Resource Description Framework
Countries that developed this resource Worldwide
Created in 2011
How to cite this record FAIRsharing.org: RDF; Resource Description Framework; DOI: https://doi.org/10.25504/FAIRsharing.p77ph9; Last edited: March 12, 2020, 4:11 p.m.; Last accessed: Aug 01 2021 11:18 p.m.
Record updated: March 3, 2020, 7:06 p.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.p77ph9' by 'The FAIRsharing Team' at 19:06, 03 Mar 2020 (approved): 'licences' has been modified: Before: After: W3C Document License|https://www.w3.org/Consortium/Legal/2015/doc-license|Data Added: W3C Document License|https://www.w3.org/Consortium/Legal/2015/doc-license|Data Removed: 'supportLinks' has been modified: Before: TeSS training|https://tess.elixir-europe.org/materials/biosamples-database-rdf-webinar online documentation|http://www.w3.org/TR/2014/REC-rdf11-concepts-20140225/ After: TeSS training|https://tess.elixir-europe.org/materials/biosamples-database-rdf-webinar online documentation|https://www.w3.org/2001/sw/wiki/RDF1.1_Errata Added: online documentation|https://www.w3.org/2001/sw/wiki/RDF1.1_Errata Removed: online documentation|http://www.w3.org/TR/2014/REC-rdf11-concepts-20140225/ 'contactORCID' has been modified: Before: After: 0000-0001-5699-0515
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Conditions of UseApplies to: Data use
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Models and Formats
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ChEMBL is an open, manually-curated, large-scale bioactivity database containing information from medicinal chemistry literature. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. Information regarding the compounds tested (including their structures), the biological or physicochemical assays performed on these and the targets of these assays are recorded in a structured form, allowing users to address a broad range of drug discovery questions.
Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest. Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions. Rhea is built on ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to describe its reaction participants. Since December 2018, Rhea is the standard for enzyme annotation in UniProt.
figshare is a data publishing platform that is free for all researchers. Some of figshare’s core beliefs are: academic research outputs should be as open as possible, as closed as necessary; academic research outputs should never be behind a paywall; academic research outputs should be human and machine readable/query-able; academic infrastructure should be interchangeable; academic researchers should never have to put the same information into multiple systems at the same institution; identifiers for everything; and the impact of research is independent of where it is published and what type of output it is. figshare supports embargoing and managed access, and will embargo data while undergoing peer review. Metadata in figshare is licenced under is CC0. All files and metadata can be accessed from docs.figshare.com. figshare has also partnered with DuraSpace and Chronopolis to offer further assurances that public data will be archived under the stewardship of Chronopolis. In the highly unlikely event of multiple AWS S3 failures, figshare can restore public user content from Chronopolis. figshare is supported through Institutional, Funder, and Governmental service subscriptions.
Human Protein Atlas
The Human Protein Atlas (HPA) portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in a number of different wild-type tissues, cancer types and human cell lines. The goal of the HPA is to map all the human proteins in cells, tissues and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. The HPA is composed of six parts: the Tissue Atlas, the Single Cell Type Atlas, the Pathology Atlas, the Blood Atlas, the Brain Atlas, and the Cell Atlas.
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.
data.eNanoMapper.net is a public database hosting nanomaterials characterization data and biological and toxicological information. The database provides various possibilities to search and explore information, and to download data in various standard formats. The database supports data upload through configurable Excel templates.
BioPortal is 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 groups ontologies by domain to aid discoverability and allows users to browse, search and visualize the content of ontologies. BioPortal also provides ontology recommendation, text annotation, ontology mapping, and a reference index to resources like PubMed.
NBDC RDF Portal
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.
AgroPortal is an ontology repository for agronomy as well as food, plant, agriculture and biodiversity sciences. It provides ontology hosting, search, versioning, visualization, comment, and recommendation; enables semantic annotation; stores and exploits ontology alignments; and enables interoperation with the semantic web. To align with the needs of the agronomy community, AgroPortal uses SKOS vocabularies and trait dictionaries) and supported features (offering detailed metadata and advanced annotation capabilities).
Ag Data Commons
The Ag Data Commons is a public, government, scientific research data catalog and repository available to help the agricultural research community share and discover research data funded by the United States Department of Agriculture and meet Federal open access requirements. Ag Data Commons holds data files managed directly by NAL and also links to datasets and resources located on other websites. The Ag Data Commons provides access to a wide variety of open data relevant to agricultural research and related domains. These may include subjects such as agronomy, genomics, hydrology, soils, agro-ecosystems, sustainability science, and economic statistics. Ag Data Commons was created to foster innovative data re-use, integration, and visualization to support bigger, better science and policy.
