Latest revision as of 19:32, 16 April 2024

Welcome to GlyGen Wiki,

The MediaWiki for the GlyGen project. This wiki system provides complementary information to the GlyGen portal and is divided into the following main sections: Help for the GlyGen portal, Help for the GlyGen data repository, Help for the GlyGen web service API, Help for the GlyGen triplestore, Frequently Asked Questions and scientific articles.

GlyGen Webinar Series

The GlyGen project organizes public webinars on diverse topics, ranging from bioinformatics databases to new glycomics analysis techniques producing interesting data. Recordings of the talks are released on the GlyGen YouTube channe

GlyGen Workshops

The GlyGen project organizes public workshops to learn more about GlyGen and glycoinformatics. The workshops are organised virtually and in-person. Recordings and material of the workshops are released on the GlyGen YouTube channel and also via the wiki page.

GlyGen Internships

The GlyGen project offers internships to undergraduate and graduate students in bioinformatics and in biology/biochemistry. These internships expose students to a wide variety of new concepts in bioinformatics and in biology/biochemistry while working on tasks and projects. The internship enable interns to develop their soft-skills and prepares them for the next stage of their career.

GlyGen Interns

The GlyGen project offers internships to undergraduate and graduate students in bioinformatics and in biology/biochemistry. Please refer to this for Interns FAQ and more information on GW Access and requirements.

GlyGen Portal

The GlyGen portal is the web interface allowing browser based access to the GlyGen data. The portal supports searching for glycans and proteins, display of detailed glycan data and protein data as well as export features to save the data to the local system. The portal also provides access to the other resources of the GlyGen project and digital resources such as posters, presentations and videos.

GlyGen Data Repository

GlyGen uses unique processing and integration workflow to retrieve and extract data from various resources. After standardization and harmonization, the high-quality datasets are created. The process of dataset creation is fully documented in BioCompute Objects.These datasets are further processed to create JSON objects and RDF triples that populate MongoDB docstore and Virtuoso triplestore backend databases respectively. The docstore is used by various GlyGen web services while the triplestore is accessed through the GlyGen SPARQL endpoint.

Frequently Asked Questions

The FAQ section contains a list of questions asked by users regarding using the portal, API and SPARQL endpoint as well as questions related to the data, data integration and quality control.

GlyGen Web Service API

The GlyGen APIs allow programmatic access of the GlyGen data objects for glycans, proteins, and glycoproteins in the MongoDB docstore. The GlyGen APIs have been documented using the Swagger framework (https://swagger.io/). Some of these web services are generic and provide searching, listing and detailed record access functionalities for GlyGen data objects, while others are custom designed to respond to specific biological questions or use cases collected from the user community.

GlyGen Triplestore

The GlyGen knowledgebase uses a Virtuoso triplestore to store GlyGen triples data. The triplestore can be accessed through the GlyGen SPARQL endpoint.

Glycan Structure Dictionary

The Glycan Structure Dictionary has been developed as a reference dictionary to provide a standardized list of widely used glycan terms that can help in the curation and mapping of glycan structures described in publications.

External links

Official

GlyGen official website

Glycan search

Glycan search — Go to GlyGen website to perform Glycan Search
Simple search
Advanced search
Tutorial — Learn how to use simple and advanced searches.

Protein search

Protein search — Go to GlyGen website to perform Protein Search
Simple search
Advanced search
Tutorial — Learn how to use Simple and Advanced searches.

Glycoprotein search

Glycoprotein search — Go to GlyGen website to perform Glycoprotein Search
Simple search
Advanced search
Tutorial — Learn how to use Simple and Advanced searches.

Quick search

Quick search — You can search by glycan, protein, species, and disease.

Try Me

Try me — To perform search select one of the frequently asked questions.

