standards > terminology artifact > DOI:10.25504/FAIRsharing.2fnz2n


ready GlycoRDF

Abbreviation: GLYCORDF


General Information
GlycoRDF is a standard representation for storing Glycomcis data (glycan structures, publication information, biological source information, experimental data) in RDF. The RDF language is defined by an OWL ontology and documented in the ontology and generated WORD files. Its GitHub repository also contains source code for the generation of RDF data for glycomics databases.

Homepage http://www.glycoinfo.org/GlycoRDF/

Countries that developed this resource Australia , Japan , United States

Created in 2014

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How to cite this record FAIRsharing.org: GLYCORDF; GlycoRDF; DOI: https://doi.org/10.25504/FAIRsharing.2fnz2n; Last edited: Feb. 5, 2019, 1:55 p.m.; Last accessed: May 19 2019 3:17 p.m.

Publication for citation  GlycoRDF: an ontology to standardize glycomics data in RDF. Ranzinger R,Aoki-Kinoshita KF,Campbell MP,Kawano S,Lutteke T,Okuda S,Shinmachi D,Shikanai T,Sawaki H,Toukach P,Matsubara M,Yamada I,Narimatsu H; Bioinformatics ; 2014; 10.1093/bioinformatics/btu732;


This record is maintained by Issaku  ORCID

Record added: Oct. 24, 2017, 9:41 a.m.
Record updated: Feb. 5, 2019, 1:55 p.m. by The FAIRsharing Team.

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No XSD schemas defined


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Publications

GlycoRDF: an ontology to standardize glycomics data in RDF.

Ranzinger R,Aoki-Kinoshita KF,Campbell MP,Kawano S,Lutteke T,Okuda S,Shinmachi D,Shikanai T,Sawaki H,Toukach P,Matsubara M,Yamada I,Narimatsu H
Bioinformatics 2014

View Paper (PubMed) View Publication

Introducing glycomics data into the Semantic Web.

Aoki-Kinoshita KF,Bolleman J,Campbell MP,Kawano S,Kim JD,Lutteke T,Matsubara M,Okuda S,Ranzinger R,Sawaki H,Shikanai T,Shinmachi D,Suzuki Y,Toukach P,Yamada I,Packer NH,Narimatsu H
J Biomed Semantics 2013

View Paper (PubMed) View Publication

GLYCORDF Ontology Display

View in BioPortal.


Disclaimer: This widget assumes the availability of the ontology resources in the NCBO BioPortal.


Related Standards

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Terminology Artifacts

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Implementing Databases (6)
GlycoNAVI
GlycoNAVI is a gateway to free suite of carbohydrate research tools. It will let you access to variety of information and assist your research.

Carbohydrate Structure Database
The Carbohydrate Structure Database (CSDB) contains manually curated natural carbohydrate structures, taxonomy, bibliography, NMR data and more. The Bacterial (BCSDB) and Plant&Fungal (PFCSDB) databases were merged in 2015, becoming the CSDB, to improve the quality of content-dependent services, such as taxon clustering and NMR simulation.

Monosaccharide Database
Database on carbohydrate building blocks / residues (monosaccharides). Provides various kinds of residue data, especially notation information.

GlycoProtDB
GlycoProtDB is a glycoprotein database providing information of Asn (N)-glycosylated proteins and their glycosylated site(s), which were constructed by employing a bottom-up strategy using actual glycopeptide sequences identified by LC/MS-based glycoproteomic technologies. The database is searchable using gene ID, gene name, and its description (protein name) as query. Each data sheet of glycproteins is based on a single amino acid sequence in Wormpep database for C.elegans and NCBI Refseq database for mouse. The sheet presents actually detected N-glycosylation site(s) which are displayed each capturing methods of glycopeptide subset, e.g., lectins Concanavalin A, wheat germ agglutinin (WGA), or HILIC (hydrophilic interaction chromatography), as well as potential N-glycosylation sites (NX[STC], X≠P). Protein sequences, which have common glycopeptide sequence(s), are linked each other.

GlycomeDB
GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links.

UniCarbKB
UniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. The knowledgebase will offer a freely accessible and information-rich resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data.

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