functional glycomics is an emerging field of science , aiming to create a cell - by - cell catalogue of glycosyltransferase expression and detected glycan structures in relation to health and diseases ( 13 ) .
however , modern analytical methods such as mass spectrometry and nmr have afforded the ability to elucidate most structural details at the concentration levels required for glycomics ( 4,5 ) .
several national and international initiatives aiming to decipher the biological function of carbohydrates have emerged for the recent years ( 68 ) . in a similar fashion to the finished human genome project  which determined the sequences of the chemical base pairs that make up a human dna 
most of these glycomics projects intend to make their data freely accessible under an open access philosophy .
unfortunately , the exchange of data between different glyco - related databases is seriously hampered by the dearth of generally accepted digital exchange formats and standardized structural and biological descriptions ( 9 ) . similar to the genomics and proteomics field , a description of glycan structures would be an appropriate way to establish an efficient connection of glyco - related information resources .
however , glycan sequences can not be described by a simple linear one - letter code as each pair of monosaccharides can be linked in several ways and branched structures can be formed .
the glycosciences.de portal ( 7 ) demonstrates that data originating from various resources can be efficiently integrated using a linear notation for unique description of carbohydrate sequences ( linucs ) ( 10 ) .
the extended alphanumeric iupac description and glycosidic linking information are applied to build up a hierarchy of the various branches starting from the reducing end of the oligosaccharide chain , which is then converted into a linear representation . however
the commercially available glycosuitedb ( 11 ) uses the so - called condensed form of the iupac description to create a linear representation , where four rules are applied to obtain a unique linear code .
the  glycan database of the us consortium for functional glycomics ( 6 ) uses the so - called linear code ( 12 ) , using a one or two character - based representation of saccharide units and linkages .
the ordering of glycan branches is established using a special lookup table where the hierarchy of monosaccharide structures is defined .
the kegg carbohydrate matcher ( kcam ) ( 8,13 ) uses a connection table based graph representation to encode carbohydrate structures , where monosaccharides are represented by nodes and glycosidic bonds as edges .
glycosciences.de , glycosuite , cfg glycan database and kegg - glycan concentrate on glycan structures found in mammalian species .
in contrast , the mission of the russian bacterial carbohydrate structure database ( bcsdb ) [ ( 14 ) , for urls see appendix ] is to provide all published glycan structures found in bacteria .
since the monosaccharide namespace as well as the type of linkages found in bacterial polysaccharides differ considerably from those found in mammals , bcsdb uses an internal representation of glycans , which diverges from those used to describe structures found in mammals . looking at various existing carbohydrate databases accessible through the internet ,
it is obvious that diverse ways to encode and store complex carbohydrates are in use .
however , users who would like to access all publicly available glyco - related data spread over many databases have not only to cope with varying graphical and non - graphical interfaces to input glycan structures , but also must be aware that the definition of building blocks and topologies may be different .
each database has developed its own set of rules to solve some problematic encoding situations such as treatment of monovalent substituents , phosphates , sulphates , repeat units , unknown linkages and other uncertain structural features of glycan structures .
it is , of course , an attractive vision [ expressed during the joint meeting of the japanese and american consortia for glycomics ( 15 ) ] to have a single user interface which will provide access to all relevant world - wide distributed resources without any technical and administrative barrier .
a prerequisite for an efficient exchange of data is the agreement to a generally accepted exchange format as well as a common application programming interface .
consequently , several proposals for an xml - based description of glycan structures have already been published ( 16,17 ) . to avoid any further confusion about xml descriptions of glycans ,
the seven larger initiatives in this field [ cfg , bcsdb , glycosciences.de , eurocarbdb , kegg , hgpi and ccrc ( for abbreviations see appendix ) ] agreed to further develop the xml description for the encoding of glycan structures on the basis of the already existing glycan data exchange ( glyde ) ( 17 ) .
the progress discussion is open to all interested scientists and takes place at the forum pages of the eurocarbdb project .
