GlyGen Wikipedia

GlyGen
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
Primary citation	GlyGen announcement.
Access
Data format	FASTA, JSON.
Website	www.glygen.org
Web service URL	Yes – Python API
Miscellaneous
License	Creative Commons General Public License
Versioning	Yes
Data release; frequency	Portal: 12 weeks Data: 12 weeks
Version	1.4 (16/ Sep/2019)
Curation policy	Yes – manual and automatic. Rules for automatic annotation generated by database curators and computational algorithms.
Bookmarkable; entities	Yes – individual protein and glycan entries and search results.

GlyGen is a database for glycans, glycoconjugates and related gene, protein and other molecular biology information. GlyGen retrieves information from multiple international data sources such as PDB, RefSeq, and UniProt, and integrates and harmonizes content to allow unique searches that cannot be executed in any of the integrated databases alone.

Organization

The GlyGen project is an international multi-institutional effort. The effort is led by the University of Georgia (UGA) and the George Washington University (GW). The two institutions collaborate in the development of the GlyGen portal. Whereas UGA is responsible for the front-end web development and GW for the back-end database. In addition, GW is also responsible for the data retrieval and data integration. To this end GW works together with the international GlyGen collaborators including: the European Bioinformatics Institute (EMBL-EBI) and the National Center for Biotechnology Information (NCBI), the Georgetown University, Soka University, and Griffith University (Institute for Glycomics).

Integrated databases

Currently GlyGen integrates data from the following publicly available databases:

Content and features

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. The GlyGen web portal allows exploration of this data and execution of unique searches that cannot be performed using any of the integrated databases in isolation.

Data Integration - Data from the different resources are accessed and downloaded in resource-specific formats (e.g. RDF, FASTA, CSV).
Data Collection - Data integration with intensive data quality control. Metadata is captured using the BioCompute Object schema.
Quick Search - Complex multi-domain search queries can be performed using the quick searches which are based on user requests.
Explore Searches - GlyGen provides users with Glycan, Protein, Glycoprotein searches via simple or advanced search options.
Data Visualization - Ability to visualize GlyGen data statistics via charts, bars, and diagrams. GlyGen integrates human, mouse, and rat proteins, glycans, and glycoproteins.
Resources - A library of glycobiology resources including databases, tools, learning material and tutorials are provided.
SPARQL Endpoint - All datasets are also RDFized using standard ontologies (e.g. UniProt RDF schema, GlycoCoO, FALDO) and made available via our public endpoint.
Feedback - Our integrated feedback system allows users to submit comments and suggestions on every web page.

Availability

We have chosen to apply the Creative Commons Attribution 4.0 International (CC BY 4.0) license to all our database sets. This allows to copy, distribute, display and make commercial use of the data in all legislations, provided users give us credit. The source code of the project is released under the GNU General Public License v3 and is available in our GlyGen GitHub repository. GlyGen data is available for free of charge and accessible via GlyGen GitHub repository, Portal, Data, API, SPARQL.

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 the National Institute of Health (NIH) under the grant 1U01GM125267-01.

References

↑ GlyGen, Article. (October 2019). "GlyGen: Computational and Informatics Resources for Glycoscience". Glycobiology. 1 (Resources for Glycoscience). doi:10.1093/glycob/cwz080. PMID 31616925.

External links

Oficial

Official website

Funding

Availability

[1] GlyGen, Article. (October 2019). "GlyGen: Computational and Informatics Resources for Glycoscience". Glycobiology. 1 (Resources for Glycoscience). doi:10.1093/glycob/cwz080. PMID 31616925.

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v t e Bioinformatics
Databases	Sequence databases: GenBank, European Nucleotide Archive and DNA Data Bank of Japan Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource Other databases: Protein Data Bank, Ensembl and InterPro Specialised genomic databases: BOLD, Saccharomyces Genome Database, FlyBase, VectorBase, WormBase, PHI-base, Arabidopsis Information Resource and Zebrafish Information Network
Software	BLAST Bowtie Clustal HMMER MUSCLE SAMtools TopHat
Other	Server: ExPASy Ontology: Gene Ontology Rosalind (education platform)
Institutions	Broad Institute Computational Biology Department (CBD) Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI) Database Center for Life Science (DBCLS) DNA Data Bank of Japan (DDBJ) European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory (EMBL) Flatiron Institute J. Craig Venter Institute (JCVI) Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) US National Center for Biotechnology Information (NCBI) Japanese Institute of Genetics Netherlands Bioinformatics Centre (NBIC) Philippine Genome Center (PGC) Scripps Research Swiss Institute of Bioinformatics (SIB) Wellcome Sanger Institute Whitehead Institute
Organizations	African Society for Bioinformatics and Computational Biology (ASBCB) Australia Bioinformatics Resource (EMBL-AR) European Molecular Biology network (EMBnet) International Nucleotide Sequence Database Collaboration (INSDC) International Society for Biocuration (ISB) International Society for Computational Biology (ISCB) Student Council (ISCB-SC) Institute of Genomics and Integrative Biology (CSIR-IGIB) Japanese Society for Bioinformatics (JSBi)
Meetings	Basel Computational Biology Conference‎ ([BC²]) European Conference on Computational Biology (ECCB) Intelligent Systems for Molecular Biology (ISMB) International Conference on Bioinformatics (InCoB) ISCB Africa ASBCB Conference on Bioinformatics Pacific Symposium on Biocomputing (PSB) Research in Computational Molecular Biology (RECOMB)
File formats	CRAM format FASTA format FASTQ format NeXML format Nexus format Pileup format SAM format Stockholm format
Related topics	Computational biology List of biological databases Molecular phylogenetics Sequencing Sequence database Sequence alignment
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