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Abstract
BackgroundGlycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as “switches” that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases.ResultsIn order to implement support for the Semantic Web most efficiently for glycomics research, the developers of major glycomics databases agreed on a minimal standard for representing glycan structure and annotation information using RDF (Resource Description Framework). Moreover, all of the participants implemented this standard prototype and generated preliminary RDF versions of their data. To test the utility of the converted data, all of the data sets were uploaded into a Virtuoso triple store, and several SPARQL queries were tested as “proofs-of-concept” to illustrate the utility of the Semantic Web in querying across databases which were originally difficult to implement.ConclusionsWe were able to successfully retrieve information by linking UniCarbKB, GlycomeDB and JCGGDB in a single SPARQL query to obtain our target information. We also tested queries linking UniProt with GlycoEpitope as well as lectin data with GlycomeDB through PDB. As a result, we have been able to link proteomics data with glycomics data through the implementation of Semantic Web technologies, allowing for more flexible queries across these domains.
Highlights
Glycoscience is a research field focusing on complex carbohydratesa, which can, for example, serve as “switches” that toggle between different functions of a glycoprotein or glycolipid
In Russia, the Bacterial Carbohydrate Structure Database (BCSDB) was developed, which contains carbohydrate structures from bacterial species collected from the scientific literature [7]
The developers of GlycomeDB were a part of the EUROCarbDB project, which was an EU-funded initiative for developing a framework for storing and sharing experimental data of carbohydrates [9]
Summary
Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as “switches” that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are publicly available and provide useful information for glycoscience research. These databases have almost no link to other life science databases. The developers of GlycomeDB were a part of the EUROCarbDB project, which was an EU-funded initiative for developing a framework for storing and sharing experimental data of carbohydrates [9]. Despite all of these efforts to develop useful and valuable glycomics databases, a lack of interoperability is hampering the development of ‘mashup’ applications that are capable of integrating glycan related data with other -omics data
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