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

Organization

• GlyGen portal with the University of Georgia (UGA) partnered with the George Washington University (GW) to create GlyGen, a glycoscience informatics portal. Wheres UGA is responsible for the front-end web development and GW for the back-end database of the GlyGen portal.
• Advocates from three different institutions the University of Georgia, the Georgetown University, and the Jackson Laboratory.
• Key Collaborators /Co-Investigators with the European Bioinformatics Institute (EMBL-EBI) and the National Center for Biotechnology Information (NCBI), the University of Georgia, the George Washington University, the Georgetown University, Soka University, the Georgetown University, and Griffith University (Institute for Glycomics).
• Glycan Array Database Partners with the Imperial College, the Harvard University, and the National Center for Biotechnology Information.

Integrated databases

Currently GlyGen integrates data from the following publicly available databases:

• BioXpress
• BioMuta
• Disease Ontology
• GlyTouCan
• Mouse Genome Database (MGI)
• NCBI HomoloGene
• NCBI PubChem
• NCBI PubMed
• NCBI RefSeq
• NCBI Taxonomy
• Orthologous MAtrix (OMA)
• The Protein Ontology (PRO)
• RCSB The Protein Data Bank (PDB)
• The Monarch Initiative
• UniCarbKB
• UniProtKB The UniProt Knowledgebase

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 means that you are free to copy, distribute, display and make commercial use of these databases in all legislations, provided you 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.

See also

See also: proteomics, glycomics, data warehouse, and sparql

External links

Oficial

• Official website

Funding

• NIH Glycoscience Common Fund Program
• Office of Strategic Coordination
• Grant 1U01GM125267-01

Availability

• GlyGen GitHub repository
• Portal
• Data
• SPARQL
• API