Agrisemantics Map of Data Standards
The Agrisemantics Map of Data Standards database is a continuation of the VEST Registry started on the FAO AIMS website and includes metadata from the AgroPortal ontology repository. The registry covers all types of vocabularies in any format, ranging from description metadata sets (XML schemas, RDFS schemas, application profiles…) to KOSs of different types (classifications, thesauri, ontologies…). Domain coverage is broad, ranging from food and agricultural data to generic vocabularies (for e.g. bibliographic references) to vocabularies from neighbouring disciplines (e.g. climate). Agrisemantics is conceived as a metadata catalog, providing descriptions and categorization of standards and links to the original website and original serialization of the standard.
TogoVar (NBDC's integrated database of Japanese genomic variation) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them. TogoVar provides variant frequencies in the Japanese population that have been aggregated across research projects. Two available datasets, JGA-NGS and JGA-SNP, are obtained by aggregating individual genomic data that have been registered in the NBDC Human Database / Japanese Genotype-phenotype Archive (JGA). In addition, TogoVar integrates information related to genotypes or phenotypes that has been compiled independently in a variety of different databases and provides information for interpreting variants in a one-stop, easy-to-understand manner. TogoVar has been developed as a joint research project of National Bioscience Database Center (NBDC), Japan Science and Technology Agency (JST) and Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS) .
Center for Expanded Data Annotation and Retrieval Workbench
The Center for Expanded Data Annotation and Retrieval (CEDAR) Workbench is a database of metadata templates that define the data elements needed to describe particular types of biomedical experiments. The templates include controlled terms and synonyms for specific data elements. CEDAR is an end-to-end process that enables community-based organizations to collaborate to create metadata templates, investigators or curators to use the templates to define the metadata for individual experiments, and scientists to search the metadata to access and analyze the corresponding online datasets.
Agronomic Linked Data
The Agronomic Linked Data (AgroLD) is a knowledge-based system relying on Semantic Web technologies and exploiting standard domain ontologies, which integrates data about plant species of high interest for the plant science community. AgroLD is an RDF knowledge base of 100M triples created by annotating and integrating more than 50 datasets from 10 data sources and linked using 10 ontologies.
NERC Vocabulary Server
The NERC Vocabulary Server provides access to standardised lists of terms and taxonomies related to a wide range of concepts which are used to facilitate data markup, interoperability and discovery in the marine and associated earth science domains. Some of these vocabularies are totally managed by BODC, others are managed by BODC on behalf of other organisations, while some are owned and, when relevant, managed by external governance authorities.
Drug Database for Inborn Errors of Metabolism
DDIEM - Drug Database for inborn errors of metabolism is a database on therapeutic strategies for inborn errors of metabolism. These strategies are classified by mechanism and outcome in DDIEM ontology. DDIEM uses this ontology to categorize the experimental treatments that have been proposed or applied. The database includes descriptions of the phenotypes addressed by the treatment and drugs participating in treatment and procedures.
Genomic Observatories Meta-Database
The Genomic Observatories Meta-Database (GEOME) is a web-based database that captures the who, what, where, and when of biological samples and associated genetic sequences. GEOME helps users with the following goals: ensure the metadata from your biological samples is findable, accessible, interoperable, and reusable; improve the quality of your data and comply with global data standards; and integrate with R, ease publication to NCBI's sequence read archive, and work with an associated LIMS. The initial use case for GEOME came from the Diversity of the Indo-Pacific Network (DIPnet) resource.
Basel Register of Thesauri, Ontologies and Classifications
The Basel Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems (KOS) and KOS -related registries. Its main goal is to list as many KOS as possible in one place in order to achieve greater visibility, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages.
Research Vocabularies Australia
Research Vocabularies Australia (RVA) helps users access and reuse vocabularies for all areas of research. Some vocabularies are hosted by the Australian Research Data Commons (ARDC) and can be accessed directly through the RVA, otherwise links are provided to the vocabulary owner’s web page. Research Vocabularies Australia also allows you to create and/or publish a vocabulary as well as integrate an existing vocabulary into your own system.
Data and Service Center for the Humanities
The Data and Service Center for the Humanities (DaSCH) digital repository allows long-term access to qualitative data in the Humanities, and provides data deposition and discovery facilities. DaSCH has been created in accordance with the FAIR principles and various international standards for interoperability. The repository accepts “simple” datasets in form of flat files as well as a project-specific “complex” datasets with data based on project/user-specific data models. Multiple data types are allowed, including qualitative data such as text, images, digital facsimile, sound files, and videos.
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