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Phyl Toukach edited this page Mar 18, 2018 · 30 revisions

GlycoRDF

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. The repository also contains source code for the generation of RDF data for glycomics databases.

Current version of GlycoRDF

Ontology: https://github.com/ReneRanzinger/GlycoRDF/blob/master/ontology/glycan.owl

Documentation: https://github.com/ReneRanzinger/GlycoRDF/blob/master/ontology/documentation.docx

Online ontology visualization: http://www.visualdataweb.de/webvowl/#opts=[sidebar=0;doc=0;filter_disjoint=false;]#iri=https://raw.githubusercontent.com/ReneRanzinger/GlycoRDF/master/ontology/glycan.owl

Updates to GlycoRDF

Users should send an email to the following

with the following information:

  • what changes have been made to which branch
  • a date by which responses should be sent when the changes will be merged to the master branch

Publications

Ranzinger R, Aoki-Kinoshita KF, Campbell MP, Kawano S, Lütteke T, Okuda S, Shinmachi D, Shikanai T, Sawaki H, Toukach P, Matsubara M, Yamada I, Narimatsu H. GlycoRDF: an ontology to standardize glycomics data in RDF. Bioinformatics. 31(6):919-925, 2015. (doi: 10.1093/bioinformatics/btu732.) (PMID: 25388145)

Aoki-Kinoshita, K.F., Bolleman, J., Campbell, M., Kawano, S., Kim, J.D., Luetteke, T., Matsubara, M., Okuda, S., Ranzinger, R., Sawaki, H., Shikanai, T., Shinmachi, D., Suzuki, Y., Toukach, P., Yamada, I., Packer, N.H., and Narimatsu, H. Introducing glycomics data into the Semantic Web, J. Biomed. Semantics. 4(1):39, 2013.

List of developers

The following table contains the people involved in the development of the standard ontology.

Name Institution
Rene Ranzinger Complex Carbohydrate Research Center, University of Georgia
Kiyoko F. Aoki-Kinoshita Faculty of Engineering, Soka University
Matthew P. Campbell Biomolecular Frontiers Research Centre, Macquarie University
Shin Kawano Database Center for Life Science, Research Organization of Information and Systems
Thomas Lütteke Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen
Shujiro Okuda Niigata University Graduate School of Medical and Dental Sciences
Hiromichi Sawaki Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology
Daisuke Shinmachi Faculty of Engineering, Soka University
Philip Toukach N.D. Zelinsky Institute of Organic Chemistry
Issaku Yamada Laboratory of Glyco-organic Chemistry, The Noguchi Institute

List of databases

The following table show the databases and online resources providing their glycan information in GlycoRDF format.

Database List of data types Documentation Example
CSDB - Glycan
- Sequence (GlycoCT, CSDB, CarbBank)
- Aglycon
- Polymerization frame positioning
- Cross references
- Biological annotation (taxon, strain)
- Bibliographic annotation (incl. abstracts)
- NMR spectra,assignment, experimental conditions
- Composition
- Analytical methods involved
CSDB documentation Single structure

All in one archive
GlycomeDB - Glycan
- Sequence (GlycoCT, GlydeII, LINUCS, CarbBank)
- Image (cfg, oxford, iupac) in png and svg
- Cross references
- Biological annotation (taxon)
- Composition
GlycomeDB documentation Single structure

All in one archive
MonosaccharideDB Monosaccharide properties and notation, including:
- Size
- Stereochemistry
- Ring type
- Core modifications
- Substituents
- Absolute Configuration (D/L)
- Alias names (GlycoCT, CSDB, CarbBank, Linucs, LinearCode, PDB, etc.)
Documentation (in development) Single structure
UniCarbKB - Glycan
- Sequence (GlycoCT, IUPAC)
- Image (cfg, oxford, iupac) in png and svg
- Biological annotation (taxon)
- Composition
- Glycoprotein information (global and site-specific)
- UniProt cross-references
- Bibliographic annotation
- Reported analytical methods
Documentation SPARQL EndPoint and Interface
GlycoNAVI - Glycan
- Chemical Synthetic Reaction
- Image (atomic) in png and/or svg
- Carbohydrate Interaction Information (STD-NMR)
- Small Molecule (solvent for analysis)
- Conformer
- TLC, Melting Point, Optical Rotation
- NMR data
- Proportion of Anomeric Isomers
GlycoNAVI documentation Single structure
GlycoEpitope - Epitope: name, identifier, carbohydrate structure, species or tis-sues expressing the epitope, and other related information
- Antibody: name, identifier, carbohydrate structure, species or tis-sues expressing the epitope, and other related information
- Glycoprotein: N-glycan or O-glycan, the glycosylation sites, epitope attachment sites, and other gene sequence related information
- Glycolipid: name, aliases, classification of the glycolipid, the sequence, carbohydrate composition, etc
- Enzyme: enzymes involved in the synthesis and degradation of the epitope, catalysis reaction, EC number, and other gene sequence information
Documentation (in development) Single structure
GlycoProtDB - Glycoprotein sequence
- Glycosylated Position (captured by lectin)
- Glycopeptide (IGOT) sequence
- Lectin (SSA, WGA, RCA120, AAL, ConA, Amide80, Gal6, DAS)
- Tissue
- Organism (C.elegans, Mus musculus, Homo sapiens)
- RefSeq cross-references
- Cross references of Protein
Documentation (in development) Single structure
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