List pages

Glycan list — GlyTouCan Accession: G17689DH
Protein list — UniProtKB Accession: P14210-1
Glycoprotein list — UniProtKB Accession: P14210-1

Detail pages

Glycan details — GlyTouCan Accession: G17689DH
Protein details — UniProtKB Accession: P14210-1
Glycoprotein details — UniProtKB Accession: P14210-1

@@ Line 1: / Line 1: @@
-{{Expand section|small=no}}
+{{DISPLAYTITLE:<span style="position: absolute; clip: rect(1px 1px 1px 1px); clip: rect(1px, 1px, 1px, 1px);">{{FULLPAGENAME}}</span>}}
+__NOTOC__
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+<div id="ggw-topbanner" style="clear:both; position:relative; box-sizing:border-box; width:100%; margin:1.2em 0 6px; min-width:47em; border:1px solid #ddd; background-color:#f9f9f9; color:#000;">
+    <div style="margin:0.4em; text-align:center;">
+        <div style="font-size:160%; padding:.1em;">Welcome to GlyGen Wiki,</div>
+        <div style="font-size:100%;">The [https://www.mediawiki.org/wiki/MediaWiki MediaWiki] for the GlyGen project. This wiki system provides complementary information to the [https://glygen.org GlyGen portal] and is divided into the following main sections: Help for the [[GlyGen portal]], Help for the [[GlyGen data repository]], Help for the [[GlyGen web service API]], Help for the [[GlyGen triplestore]], [[Frequently Asked Questions]] and scientific articles.</div>
+    </div>
+</div>
+<div style="clear: both;"></div>
-{{Mirage
+<div style="clear: both;"><br />
-|style = background-color: #F79646; border:2px solid #B66D31; border-radius: 15px;
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><div id="ggw_row3" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
-|header = Mirage headline
+    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
-|text = This is a custom text. With this template, you can customize infobox style, text, and image. See documentation for details
+        <h3>[[GlyGen Webinar Series]]</h3>
-}}
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
+{{main|GlyGen Webinar Series}}The GlyGen project organizes public webinars on diverse topics, ranging from bioinformatics databases to new glycomics analysis techniques producing interesting data. Recordings of the talks are released on the GlyGen YouTube channe<br />
+</div>
+    </div>
+</div>
+</div><div style="clear: both;"><div style="border-top: 1px solid #CCC; padding-top: 0.5em;"><div id="ggw_row3" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
+    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
+        <h3>[[GlyGen Workshops]]</h3>
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">{{main|GlyGen Workshops}}The GlyGen project organizes public workshops to learn more about GlyGen and glycoinformatics. The workshops are organised virtually and in-person. Recordings and material of the workshops are released on the GlyGen YouTube channel and also via the wiki page.
+</div>
+    </div>
+</div></div><div id="ggw_row3" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
+    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
+        <h3>[[GlyGen Internships]]</h3>
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
+{{main|GlyGen Internships}}The GlyGen project offers internships to undergraduate and graduate students in bioinformatics and in biology/biochemistry. These internships expose students to a wide variety of new concepts in bioinformatics and in biology/biochemistry while working on tasks and projects. The internship enable interns to develop their soft-skills and prepares them for the next stage of their career.
+</div>
+    </div>
+</div></div>
-'''Computational and Informatics Resources and Tools for Glycoscience Research'''. <br> 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.
+</div></div><div id="ggw_row3" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
+    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
+<h3>[[GlyGen Interns]]</h3>
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
+{{main|GlyGen Internships}}The GlyGen project offers internships to undergraduate and graduate students in bioinformatics and in biology/biochemistry. Please refer to this for Interns FAQ and more information on GW Access and requirements.
+</div>
+    </div>
+</div></div>
-=Search pages=
-{{Expand section|small=no}}
-==Glycan search==
+ <div id="ggw_row2" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
-{{Expand section|small=no}}
+    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
-[[Glycan search]]
+        <h3>[[GlyGen portal|GlyGen Portal]]</h3>
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
+{{main|GlyGen portal}}
+The [[GlyGen portal]] is the web interface allowing browser based access to the GlyGen data. The portal supports searching for [[Glycan search|glycans]] and [[Protein search|proteins]], display of detailed [[Glycan details|glycan data]] and [[Protein details|protein data]] as well as export features to save the data to the local system. The portal also provides access to the other resources of the GlyGen project and digital resources such as posters, presentations and videos.
