GlyGen Wikipedia

GlyGen

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Content
Description	GlyGen is the Computational and Informatics Resources for Glycoscience.
Data types captured	Glycans, Proteins, and Glycoproteins
Organisms	Homo sapiens, Mus musculus, and Rattus norvegicus.
Contact
Research center	EMBL-EBI, UK; SIB, Switzerland; PIR, US.
Primary citation	UniProt Consortium
Access
Data format	Custom flat file, FASTA, GFF, RDF, XML.
Website	www.uniprot.org www.uniprot.org/news/
Download URL	www.uniprot.org/downloads & for downloading complete data sets ftp.uniprot.org
Web service URL	Yes – PYTHON API see all frameworks here
Miscellaneous
Versioning	Yes
Data release frequency	12 weeks
Curation policy	Yes – manual and automatic. Rules for automatic annotation generated by database curators and computational algorithms.

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. This web portal allows exploring this data and performing unique searches that cannot be executed in any of the integrated databases alone.

About

GlyGen is a Computational and Informatics Resources for Glycoscience. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. GlyGen allows for exploring these data by performing unique searches that cannot be executed in any of the existing databases alone.

The GlyGen mission is to provide computational and informatics resources and tools for glycosciences research. Integrate data and knowledge from diverse disciplines relevant to glycobiology. Address needs inside and outside the glycoscience community.

The major goal of GlyGen is to develop an integrated, extendable, and cross-disciplinary resource providing tools and data to address specific questions in glycoscience. Currently, these questions can be answered only by extensive literature-based research and/or manual collection of data from disparate databases and websites. The GlyGen project is built using insight gained during workshops that evaluated existing resources and identified pressing community needs.

The GlyGen Effort. GlyGen is a cooperative, global, community-driven project. An open, standardized environment for independent development and integration of additional research tools by other investigators. More than 15 investigators in four countries play key roles in the project. Two years of organized discussion and planning involving nearly 100 investigators.

GlyGen as the Resource. Ongoing technical advances are accelerating the pace and sophistication of glycoscience data acquisition, the transformation of data to glycobiology knowledge, and insight. Understanding is compromised by the lack of glycoinformatics databases and tools to combine information from related disciplines. The functional and biomedical interpretation of glycobiology data is slowed by our limited ability to integrate it with biological knowledge from diverse disciplines. GlyGen addresses these needs as a broadly relevant and sustainable glycoinformatics resource that provides a roadmap to explore data from diverse domains in the context of glycoscience.

Funding

GlyGen is an international project funded by The National Institutes of Health to facilitate glycoscience research by integrating diverse kinds of information, including glycomics, genomics, proteomics (and glycoproteomics), cell biology, developmental biology and biochemistry. GlyGen is supported and funded by the NIH Glycoscience Common Fund Program managed by the Office of Strategic Coordination at National Institute of Health (NIH) under the grant 1U01GM125267-01.

Databases

Data resources

A list of publicly available databases, repositories and knowledgebases providing glycan-related information.

Category	Website	Description	Publications
Database	CAZy	The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.
Database	CSDB: Carbohydrate Structure Database	A set of manually curated carbohydrate structure databases with associated metadata (taxonomic annotation, bibliography, and NMR data). There are subdatabases focusing on bacterial carbohydrates, plant and fungal carbohydrates as well as a database for glycosyltransferases.	Yes
Database	GlycoStore	GlycoStore is a curated chromatographic, electrophoretic and mass-spectrometry composition database of N-, O-, glycosphingolipid (GSL) glycans and free oligosaccharides associated with a range of glycoproteins, glycolipids and biotherapeutics. This database associates glycan structures with standardized retention times (UPLC, HILIC-UPLC, CE-LIF, HILIC-HPLC, PGC-LC-ESI-MS/MS).	Yes
Database	DAGR	Database of Anti-Glycan Reagents (DAGR) is a publicly available, comprehensive resource for anticarbohydrate antibodies, their applications, availability, and quality. DAGR allows to search and identify antibodies and reagent lectins to various carbohydrates as well as to obtain information about those antibodies. In addition, users can add new antibodies/lectins to the database or information about them.	Yes
Knowledgebase	CAZypedia	CAZypedia is a community-driven resource to assemble a comprehensive encyclopedia of the carbohydrate-active enzymes and associated carbohydrate-binding modules involved in the synthesis and degradation of complex carbohydrates. CAZypedia is closely connected with, the actively curated CAZy Database.
Knowledgebase	UniCarbKB	UniCarbKB is a curated knowledgebase of glycosylated proteins, the attached glycan structures and if known, the glycosylation site.	Yes
Knowledgebase	GlycoPOD	GlycoPOD is the glycosciences protocol database. This resource contains an extensive and curated list of experimental protocols and detailed instructions on the execution of these protocols as well as the necessary reagents and hardware.	Yes
Repository	GlyTouCan	GlyTouCan is the international glycan structure repository. This repository is the uncurated registry for glycan structures that assigns globally unique accession numbers to any glycan independent of the level of information provided by the experimental method used to identify the structure.	Yes