Bio-medical Ontologies Maintenance and Change Management
Bio-medical Ontologies Maintenance and Change Management
Bio-medical Ontologies Maintenance and Change Management
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Towards <strong>Bio</strong>informatics Resourceomes 31<br />
A Resourceome has a three level view: two conceptual ones (concepts of<br />
resources <strong>and</strong> domain) <strong>and</strong> a physical one (individuals of resources). In a<br />
Resourceome, the arcs representing the relationships between different resources,<br />
allow for a better customization. The features of the resource are<br />
represented by the properties described at their physical level. The access to<br />
the resources can be made through specific relations with other resources.<br />
For example, a resource such as a Web Service like ClustalW 23 , can be characterized<br />
by its WSDL descriptor property <strong>and</strong> by a relation like stub with<br />
to the WSDL2Java resource. The stub with relation specifies that the Web<br />
Service resource ClustalW, needs the tool resource WSDL2Java for being accessed.<br />
In this way, access to heterogeneous resources is guaranteed. Another<br />
important difference between <strong>Bio</strong>Navigation <strong>and</strong> a Resourceome is that the<br />
first concerns only biological data sources, whereas a Resourceome is general<br />
purpose <strong>and</strong> embraces every kind of resource. Furthermore, the ontologies of<br />
a Resourceome are published on the Semantic Web.<br />
4.3 Resourceomes <strong>and</strong> Web Services<br />
In a Resourceome, Web Services are just a specific class of resources, whose<br />
function can be described in term of domain concepts. Further semantic descriptors<br />
which characterize the Semantic Web Service <strong>and</strong> systems for their<br />
interoperability represent a further advantage for the use of those resources.<br />
ServicesSemanticMap [45] is a project compatible with <strong>Bio</strong>Moby. ServicesSemanticMap<br />
provides a system for the registration of Web Services<br />
<strong>and</strong> a visualization interface for ontology <strong>and</strong> service map exploration. ServiceSematicMap<br />
<strong>and</strong> <strong>Bio</strong>Moby represent Web Services registries like UDDI 24 )<br />
enriched with semantics. Also in this case, Resourceome can play the same<br />
role. In any case, <strong>Bio</strong>Moby <strong>and</strong> ServiceSemanticMap are dedicated only to<br />
resources of Web Services type. The SemBowser [57] registry is aimed to help<br />
glycoproteomics researchers to find the proper Web Service among a number<br />
of available ones. It represents an ontology based implementation of the<br />
UDDI specification (non W3C), which classify a Web Service according to<br />
the task performed <strong>and</strong> the domain it is associated with.<br />
4.4 Resourceomes <strong>and</strong> TAMBIS<br />
The TAMBIS ontology (TaO) [2] describes a wide range of bioinformatics<br />
tasks <strong>and</strong> resources, <strong>and</strong> has a central role within the TAMBIS system. An<br />
interesting difference between the TaO <strong>and</strong> some of the other ontologies reviewed<br />
here, is that the TaO does not contain any instances. The TaO only<br />
contains knowledge about bioinformatics <strong>and</strong> molecular biology concepts <strong>and</strong><br />
their relationships. The instances they represent still reside in an external<br />
database. As concepts represent instances, a concept can act as a question.<br />
23 http://www.ebi.ac.uk/Tools/webservices/services/clustalw<br />
24 http://www.uddi.org
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