Bioinformatics applications that are available as web services are numerous and are growing in number. More bioinformatics service providers are supplying web service versions of their applications and more 'legacy' command-line and web page applications are being made available as web services via SoapLab and GowLab wrapping. Consequently, service discovery is becoming increasingly important.
Feta is a semantic discovery tool that can be used to search available services and find those that best match the requirements of the user.

Motivation

It is often difficult to ascertain the function(s) of a web service application from its name. Experienced bioinformaticians may be familiar with a number of applications, but perhaps not all of them. Laboratory-based biologists, who may also wish to use myGrid tools, are even less likely to be familiar with the web services they can use in workflow designs.

myGrid has addressed this problem by implementing Feta, a system to search for web services not only by name, but also by function or input or output parameters.
Feta can assist the user in workflow design, shortening time taken to discover services and incorporate them into workflows. Feta can also provide extra information on the format required or produced for inputs or outputs.
Another important function of Feta is that it can provide information on alternative services. Several organisations can provide different implementations of the same application, or provide applications that are very similar and essentially perform the same function. The semantic discovery capabilities can be used to find alternative services if a particular web service is unavailable, or if past experience has shown that a particular web service is unreliable or slow.

myGrid Ontology

Feta builds upon the myGrid ontology, which is actually a suite of ontologies that describe molecular biology and bioinformatics concepts as well as organisational, service and workflow concepts. The ontology suite describes the kinds of data being interrogated, the requirements and actions of the services performing the interrogation and the kinds of data being produced. This allows the annotation of data, workflows and services and allows their classification.

Papers / Documents

A suite of DAML+OIL Ontologies to Describe Bioinformatics Web Services and Data. in International Journal of Cooperative Information Systems special issue on Bioinformatics, March 2003. ISSN: 0218-8430 - Chris Wroe, Robert Stevens, Carole Goble, Angus Roberts, Mark Greenwood (2003)
Abstract: The growing quantity and distribution of bioinformatics resources means that finding and utilising them requires a great deal of expert knowledge, especially as many resources need to be tied together into a workflow to accomplish a useful goal. We want to formally capture at least some of this knowledge within a virtual workbench and middleware framework to assist a wider range of biologists in utilising these resources. Different activities require different representations of knowledge. Finding or substituting a service within a workflow is often best supported by a classification. Marshalling and configuring services is best accomplished using a formal description. Both representations are highly interdependent and maintaining consistency between the two by hand is difficult. We report on a description logic approach using the web ontology language DAML+OIL that uses property based service descriptions. The ontology is founded on DAML-S to dynamically create service classifications. These classifications are then used to support semantic service matching and discovery in a large grid based middleware project myGrid. We describe the extensions necessary to DAML-S in order to support bioinformatics service description; the utility of DAML+OIL in creating dynamic classifications based on formal descriptions; and the implementation of a DAML+OIL ontology service to support partial user-driven service matching and composition
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Created on 2004-12-01 13:01:59 by katy Updated on 2006-10-12 10:21:21 by katy