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Introducing glycomics data into the Semantic Web
BACKGROUND: 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 chara...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177142/ https://www.ncbi.nlm.nih.gov/pubmed/24280648 http://dx.doi.org/10.1186/2041-1480-4-39 |
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author | Aoki-Kinoshita, Kiyoko F Bolleman, Jerven Campbell, Matthew P Kawano, Shin Kim, Jin-Dong Lütteke, Thomas Matsubara, Masaaki Okuda, Shujiro Ranzinger, Rene Sawaki, Hiromichi Shikanai, Toshihide Shinmachi, Daisuke Suzuki, Yoshinori Toukach, Philip Yamada, Issaku Packer, Nicolle H Narimatsu, Hisashi |
author_facet | Aoki-Kinoshita, Kiyoko F Bolleman, Jerven Campbell, Matthew P Kawano, Shin Kim, Jin-Dong Lütteke, Thomas Matsubara, Masaaki Okuda, Shujiro Ranzinger, Rene Sawaki, Hiromichi Shikanai, Toshihide Shinmachi, Daisuke Suzuki, Yoshinori Toukach, Philip Yamada, Issaku Packer, Nicolle H Narimatsu, Hisashi |
author_sort | Aoki-Kinoshita, Kiyoko F |
collection | PubMed |
description | BACKGROUND: 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 now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases. RESULTS: In 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. CONCLUSIONS: We 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. |
format | Online Article Text |
id | pubmed-4177142 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-41771422014-09-28 Introducing glycomics data into the Semantic Web Aoki-Kinoshita, Kiyoko F Bolleman, Jerven Campbell, Matthew P Kawano, Shin Kim, Jin-Dong Lütteke, Thomas Matsubara, Masaaki Okuda, Shujiro Ranzinger, Rene Sawaki, Hiromichi Shikanai, Toshihide Shinmachi, Daisuke Suzuki, Yoshinori Toukach, Philip Yamada, Issaku Packer, Nicolle H Narimatsu, Hisashi J Biomed Semantics Short Report BACKGROUND: 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 now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases. RESULTS: In 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. CONCLUSIONS: We 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. BioMed Central 2013-11-26 /pmc/articles/PMC4177142/ /pubmed/24280648 http://dx.doi.org/10.1186/2041-1480-4-39 Text en Copyright © 2013 Aoki-Kinoshita et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Short Report Aoki-Kinoshita, Kiyoko F Bolleman, Jerven Campbell, Matthew P Kawano, Shin Kim, Jin-Dong Lütteke, Thomas Matsubara, Masaaki Okuda, Shujiro Ranzinger, Rene Sawaki, Hiromichi Shikanai, Toshihide Shinmachi, Daisuke Suzuki, Yoshinori Toukach, Philip Yamada, Issaku Packer, Nicolle H Narimatsu, Hisashi Introducing glycomics data into the Semantic Web |
title | Introducing glycomics data into the Semantic Web |
title_full | Introducing glycomics data into the Semantic Web |
title_fullStr | Introducing glycomics data into the Semantic Web |
title_full_unstemmed | Introducing glycomics data into the Semantic Web |
title_short | Introducing glycomics data into the Semantic Web |
title_sort | introducing glycomics data into the semantic web |
topic | Short Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177142/ https://www.ncbi.nlm.nih.gov/pubmed/24280648 http://dx.doi.org/10.1186/2041-1480-4-39 |
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