identifiers for related objects in life sciences.|
|DisGeNET RDF API||An RDF SPARQL Endpoint for DisGeNET, a knowledge platform on human disease genes and variants|
|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.|
|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.|
|PLAZA||Provides an integrative resource for functional, evolutionary, and comparative genomics in plants.|
Further information: Peter Maccallum (peter.maccallum [at] elixir-europe.org).