+        </div>
+    </div>
+    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
+        <h3>[[GlyGen data repository|GlyGen Data Repository]]</h3>
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
+{{main|GlyGen data repository}}GlyGen uses unique processing and integration workflow to retrieve and extract data from various resources. After standardization and harmonization, the high-quality datasets are created. The process of dataset creation is fully documented in BioCompute Objects.These datasets are further processed to create JSON objects and RDF triples that populate MongoDB docstore and Virtuoso triplestore backend databases respectively. The docstore is used by various GlyGen web services while the triplestore is accessed through the GlyGen SPARQL endpoint.
+</div>
+    </div>
+    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
+        <h3>[[Frequently Asked Questions]]</h3>
+	<div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
+{{main|Frequently Asked Questions}}
+The FAQ section contains a list of questions asked by users regarding using the portal, API and SPARQL endpoint as well as questions related to the data, data integration and quality control.
+        </div>
+    </div>
+</div>
-==Protein search==
+<div id="ggw_row3" style="display: flex; flex-flow: row wrap; justify-content: space-between; padding: 0; margin: 0 -5px 0 -5px;">
-{{Expand section|small=no}}
+    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
-[[Protein search]]
+        <h3>[[GlyGen web service API|GlyGen Web Service API]]</h3>
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
-==Glycoprotein search==
+{{main|GlyGen web service API}}The GlyGen APIs allow programmatic access of the GlyGen data objects for glycans, proteins, and glycoproteins in the MongoDB docstore. The GlyGen APIs have been documented using the Swagger framework (https://swagger.io/). Some of these web services are generic and provide searching, listing and detailed record access functionalities for GlyGen data objects, while others are custom designed to respond to specific biological questions or use cases collected from the user community.
-{{Expand section|small=no}}
+</div>
-[[Glycoprotein search]]
+    </div>
+    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
-==Quick search==
+        <h3>[[GlyGen triplestore|GlyGen Triplestore]]</h3>
-{{Expand section|small=no}}
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
+{{main|GlyGen triplestore}}The GlyGen knowledgebase uses a Virtuoso triplestore to store GlyGen triples data. The triplestore can be accessed through the GlyGen SPARQL endpoint.
-[[Quick search]]
+</div>
+    </div>
-=List pages=
+    <div style="flex: 1; margin: 5px; min-width: 210px; border: 1px solid #CCC;	padding: 0 10px 10px 10px; box-shadow: 0 2px 2px rgba(0,0,0,0.1); background: #f5faff;">
-{{Expand section|small=no}}
+        <h3>[[Glycan structure dictionary|Glycan Structure Dictionary]]</h3>
+        <div style="border-top: 1px solid #CCC; padding-top: 0.5em;">
-'''Glycan list''' &mdash; [[Glycan list|Glycan list]]
+{{main|Glycan structure dictionary}}The Glycan Structure Dictionary has been developed as a reference dictionary to provide a standardized list of widely used glycan terms that can help in the curation and mapping of glycan structures described in publications.
+</div>
-'''Protein list''' &mdash; [[Protein list|Protein list]]
+    </div>
+</div>
-'''Glycoprotein list''' &mdash; [[Glycoprotein list|Glycoprotein list]]
-=Detail pages=
-{{Expand section|small=no}}
-'''Glycan details''' &mdash; [[Glycan details|Glycan details]]
-'''Protein details''' &mdash; [[Protein details|Protein details]]
-'''Glycoprotein details''' &mdash; [[Glycoprotein details|Glycoprotein details]]
 =External links=
@@ Line 51: / Line 93: @@
 ;Official
-*[http://glygen.org/ GlyGen official website]
+*[https://www.glygen.org/ GlyGen official website]
 ;Glycan search
@@ Line 58: / Line 100: @@
 *[http://glygen.org/glycan_search.html#simple_search Simple search]
 *[http://glygen.org/glycan_search.html#advanced_search Advanced search]
-*[http://glygen.org/glycan_search.html#tutorial tutorial] &mdash; Learn how to use simple and advanced searches.
+*[http://glygen.org/glycan_search.html#tutorial Tutorial] &mdash; Learn how to use simple and advanced searches.
 ;Protein search
@@ Line 93: / Line 135: @@
 *[http://glygen.org/protein_detail.html?uniprot_canonical_ac=P14210-1 Protein details] &mdash; UniProtKB Accession: P14210-1
 *[http://glygen.org/glycoprotein_detail.html?uniprot_canonical_ac=P14210-1 Glycoprotein details] &mdash; UniProtKB Accession: P14210-1
-=GlyGen Wikipedia=
-'''GlyGen Wikipedia page''' &mdash; [[GlyGen Wikipedia|GlyGen Wikipedia]]

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