GlyGen Wikipedia: Difference between revisions
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{{infobox biodatabase | {{infobox biodatabase | ||
|title = GlyGen | |title = GlyGen | ||
|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 | |organism = [[Homo sapiens]], [[Mus musculus]], and [[Rattus norvegicus]]. | ||
|center = | |||
|laboratory = | |laboratory = | ||
|author = | |author = | ||
|citation = | |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 = | ||
|format = | |format = [[FASTA]], [[JSON]]. | ||
|url = {{URL|www. | |url = {{URL|www.glygen.org}} | ||
|download = | |download = | ||
|webservice = Yes – [[Python (programming language)| | |webservice = Yes – [[Python (programming language)|Python]] [https://api.glygen.org/ API] | ||
|sql = | |sql = | ||
|sparql = | |sparql = | ||
|webapp = | |webapp = | ||
|standalone = | |standalone = | ||
|license = | |license = [[Creative Commons]] [[General Public License]] | ||
|versioning = Yes | |versioning = Yes | ||
|frequency = 12 weeks | |frequency = '''Portal:''' 12 weeks '''Data:''' 12 weeks | ||
|curation = Yes – manual and automatic. Rules for automatic annotation generated by database curators and computational algorithms. | |curation = Yes – manual and automatic. Rules for automatic annotation generated by database curators and computational algorithms. | ||
|bookmark = | |bookmark = Yes – individual protein and glycan entries and search results. | ||
|version = | |version = 1.4 (16/ Sep/2019) | ||
}} | }} | ||
'''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: | |||
* [[BioXpress]] | |||
* [[BioMuta]] | |||
* [[Disease Ontology]] | |||
* [[GlyTouCan]] | |||
* [[Mouse Genome Database]] ([[MGI]] | |||
* [[PubChem|NCBI PubChem]] | |||
* [[PubMed|NCBI PubMed]] | |||
* [[RefSeq|NCBI RefSeq]] | |||
* [[Taxonomy_(biology)|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 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]]. | |||
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 | |||
==Funding== | ==Funding== | ||
GlyGen is an international project funded by | 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 [[GlyGen Wikipedia#External links|NIH Glycoscience Common Fund Program]] managed by the [[GlyGen Wikipedia#External links|Office of Strategic Coordination]] at the [[National Institute of Health]] (NIH) under the grant [[GlyGen Wikipedia#External links|1U01GM125267-01]]. | ||
== See also == | |||
{{See also|proteomics|glycomics|data warehouse|sparql}} | |||
| | |||
| | |||
|} | |||
==References== | |||
{{reflist}} | |||
==External links== | ==External links== | ||
;Oficial | ;Oficial | ||
*[ | *[https://www.glygen.org/ Official website] | ||
;Funding | ;Funding | ||
*[https://commonfund.nih.gov/glycoscience| NIH Glycoscience Common Fund Program] | *[https://commonfund.nih.gov/glycoscience| NIH Glycoscience Common Fund Program] | ||
*[https://commonfund.nih.gov/about/osc| Office of Strategic Coordination] | *[https://commonfund.nih.gov/about/osc| Office of Strategic Coordination] | ||
*[https://projectreporter.nih.gov/project_info_details.cfm?aid=9391499&icde=0| Grant 1U01GM125267-01] | *[https://projectreporter.nih.gov/project_info_details.cfm?aid=9391499&icde=0| Grant 1U01GM125267-01] | ||
; | ;Availability | ||
*[https:// | *[https://github.com/glygener/ GlyGen GitHub repository] | ||
*[https:// | *[https://www.glygen.org/ Portal] | ||
*[https:// | *[https://data.glygen.org/ Data] | ||
*[https://sparql.glygen.org/ SPARQL] | |||
*[https://api.glygen.org/ API] | |||
{{Bioinformatics}} | |||
<!-- Categories --> | |||
[[Category:Biological databases]] | |||
[[Category:Online databases]] | |||
[[Category:Proteomics]] | |||
[[Category:Glycomics]] |
Latest revision as of 14:03, 10 December 2019
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.[1] |
Access | |
Data format | FASTA, JSON. |
Website | www |
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:
- BioXpress
- BioMuta
- Disease Ontology
- GlyTouCan
- Mouse Genome Database (MGI
- 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 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
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
- Funding
- Availability