concerning the technical realization of the online connection between existing databases , it seems that the simple object access protocol ( soap ) is now the broadly accepted procedure for automated communication between web - applications .
being designed to communicate via the internet , it is well suited to be also used for the exchange of glycan - related data between distributed computers . taken together , it seems like the field has matured to the point where it is feasible to establish an online connection of distributed databases , at least between the larger of the established projects .
the bacterial carbohydrate structure database ( bcsdb ) [ ( 14 ) , for urls see appendix ] is a database containing data on natural carbohydrates with known structure .
in addition to the structure and bibliography , each record in the bcsdb contains the abstract of the publication , data on the carbohydrate source , methods of structure elucidation , information on the availability of spectral data and assignment of nmr spectra when available , data on conformation , biological activity , chemical and enzymatic synthesis , biosynthesis , genetics and other related data .
the search criteria can be fragment(s ) of the structure ; fragment(s ) of the nmr spectrum ; and indexed tags , including microorganism , bibliography and keywords .
currently , the bcsdb contains 8200 records on bacterial carbohydrates , including the corresponding part of carbbank ( 18 ) ( 3500 records on structures reported before 1995 ) .
data from both literature and carbbank have been carefully checked for consistency before the upload , and corrected when necessary .
the bcsdb interface includes the web - based user part , web - based administrator part and programming gateways for the automated data interchange .
the bcsdb is available on the internet for free usage and validated user data submission .
the glycosciences.de portal ( 7 ) is an attempt to link glycan - related data originating from various resources through a unique structural description .
the linucs ( linear notation for unique description of carbohydrate sequences ) ( 10 ) notation is used to uniquely encode fully characterized glycans . currently , the glycosciences portal provides access to 24  000 different entries with nearly 14  000 different carbohydrate moieties .
these structures are sourced from a number of sources , including the former carbbank and sugabase - project ( 19 ) , automatic extraction from the protein data base ( pdb ) ( 20 ) , and the curation of new entries altogether .
the structure - oriented approach to the database allows the data related to a single glycan , but originating from various sources ( e.g. experimental nmr spectra , theoretically calculated fragment ions for mass spectra interpretation or experimental or simulated 3d structures ) to be easily linked and accessed using a single database query .
according to the varying needs of specific research questions , the glycosciences portal provides several structure - oriented options to recall glycan - related data .
the retrieval of glycans matching an exact structure is the most traditional way to access a database .
the motif search enables to retrieve all entries , which possess substructures having names such as lewis , blood group h antigen or gm3 .
all glycan - related scientific data of the glycosciences.de portal are freely accessible via the internet following the open access philosophy :  free availability and unrestricted use.
the soap - based web - services are available on the websites of the two projects and are documented in the form of wsdl ( for urls see appendix ) descriptions that provide the possibility of platform - independent formalization of server - side features .
wsdl files can be easily integrated into the existing code by using features from various soap libraries which allow the transparent work with the soap interface under perl , php , java , etc .
glycan data exchange ( glyde ) version 1.2 ( 17 ) was chosen as the structure exchange format .
it supports almost all known peculiarities of carbohydrate structures , such as uncertainities in configuration and ring sizes , various combinations of repeating and non - repeating parts , non - carbohydrate linkers , cyclic structures , etc .. glyde uses a tree - based approach to structure description . within this approach
the tree root is the reducing and or the rightmost residue in the repeating unit , while all the substituents are the  children of the residue they are attached to .
configurations , ring - size and other related information is stored as attributes of the residue .
two approaches are used : the raw data ( as array of strings corresponding to authors , title terms , journal name , etc . ) or pubmed xml .
a well - known identifier for an organism is a taxid provided by ncbi taxonomy database .
however , the ranking of taxid is limited to species ; thus , no possibility to cross - search for particular strains / serogroups is provided . as this detailed ranking is significant mainly for bacteria , the capability to perform deep species searching
taxids are stored in the glycosciences.de database together with structures , while bcsdb generates taxids based on genus and species name , making use of an ncbi web service .
