<it>GlycomeDB </it>– integration of open-access carbohydrate structure databases
<p>Abstract</p> <p>Background</p> <p>Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for c...
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| Format: | Article |
| Language: | English |
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BMC
2008-09-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/9/384 |
| _version_ | 1818789248885587968 |
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| author | von der Lieth Claus-Wilhelm Wetter Thomas Herget Stephan Ranzinger René |
| author_facet | von der Lieth Claus-Wilhelm Wetter Thomas Herget Stephan Ranzinger René |
| author_sort | von der Lieth Claus-Wilhelm |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases.</p> <p>Results</p> <p>We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called <it>GlycomeDB</it>, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in <it>GlycomeDB </it>using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators.</p> <p>Conclusion</p> <p><it>GlycomeDB </it>is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application <it>GlycoUpdateDB </it>is also available for establishing and updating a local installation of <it>GlycomeDB</it>. With the advent of <it>GlycomeDB</it>, the distributed islands of knowledge in glycomics are now bridged to form a single resource.</p> |
| first_indexed | 2024-12-18T14:36:33Z |
| format | Article |
| id | doaj.art-3955fa887f2c41919cd8622ea405d015 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-18T14:36:33Z |
| publishDate | 2008-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-3955fa887f2c41919cd8622ea405d0152022-12-21T21:04:29ZengBMCBMC Bioinformatics1471-21052008-09-019138410.1186/1471-2105-9-384<it>GlycomeDB </it>– integration of open-access carbohydrate structure databasesvon der Lieth Claus-WilhelmWetter ThomasHerget StephanRanzinger René<p>Abstract</p> <p>Background</p> <p>Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases.</p> <p>Results</p> <p>We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called <it>GlycomeDB</it>, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in <it>GlycomeDB </it>using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators.</p> <p>Conclusion</p> <p><it>GlycomeDB </it>is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application <it>GlycoUpdateDB </it>is also available for establishing and updating a local installation of <it>GlycomeDB</it>. With the advent of <it>GlycomeDB</it>, the distributed islands of knowledge in glycomics are now bridged to form a single resource.</p>http://www.biomedcentral.com/1471-2105/9/384 |
| spellingShingle | von der Lieth Claus-Wilhelm Wetter Thomas Herget Stephan Ranzinger René <it>GlycomeDB </it>– integration of open-access carbohydrate structure databases BMC Bioinformatics |
| title | <it>GlycomeDB </it>– integration of open-access carbohydrate structure databases |
| title_full | <it>GlycomeDB </it>– integration of open-access carbohydrate structure databases |
| title_fullStr | <it>GlycomeDB </it>– integration of open-access carbohydrate structure databases |
| title_full_unstemmed | <it>GlycomeDB </it>– integration of open-access carbohydrate structure databases |
| title_short | <it>GlycomeDB </it>– integration of open-access carbohydrate structure databases |
| title_sort | it glycomedb it integration of open access carbohydrate structure databases |
| url | http://www.biomedcentral.com/1471-2105/9/384 |
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