BioNemus Web Services generation tool


BioNemus is a web services generation tool based on BioMoby services' descriptions. The tool works directly with BioMoby Registry servers and generates Document/Literal SOAP 1.1 web services that act as a proxy to original BioMoby counterparts. It also preserves BioMoby annotations as Semantical Annotaions. Apart of SOAP-based web services it can also generate HTTP-based ones (REST). It is also possible to create new web services from scratch or based on BioMoby datatype ontology.

Generated aplication is a standard JAX-WS based web application that can be run on any compatible Java Application Server. The proxy supports both synchronous and asynchronous modes through WS-Addressing.

BioNemus architecture

BioNemus architecture

All BioMoby datatype relationships (ISA, HAS, HASA) can be easily represented in XML Schema:

BioNemus datatypes

Because generated SOAP-based web services are directly created from BioMoby definitions users should not have problems with their usage.
Some BioNemus entities are directly translated to their BioMoby counterparts:

BioMoby BioNemus description
id nemusId a biological entity identifier of any kind (ie "PDB_ID", "UNIPROT_ID" ...)
namespace nemusNamespace a concept of data origin, usually goes along with an identifier ([id="P00807", namespace="UniProt"], [id="1PIO", namespace="PDB"]...)
SecondaryParameters parameters usually specifies additional parameters for a service (ie BLAST parameters in runNCBIBlastp service)
xrefs reference A cross reference is an optional component of any object.