Informatics:Cross-Database Search (WGGDS)

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Starting in 2010, as part of a CFG bridging grant project and with support from the Working Group for Glycomcis Data(base) Standards (WGGDS) , an cross-database search interface based on REST web services was defined to allow searches between the CFG glycan database and EUROCarbDB databases. Since the interface and protocol is formulated independent of the database backend, several groups have expressed interest in joining this initiative and implementing the interface on other databases. The documentation of the interface can be found in a sub article.

Contents

CFG

The implementation of the standard interface at the CFG database is ongoing. A Test webpage is available showing the current development status and providing input interfaces and test inputs for the webservices.

Mass search

The mass search is implemented but not all options are available at this point.

ppm
Only false is supported allowing to specify the search interval in dalton.
persubstitution
Only none is supported. Other per-derivatisations will be added soon.
monoisotopic
Only false is supported which means the search performed with average masses.
format
JSON is not supported.

Substructure search

The substructure search is not implemented at this point.

Composition search

The composition search is not implemented at this point.

Result list operation

The combination of search results is not implemented at this point.

Full information service

This service is not implemented at this point.

EUROCarbDB

The implementation of the standard interface at the EUROCarbDB database is ongoing. A Test webpage is available showing the current development status and providing input interfaces and test inputs for the webservices.

Mass search

The mass search is not implemented at this point.

Substructure search

The substructure search is not implemented at this point.

Composition search

The composition search is not implemented at this point.

Result list operation

The combination of search results is not implemented at this point.

Full information service

This service is not implemented at this point.

GlycomeDB

The implementation of the standard interface at the GlycomeDB database will start in October 2010. However, a Test webpage is available showing the development status and providing input interfaces and test inputs for the webservices.

Mass search

The mass search is not implemented at this point.

Substructure search

The substructure search is not implemented at this point.

Composition search

The composition search is not implemented at this point.

Result list operation

The combination of search results is not implemented at this point.

Full information service

This service is not implemented at this point.

KEGG (DBCLS)

The implementation of the standard interface at the KEGG database is almost complete. A Test webpage is available showing the development status and providing input interfaces and test inputs for the webservices.

Mass search

The mass search is implemented but not all options are available at this point.

ppm
unsupported - any value is ignored.
persubstitution
unsupported - any value is ignored.
monoisotopic
unsupported - any value is ignored.
format
only xml will be returned.

Substructure search

The substructure search is implemented but only exactMatch option is supported (gapped vs. ungapped). The other options are ignored.

Composition search

The composition search is implemented but compositions are currently taken in CarbBank format.

Result list operation

The combination of search results is implemented for AND, OR and XOR only at this point. However it currently errors out due to some technical issues on the server.

Full information service

This service is implemented.

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