example 1 , using the bibliographic search of glycosciences.de , shows all references found in both resources for author  brade in year 2002 .
example 2 depicts a substructure search containing a specified disaccharide fragment [ -d - neup5nac-(2 - 3)--d - galp ] in glycosciences.de .
the data associated with two entries containing the disaccharide fragment are shown in example 2b .
example 3 demonstrates a substructure search in bcsdb using glycosciences.de to input the trisaccharide fragment -d - galp-(1 - 3)--d - manp-(1 - 4)--l - rhap .
substructure search for a - d - neup5nac-(2 - 3)-b - d - galp in glycosciences.de using the bcsdb input wizard .
result querying glycosciences for all structures containing a specified disaccharide fragment -d - neup5ac-(23)-d - galp .
querying bcsdb for all structures containing the specified trisaccharide fragment -d - galp-(1 - 3)--d - manp-(1 - 4)--l - rhap .
the glycosciences.de substructure input spreadsheet is used . the data associated with bcsdb entry 10147 are additionally shown .
the capability of web services to make distributed scientific data accessible is clearly demonstrated . to our knowledge ,
the implemented mutual online access between bcsdb and glycosciences.de is the first reported attempt of a structure - based interconnection of two glyco - related databases . for users the advantages are obvious
: they can use and have to learn only one interface , always have access to the latest data from both services , and the results of both searches are presented in a consistent way . for the database design and its functionality the establishment of a connection helped to find shortcomings and inconsistencies in both underlying data concepts and structural representations . for the maintenance of the databases , duplication of work can be easily avoided .
it can be expected that more frequent use of both services will improve the quality of data .
this will hopefully lead to a better worldwide acceptance of both services within the community of glycoscientists . since the exchange of data is accomplished through standard , well - documented xml - based descriptions and soap protocols ; other interested providers of glyco - related databases may easily be linked so that a larger network could grow .
it can be envisaged that online connection of thematically related scientific data collections will have a bright future , and not only in the area of glycosciences .
one of the main bottlenecks is currently that broadly accepted standard xml exchange formats are often not yet available .
it will definitively be a time - consuming task to come to agreements about such standard descriptions within the various communities .
with glyde 1.2 an xml - based encoding scheme of glycan structures exists , which is sufficiently flexible to link the vast majority of structures contained in bcsdb and glycosciences.de . however , glyde 1.2 has some shortcomings regarding uncertainties in terminal residues and other fuzzy encodings , which will become more important for glycomics projects .
the current focus of discussion is to base a more flexible encoding on the concept of a connection table approach , instead of a tree - like structure as used in glyde 1.2 .
recently ( september 2006 , nih meeting  frontier in glycomics ) , the seven larger projects already mentioned above have agreed to support glyde - ct as the main database format for the exchange of glycan structures .
a less favourable situation would be that several exchange format exit and parsers must be available for each database .
 functional glycomics , the scientific attempt to identify and assign functions to all glycan molecules synthesized by an organism , is an emerging field of science . in recent years , 
 several databases have been started , all aiming to support deciphering the biological function of carbohydrates . 
 however , diverse encoding and storage schemes are in use amongst these databases , significantly hampering the interchange of data . the mutual online access between the bacterial carbohydrate structure database ( bcsdb ) and the glycosciences.de portal , as a first reported attempt of a structure - based direct interconnection of two glyco - related databases is described . in this approach 
 , users have to learn only one interface , will always have access to the latest data of both services , and will have the results of both searches presented in a consistent way . 
 the establishment of this connection helped to find shortcomings and inconsistencies in the database design and functionality related to underlying data concepts and structural representations . 
 for the maintenance of the databases , duplication of work can be easily avoided , and will hopefully lead to a better worldwide acceptance of both services within the community of glycoscienists . 
 bcsdb is available at   and the glycosciences.de portal at 
INTRODUCTION
BACTERIAL CARBOHYDRATE STRUCTURE DATABASE
GLYCOSCIENCES.de
WEB-SERVICES
DATA TRANSFER FORMATS
EXAMPLES
CONCLUSIONS