GlycoCT sequence format for carbohydrates.
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GlycoCT sequence format for carbohydrates.
metasource: Fairsharing.org
version: FAIRsharing.org: GlycoCT XML; GlycoCT sequence format for carbohydrates.; DOI: https://doi.org/10.25504/FAIRsharing.qz30cx; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
GlycoCT XML
metasource: Fairsharing.org
version: FAIRsharing.org: GlycoCT XML; GlycoCT sequence format for carbohydrates.; DOI: https://doi.org/10.25504/FAIRsharing.qz30cx; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Names
More detailed information about this field from each metasource.
GlycoCT sequence format for carbohydrates.
metasource: Fairsharing.orgversion: FAIRsharing.org: GlycoCT XML; GlycoCT sequence format for carbohydrates.; DOI: https://doi.org/10.25504/FAIRsharing.qz30cx; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
GlycoCT XML
metasource: Fairsharing.orgversion: FAIRsharing.org: GlycoCT XML; GlycoCT sequence format for carbohydrates.; DOI: https://doi.org/10.25504/FAIRsharing.qz30cx; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Names
More detailed information about this field from each metasource.
GlycoCT sequence format for carbohydrates.
metasource: Fairsharing.orgversion: FAIRsharing.org: GlycoCT XML; GlycoCT sequence format for carbohydrates.; DOI: https://doi.org/10.25504/FAIRsharing.qz30cx; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
GlycoCT XML
metasource: Fairsharing.orgversion: FAIRsharing.org: GlycoCT XML; GlycoCT sequence format for carbohydrates.; DOI: https://doi.org/10.25504/FAIRsharing.qz30cx; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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GlycoCT format is devised to describe the carbohydrate sequences, with a controlled vocabulary to name monosaccharides, adopting IUPAC rules to generate a consistent, machine-readable nomenclature, based on a connection table approach, instead of a linear encoding scheme. The format uses a block concept to describe frequently occurring special features of carbohydrate sequences like repeating units. It exists in two variants, a condensed form and a more verbose XML syntax. Sorting rules assure the uniqueness of the condensed form, thus making it suitable as a direct primary key for database applications, which rely on unique identifiers. GlycoCT encompasses the capabilities of the heterogeneous landscape of digital encoding schemata in glycomics and is thus a step forward on the way to a unified and broadly accepted sequence format in glycobioinformatics.
Description
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GlycoCT format is devised to describe the carbohydrate sequences, with a controlled vocabulary to name monosaccharides, adopting IUPAC rules to generate a consistent, machine-readable nomenclature, based on a connection table approach, instead of a linear encoding scheme. The format uses a block concept to describe frequently occurring special features of carbohydrate sequences like repeating units. It exists in two variants, a condensed form and a more verbose XML syntax. Sorting rules assure the uniqueness of the condensed form, thus making it suitable as a direct primary key for database applications, which rely on unique identifiers. GlycoCT encompasses the capabilities of the heterogeneous landscape of digital encoding schemata in glycomics and is thus a step forward on the way to a unified and broadly accepted sequence format in glycobioinformatics.
metasource: Fairsharing.orgversion: FAIRsharing.org: GlycoCT XML; GlycoCT sequence format for carbohydrates.; DOI: https://doi.org/10.25504/FAIRsharing.qz30cx; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Webpage:
http://www.eurocarbdb.org/recommendations/encoding/GlycoCT_V3.pdfWebpage
More detailed information about this field from each metasource.
http://www.eurocarbdb.org/recommendations/encoding/GlycoCT_V3.pdf
metasource: Fairsharing.orgversion: FAIRsharing.org: GlycoCT XML; GlycoCT sequence format for carbohydrates.; DOI: https://doi.org/10.25504/FAIRsharing.qz30cx; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
GlycoCT-a unifying sequence format for carbohydrates
PMID: 18436199
metasource: Fairsharing.org
version: FAIRsharing.org: GlycoCT XML; GlycoCT sequence format for carbohydrates.; DOI: https://doi.org/10.25504/FAIRsharing.qz30cx; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications
More detailed information about this field from each metasource.
GlycoCT-a unifying sequence format for carbohydrates
PMID: 18436199
metasource: Fairsharing.org
version: FAIRsharing.org: GlycoCT XML; GlycoCT sequence format for carbohydrates.; DOI: https://doi.org/10.25504/FAIRsharing.qz30cx; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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GlycoCT-a unifying sequence format for carbohydrates
PubMed citations: 64.
