Services: Interoperability And Standards

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.