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GlycomeDB - integration of open-access carbohydrate structure databases.

Ranzinger R, Herget S, Wetter T, von der Lieth CW - BMC Bioinformatics (2008)

Bottom Line: 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.More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: German Cancer Research Center DKFZ, Core Facility Molecular Structural Analysis, Im Neuenheimer Feld 280, Heidelberg, Germany. r.ranzinger@dkfz.de

ABSTRACT

Background: 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.

Results: 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 GlycomeDB, 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 GlycomeDB 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.

Conclusion: GlycomeDB 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 GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource.

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Encoding schemes used in various carbohydrate sequence databases. The N-glycan core structure has been chosen to illustrate the different encoding schemes used in the various databases for a given carbohydrate sequence. (A) Pictorial representation in CFG style with reducing end at the right. (B) LINUCS encoding used in GLYCOSCIENCES.de (reducing end at the left). (C) BCSDB encoding (reducing end at the right). (D) ASCII 2D graph as employed in CarbBank (reducing end at the right). (E) Notation used by GlycoBase (Lille). (F) KCF notation used by KEGG. (G) GlycoMinds encoding used in the CFG database (reducing end at the right). (H) Oxford notation used in GlycoBase (Dublin).
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Figure 2: Encoding schemes used in various carbohydrate sequence databases. The N-glycan core structure has been chosen to illustrate the different encoding schemes used in the various databases for a given carbohydrate sequence. (A) Pictorial representation in CFG style with reducing end at the right. (B) LINUCS encoding used in GLYCOSCIENCES.de (reducing end at the left). (C) BCSDB encoding (reducing end at the right). (D) ASCII 2D graph as employed in CarbBank (reducing end at the right). (E) Notation used by GlycoBase (Lille). (F) KCF notation used by KEGG. (G) GlycoMinds encoding used in the CFG database (reducing end at the right). (H) Oxford notation used in GlycoBase (Dublin).

Mentions: The biggest obstacle for data integration was the use of various sequence encoding formats by the different initiatives (Figure 2).


GlycomeDB - integration of open-access carbohydrate structure databases.

Ranzinger R, Herget S, Wetter T, von der Lieth CW - BMC Bioinformatics (2008)

Encoding schemes used in various carbohydrate sequence databases. The N-glycan core structure has been chosen to illustrate the different encoding schemes used in the various databases for a given carbohydrate sequence. (A) Pictorial representation in CFG style with reducing end at the right. (B) LINUCS encoding used in GLYCOSCIENCES.de (reducing end at the left). (C) BCSDB encoding (reducing end at the right). (D) ASCII 2D graph as employed in CarbBank (reducing end at the right). (E) Notation used by GlycoBase (Lille). (F) KCF notation used by KEGG. (G) GlycoMinds encoding used in the CFG database (reducing end at the right). (H) Oxford notation used in GlycoBase (Dublin).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2567997&req=5

Figure 2: Encoding schemes used in various carbohydrate sequence databases. The N-glycan core structure has been chosen to illustrate the different encoding schemes used in the various databases for a given carbohydrate sequence. (A) Pictorial representation in CFG style with reducing end at the right. (B) LINUCS encoding used in GLYCOSCIENCES.de (reducing end at the left). (C) BCSDB encoding (reducing end at the right). (D) ASCII 2D graph as employed in CarbBank (reducing end at the right). (E) Notation used by GlycoBase (Lille). (F) KCF notation used by KEGG. (G) GlycoMinds encoding used in the CFG database (reducing end at the right). (H) Oxford notation used in GlycoBase (Dublin).
Mentions: The biggest obstacle for data integration was the use of various sequence encoding formats by the different initiatives (Figure 2).

Bottom Line: 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.More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: German Cancer Research Center DKFZ, Core Facility Molecular Structural Analysis, Im Neuenheimer Feld 280, Heidelberg, Germany. r.ranzinger@dkfz.de

ABSTRACT

Background: 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.

Results: 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 GlycomeDB, 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 GlycomeDB 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.

Conclusion: GlycomeDB 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 GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource.

Show MeSH