GlycomeDB – integration of open-access carbohydrate structure databases

BMC Bioinformatics

Table 1 Mechanisms of data access from source databases

Database	Access Mode	URL	File Type
BCSDB	CGI	http://www.glyco.ac.ru/bcsdb/admin/export_data.cgi	Text
CarbBank	HTTP	http://www.glycome-db.org/downloads/CarbBank/carbbank.zip	Text
CFG	CGI	http://www.functionalglycomics.org/glycomics/molecule/jsp/carbohydrate/table_export.jsp	CSV
GlycoBase (Dublin)	HTTP	http://glycobase.nibrt.ie/dump_sql/rene.text	CSV
GlycoBase (Lille)	CGI	http://glycobase.univ-lille1.fr/base/xml_dump.php	XML
GLYCOSCIENCES.de	HTTP	http://www.dkfz.de/spec/B090/export/data.csv.gz and http://www.dkfz.de/spec/B090/export/taxonomy.csv.gz	CSV
KEGG	FTP	ftp://ftp.genome.jp/pub/kegg/ligand/glycan/glycan	Text

The source databases used to obtain carbohydrate structures for GlycomeDB are listed together with their access mode, file type and URL. FTP and HTTP access is via normal file downloads; CGI means that a HTTP-GET or HTTP-POST request is made to a script residing on the remote server. File types are: Text = text with keywords, CSV = comma-separated values, XML = extensible markup language.

ISSN: 1471-2105