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|logo = [[File:Logo-glygen-blue-top.svg]]
|logo = [[File:Logo-glygen-blue-top.svg]]
|description = '''GlyGen''' is the '''Computational and Informatics Resources for Glycoscience.'''
|description = '''GlyGen''' is the '''Computational and Informatics Resources for Glycoscience.'''
|scope = Glycans, Proteins, and Glycoproteins  
|scope = [[Glycans]], [[Proteins]], and [[Glycoproteins]].
|organism = Homo sapiens, Mus musculus, and Rattus norvegicus.
|organism = [[Homo sapiens]], [[Mus musculus]], and [[Rattus norvegicus]].
|center =  
|center =  
|laboratory =  
|laboratory =  
|author =  
|author =  
|citation = {{cite journal| last=GlyGen| first=Article.| title=GlyGen: Computational and Informatics Resources for Glycoscience.|journal=Glycobiology|date=October 2019|volume=1|issue=Resources for Glycoscience|pmid=31616925|doi=10.1093/glycob/cwz080}}
|citation = GlyGen announcement.<ref>{{cite journal|last1=GlyGen|first1=Article.|title=GlyGen: Computational and Informatics Resources for Glycoscience.|journal=Glycobiology|date=October 2019|volume=1|issue=Resources for Glycoscience|pmid=31616925|doi=10.1093/glycob/cwz080}}</ref>
|released =  
|released =  
|standard =  
|standard =  
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|url = {{URL|www.glygen.org}}
|url = {{URL|www.glygen.org}}
|download =  
|download =  
|webservice = Yes – [[Python (programming language)|PYTHON]], [https://api.glygen.org/ API]
|webservice = Yes – [[Python (programming language)|Python]] [https://api.glygen.org/ API]
|sql =
|sql =
|sparql =  
|sparql =  
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|version = 1.4 (16/ Sep/2019)
|version = 1.4 (16/ Sep/2019)
}}
}}
'''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.
 
'''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==
==Organization==
* ''GlyGen portal'' with the [[University of Georgia]] (UGA) partnered with the [[George Washington University]] (GW) to create [[GlyGen Wikipedia#External links|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.
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).
* ''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==
==Integrated databases==
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* [[Disease Ontology]]
* [[Disease Ontology]]
* [[GlyTouCan]]  
* [[GlyTouCan]]  
* [[Mouse Genome Database]] ([[MGI]])
* [[Mouse Genome Database]] ([[MGI]]  
* [[HomoloGene|NCBI HomoloGene]]  
* [[PubChem|NCBI PubChem]]
* [[PubChem|NCBI PubChem]]
* [[PubMed|NCBI PubMed]]
* [[PubMed|NCBI PubMed]]
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== Availability ==
== 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.
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 Wikipedia#External links|GlyGen GitHub repository]].
The source code of the project is released under the GNU [[General Public License]] v3 and is available in our [[GlyGen Wikipedia#External links|GlyGen GitHub repository]].
GlyGen data is available for free of charge and accessible via [[GlyGen Wikipedia#External links|GlyGen GitHub repository]], [[GlyGen Wikipedia#External links|Portal]], [[GlyGen Wikipedia#External links|Data]], [[GlyGen Wikipedia#External links|API]], [[GlyGen Wikipedia#External links|SPARQL]].
GlyGen data is available for free of charge and accessible via [[GlyGen Wikipedia#External links|GlyGen GitHub repository]], [[GlyGen Wikipedia#External links|Portal]], [[GlyGen Wikipedia#External links|Data]], [[GlyGen Wikipedia#External links|API]], [[GlyGen Wikipedia#External links|SPARQL]].
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==References==
==References==
{{reflist|2}}
{{reflist}}


==External links==
==External links==
;Oficial
;Oficial
*[http://glygen.org/ Official website]
*[https://www.glygen.org/ Official website]


;Funding
;Funding

Latest revision as of 14:03, 10 December 2019

GlyGen
Content
DescriptionGlyGen is the Computational and Informatics Resources for Glycoscience.
Data types
captured		Glycans, Proteins, and Glycoproteins.
OrganismsHomo sapiens, Mus musculus, and Rattus norvegicus.
Contact
Primary citationGlyGen announcement.[1]
Access
Data formatFASTA, JSON.
Websitewww.glygen.org
Web service URLYes – Python API
Miscellaneous
LicenseCreative Commons General Public License
VersioningYes
Data release
frequency		Portal: 12 weeks Data: 12 weeks
Version1.4 (16/ Sep/2019)
Curation policyYes – 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.

See also

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

References

  1. ↑ 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
Funding
Availability


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