Main Page

Welcome to HIVE Wiki,

The HIVE Lab group is involved in developing the High-performance Integrated Virtual Environment (HIVE) which is a collaborative project between HIVE group at the CBER Food and Drug Administration (FDA) and Dr. Raja Mazumder's HIVE Lab team at George Washington University (GW). Both groups are coordinating their efforts to integrate various high throughput data analysis tools into the HIVE platform.

The MediaWiki for the HIVE project. This wiki system provides complementary information to the HIVE Lab and is divided into the following main sections:

Projects

Template:Main
HIVE team projects fall into two major categories:
1) Developing infrastructure for biomedical data analysis
2) Using that infrastructure to integrate and mine the data for knowledge.

GlyGen Workshops

Template:MainThe 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

Template:MainThe 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

Template:MainThe 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

Template:Main 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

Template:MainGlyGen 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

Template:Main 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

Template:MainThe 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

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

Glycan Structure Dictionary

Template:MainThe 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