CATH/Gene3D Database Lookup Services

By | September 22, 2011

The CATH/Gene3D Database lookup service provides an interface that exposes the backend CATH/Gene3D databases to simple lookup queries. This enables users to quickly answers questions such as:

  • return all the GO terms for a given CATH superfamily (PdbSuperfamily2GoTerms)
  • return all the CATH domains for a given UniProt ID (UniProtId2DomainIds)

The operations offered currently all take the form QueryType2MatchTypes (e.g. PdbSuperfamily2GoTerms) where the QueryType is essentially the database column used for the lookup and MatchType specifies what type of matching data will be returned.

These services (WSDL, server, backend) are all automatically generated from a small configuration file which simply provides a database connection and the query for each operation (table, input column). This process uses a combination of perl tools: Catalyst (MVC Web Framework), DBIx::Class (database manipulation/introspection), XML::Compile (WSDL) and was written as a generic bootstrapping module. The intention is to release this to CPAN (DataService) so that others could use it to provide their own database lookup webservices with minimal fuss.

Name
CATH/Gene3D Database Lookup Services
Documentation
http://api-v3-1.cathdb.info/static/wsdl/DataServices.wsdl
Protocol
SOAP
WSDL
Endpoint
http://ws.cathdb.info/api/soap/DataServices
Topic
Biology, Domains, Pathways
Type
Analysis, Data Retrieval
Tags
, , , , , , , , , , , , , ,
Description

The CATH/Gene3D Database lookup service provides an interface that exposes the backend CATH/Gene3D databases to simple lookup queries. This enables [...]

Further information

The CATH/Gene3D Database lookup service provides an interface that exposes the backend CATH/Gene3D databases to simple lookup queries. This enables users to quickly answers questions such as:

  • return all the GO terms for a given CATH superfamily (PdbSuperfamily2GoTerms)
  • return all the CATH domains for a given UniProt ID (UniProtId2DomainIds)

The operations offered currently all take the form QueryType2MatchTypes (e.g. PdbSuperfamily2GoTerms) where the QueryType is essentially the database column used for the lookup and MatchType specifies what type of matching data will be returned.

These services (WSDL, server, backend) are all automatically generated from a small configuration file which simply provides a database connection and the query for each operation (table, input column). This process uses a combination of perl tools: Catalyst (MVC Web Framework), DBIx::Class (database manipulation/introspection), XML::Compile (WSDL) and was written as a generic bootstrapping module. The intention is to release this to CPAN (DataService) so that others could use it to provide their own database lookup webservices with minimal fuss.

Original source
BioCatalogue

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