64 articles citing: GlycoCT-a unifying sequence format for carbohydrates
Dealing with the Ambiguity of Glycan Substructure Search. PMID:35011294
SugarDrawer: A Web-Based Database Search Tool with Editing Glycan Structures. PMID:34885724
Trop2 Forms a Stable Dimer with Significant Structural Differences within the Membrane-Distal Region as Compared to EpCAM. PMID:34638982
Informatics Ecosystems to Advance the Biology of Glycans. PMID:34626414
O-Glycologue: A Formal-Language-Based Generator of O-Glycosylation Networks. PMID:34611872
An Interactive View of Glycosylation. PMID:34611864
GlycoStore: A Platform for H/UPLC and Capillary Electrophoresis Glycan Data. PMID:34611863
Glycoinformatics Tools for Comprehensive Characterization of Glycans Enzymatically Released from Proteins. PMID:34611862
Enhancing the interoperability of glycan data flow between ChEBI, PubChem and GlyGen. PMID:34314492
Glycowork: A Python package for glycan data science and machine learning. PMID:34192308
FGDB: Database of follicle stimulating hormone glycans. PMID:33897975
Simulating the enzymes of ganglioside biosynthesis with Glycologue. PMID:33828618
Molecular representations in AI-driven drug discovery: a review and practical guide. PMID:33431035
GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans. PMID:33322545
Insights into Bioinformatic Applications for Glycosylation: Instigating an Awakening towards Applying Glycoinformatic Resources for Cancer Diagnosis and Therapy. PMID:33302373
A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR). PMID:33178355
The international glycan repository GlyTouCan version 3.0. PMID:33125071
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer. PMID:33093930
Computational tools for drawing, building and displaying carbohydrates: a visual guide. PMID:33082879
Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations. PMID:33076365
Glycosaminoglycan-Protein Interactions: The First Draft of the Glycosaminoglycan Interactome. PMID:32757871
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
GlycoGlyph: a glycan visualizing, drawing and naming application. PMID:32170934
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. PMID:31735951
The MetaCyc database of metabolic pathways and enzymes - a 2019 update. PMID:31586394
Towards a standardized bioinformatics infrastructure for N- and O-glycomics. PMID:31332201
glypy: An Open Source Glycoinformatics Library. PMID:31310539
A Bioinformatics View of Glycan⁻Virus Interactions. PMID:31018588
SugarSketcher: Quick and Intuitive Online Glycan Drawing. PMID:30563078
GlycanFormatConverter: a conversion tool for translating the complexities of glycans. PMID:30535258
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. PMID:30371822
Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update). PMID:30357361
UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D structures and interacting ligands. PMID:30239928
Glycomics@ExPASy: Bridging the Gap. PMID:30097532
The Glycoscience of Immunity. PMID:29759949
Emerging glycobiology tools: A renaissance in accessibility. PMID:29759530
GLYDE-II: The GLYcan data exchange format. PMID:28955652
Glycoblocks: a schematic three-dimensional representation for glycans and their interactions. PMID:28177314
An editor for the generation and customization of geometry restraints. PMID:28177308
Glycosaminoglycanomics: where we are. PMID:27900575
A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts. PMID:27054587
Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search. PMID:26656740
SugarBindDB, a resource of glycan-mediated host-pathogen interactions. PMID:26578555
GlyTouCan 1.0--The international glycan structure repository. PMID:26476458
Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts. PMID:26286194
Integration of systems glycobiology with bioinformatics toolboxes, glycoinformatics resources, and glycoproteomics data. PMID:25871730
GlycoRDF: an ontology to standardize glycomics data in RDF. PMID:25388145
GlycoPattern: a web platform for glycan array mining. PMID:25143288
X-ray structure of the mouse serotonin 5-HT3 receptor. PMID:25119048
Toolboxes for a standardised and systematic study of glycans. PMID:24564482
Introducing glycomics data into the Semantic Web. PMID:24280648
UniCarbKB: building a knowledge platform for glycoproteomics. PMID:24234447
Exploring site-specific N-glycosylation microheterogeneity of haptoglobin using glycopeptide CID tandem mass spectra and glycan database search. PMID:23829323
The use of glycoinformatics in glycochemistry. PMID:23015842
Glycan fingerprints: calculating diversity in glycan libraries. PMID:22373368
Semi-automated identification of N-Glycopeptides by hydrophilic interaction chromatography, nano-reverse-phase LC-MS/MS, and glycan database search. PMID:22239659
Understanding glycomechanics using mathematical modeling: a review of current approaches to simulate cellular glycosylation reaction networks. PMID:22090146
GlycomicsDB - A Data Integration Platform for Glycans and their Strucutres. PMID:21603090
Systems glycobiology: biochemical reaction networks regulating glycan structure and function. PMID:21436236
EUROCarbDB: An open-access platform for glycoinformatics. PMID:21106561
GlycomeDB--a unified database for carbohydrate structures. PMID:21045056
Bioinformatics and molecular modeling in glycobiology. PMID:20364395
GlycomeDB - integration of open-access carbohydrate structure databases. PMID:18803830
Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans. PMID:18694500
Tags:
Tags
More detailed information about this field from each metasource.
carbohydrate
metasource: Fairsharing.org
version: FAIRsharing.org: GlycoCT XML; GlycoCT sequence format for carbohydrates.; DOI: https://doi.org/10.25504/FAIRsharing.qz30cx; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Tags
More detailed information about this field from each metasource.
carbohydrate
metasource: Fairsharing.orgversion: FAIRsharing.org: GlycoCT XML; GlycoCT sequence format for carbohydrates.; DOI: https://doi.org/10.25504/FAIRsharing.qz30cx; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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