Interoperability and standards services

A reusable platform-independent API call component for protein metadata alignment, annotation, and integration across major protein data resources.

ANISEED is the main model organism database for the worldwide community of scientists working on a class of marine invertebrates, the tunicates (sister-group of vertebrates). It integrates for each species: a main knowledge base with extended information on gene function, gene expression, phylogeny and embryonic anatomy at single cell resolution; a genomic browser and a Genomicus gene synteny browser.

APICURON is a database to credit and acknowledge the work of biocurators. It collects and aggregates biocuration events from third party resources generating achievements and leaderboards.

Aruna Object Storage is a data lake storage system that manages scientific data and a rich set of associated metadata according to FAIR principles.

 BIII Bio Image informatics Index (www.biii.eu) is a knowledge database of software tools, test image databases and training materials for bio image analysis. Software tools are organized as full protocol of analysis (workflow), specific brick (component) to construct a workflow, or software platform or library (collection).  They are described using Edam Bio Imaging, which is iteratively defined using this website. All entries are exposed following FAIR principles and accessible for other usage with  (ODC-By) v1.0 license.

Provides an R interface to BioMart services. In particular this is the most widely used programmatic access route to query EMBL-EBI’s Ensembl database.

A framework to map identifiers between various databases.

ELIXIR-NL can help organise standard events that make data sources more FAIR by applying Linked Data, or help make data repository software more FAIR. Such meetings focus on one or two data sources, and will bring together your experts on the data content and on the usage of the data with experts in data modeling. As an important side-effect such events also educate the participants on what it means to make data FAIR in practice.

General‐purpose software for making genotype–phenotype data discoverable in restricted or open access contexts.

Gold standard of oncology clinical cases annotated with CIE-O 3 terminology

Conceptual modelling, especially OntoUML, UML, BORM, DEMO and BPMN and consultancy. Software solutions design, software development and consultancy.

Expertise on very diverse subjects of data processing, analysis and curation as well as connections to existing infrastructure RI's like EUDAT. This expertise can be made available to research projects and organisations.  

COPO is a portal for scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results. COPO can link your outputs to your ORCiD profile.

Support regarding data uploads into public repositories (esp. PRIDE), standard data formats and converters.

The Data Stewardship Wizard is an international project to help serious researchers and data stewards with building smart Data Management Plans for FAIR Open Science.

Data, Otimization, Model and Evaluation: Recommendations for supervised machine learning validation in biology.

DSW@IFB is the support service for the development of data management plans in life sciences hosted by the French Bioinformatics Institute (IFB / ELIXIR-FR) and based an instance of the Data Stewardship Wizard<https://ds-wizard.org/>.

Plant Genomics and Phenomics Research Data Repository (e!DAL-PGP) is an infrastructure to comprehensively publish plant research data.

An ontology primarily dedicated to categorising computational tools and data resources

Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help the research communities to make and keep data Findable, Accessible, Interoperable and Reusable (FAIR). The FAIR Cookbook guides researchers and data stewards of the Life Science domain in their FAIRification journey and provides policy makers and trainers with practical examples to recommend in their guidance and use in their educational material. As a UK-LU joint Node Service, we will continue the development the FAIR Cookbook as well as collaborate towards its sustainability.

This is a joint Node Service between ELIXIR Luxembourg and ELIXIR UK.

Data publication technology/tooling based on Linked Data, with associated data management processes. See the FAIR data tools.

FAIR-Checker is a generic tool built on semantic web W3C standards and technologies that aims at assessing the alignement to FAIR principles of web resources, in line with the GO-FAIR and RDA FAIR data maturity model.

The SEEK platform is a web-based resource for sharing heterogeneous scientific research datasets, models or simulations, processes and research outcomes. 

Open source web platform for sharing scientific research assets, models, processes and outcomes. Offering the FAIRDOMHub instance, as well as the SEEK software for own installations. Associated tooling and training.

An information and educational resource of inter-related data standards, databases and policies. 

FAIRtracks is 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 is a bioinformatics toolkit for characterising and manipulating gene lists of high-throughput genomic data.

The Gene Ontology (GO) project addresses the need for consistent descriptions of gene products across databases. It has developed three structured, controlled vocabularies (ontologies) that describe gene products.

HUGO Gene Nomenclature Committee, responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication.

Identifiers.org is a system providing resolvable persistent URIs used to identify data for the scientific community, with a current focus on the Life Sciences domain.

An ontology for IDP community: it enables the annotation of structural and functional properties of intrinsically disordered proteins and their interaction partners.

An integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) of human and other vertebrate species. 

A database framework widely used to support model organism databases. 

A suite of open source tools and formats to enable standards-compliant collection, curation, management, publication and reuse of experiments. 

The Italian COVID-19 Data Portal provides information, guidelines, tools and services to support researchers in creating and sharing research data on COVID-19.

A Galaxy-based workbench providing established tools (e.g BioMaS, Mothur and qiime2) targeted at global taxonomic analysis of eukaryotic communities based on Internal Transcribed Spacer 1 variants high-throughput sequencing.

A comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. KnetMiner is a web application to search and visualise genome-scale knowledge networks. It is used by scientists in academia and industry to accelerate gene-trait discovery research. KnetMiner offers features such as keyword, gene list and genome region search, query refinement, gene ranking, gene set enrichment analysis and interactive visualisation of knowledge networks and genomic information.

A web tool and a mobile app for exploring the entire Tree of Life

Provides access to lipid nomenclature, databases, tools, protocols, standards, tutorials, meetings, publications, and other resources and serving the international lipid research community.

The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes and much more.

A software package to help researchers set up an online database application that supports data queries and allows data sharing.

The NERC Environmental Omics Facility (NEOF) will enable environmental researchers in the UK to access the full range of omics supporting technology.

The Omics Discovery Index provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics). It indexes metadata from more than 20 omics resources across four continents.

Terms that are commonly encountered while conducting, reporting, storing, harmonizing, integrating, and describing nutritional studies. ONS builds upon a subset of the Ontology for Biomedical Investigations (OBI), reuses already formalized information by importing terms already defined in other ontologies, and defines de novo key classes/terms to tailor concept to the nutritional field

OpenEBench (https://openebench.bsc.es) is the ELIXIR benchmarking and technical monitoring platform for bioinformatics tools, web servers and workflows. 

Orphadata provides the scientific community with comprehensive, quality data sets related to rare diseases and orphan drugs from the Orphanet knowledge base, in reusable formats.

Orphanet is the reference resource for information and data on rare diseases and orphan drugs. Orphanet derives from its knowledge base an ontology of rare diseases, information on rare diseases and data on rare diseases.

A service for the publishing, archiving and re-using data.

ParameciumDB is a community model organism database for the ciliate Paramecium. The web site gives access to genomes of many Paramecium species and their annotations. ParameciumDB also  integrates  genome-wide datasets (DNA-seq, RNA-seq, ChIP-seq) provided by the community. This portal is used to query, retrieve, visualize and compare the most up-to-date public data.

A comprehensive ontology for the plant domain, that is useful for data integration and querying heterogeneous data.

Plant-oriented online resource for comparative, evolutionary and functional genomics.

The ELIXIR Research Data Management Kit (RDMkit) is an online guide containing best practices in data management applicable to research projects from the beginning to the end. RDMkit is developed and managed by people who work every day with life science data. 

Either as a cooperation or consultancy service.

The Ontology Lookup Service (OLS) provides a web service interface to query multiple ontologies from a single location with a unified output format.

Diverse tools under development, in use in BYOD events to facilitate making data FAIR using linked data technology.

An open, collaborative platform dedicated to the curation of biological pathways