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Standards > model/format > bsg-s000559

ready Resource Description Framework


General Information
The Resource Description Framework (RDF) is a framework for representing information in the Web. This document defines an abstract syntax (a data model) which serves to link all RDF-based languages and specifications. The abstract syntax has two key data structures: RDF graphs are sets of subject-predicate-object triples, where the elements may be IRIs, blank nodes, or datatyped literals. They are used to express descriptions of resources. RDF datasets are used to organize collections of RDF graphs, and comprise a default graph and zero or more named graphs. RDF 1.1 Concepts and Abstract Syntax also introduces key concepts and terminology, and discusses datatyping and the handling of fragment identifiers in IRIs within RDF graphs.

This record is maintained by rafaelrichards

Record updated: July 6, 2017, 2:31 p.m. by The FAIRsharing Team.



Additional Information

TeSS training resources 

Biosamples database rdf webinar


    No tools defined


No XSD schemas defined

Access / Retrieve Data

Conditions of Use


Implementing Databases (7)
UniProt Knowledgebase
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The UniProt Knowledgebase consists of two sections: a reviewed section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis (aka "UniProtKB/Swiss-Prot"), and an unreviewed section with computationally analyzed records that await full manual annotation (aka "UniProtKB/TrEMBL").

RegenBase is a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details from publications, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase enables researchers to organize and interrogate experimental data generated by spinal cord injury (SCI) research, with the ultimate goal of translating SCI experimental findings in model organisms into human therapies.

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S), Open Biological and Biomedical Ontologies (OBO) format, and Protégé frames and Rich Release Format. BioPortal has a service-oriented architecture; the NCBO Web services provide the functionality found in BioPortal and these Web services can be incorporated into other software applications to access and use ontology content. BioPortal groups ontologies by domain to ease finding relevant ontologies and allows users to browse, search and visualize the content of ontologies. BioPortal also provides value-added features like ontology recommendation, text annotation, ontology mapping, and a reference index to resources like PubMed.

The NBDC RDF Portal provides a collection of life science datasets in RDF (Resource Description Framework). The portal aims to accelerate integrative utilization of the heterogeneous datasets deposited by various research institutions and groups. In this portal, each dataset comes with a summary, downloadable files and a SPARQL endpoint.

Free knowledge database project hosted by Wikimedia and edited by volunteers.

A linked data server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. Ontobee dynamically dereferences and presents individual ontology term URIs to (i) HTML web pages for user-friendly web browsing and navigation, and to (ii) RDF source code for Semantic Web applications. Ontobee is the default linked data server for most OBO Foundry library ontologies. Ontobee has also been used for many non-OBO ontologies.

Xenobiotics Metabolism Database
XMetDB is an open access and open source database and web interface for the submission and retrieval of experimental metabolite data for drugs and other xenobiotics. It will also feature an open API for access to the database.

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