Bio-medical Ontologies Maintenance and Change Management

2 The New Waves
Towards Bioinformatics Resourceomes 19
Here we briefly summarize some recent innovations in Information Technology
and their impact in bioinformatics.
2.1 Ontologies
In philosophy, ontology is, since the ancient Greeks, the study of being or
existence. In applied computer science recently we witnessed a massive diffusion
of ontologies. They are now used to model, by mean of a ontology formal
language, the knowledge concerning a particular domain. The concepts of the
domain can be precisely defined as well as the relationships between those
concepts. The actual objects of the domain are represented as instances of
the concepts and it is possible to perform formal reasoning on them, automatically
inferring new knowledge.
Bioinformatics and biomedicine undoubtedly contributed to (and benefited
of) this generalized diffusion of ontologies (or ontology-like structures [35])
in science. In order to provide some coordination to these efforts the Open
Biomedical Ontologies (OBO 10 ) consortium was established. The renewed
OBO Foundry website lists today more than sixty ontologies, ranging from
“Animal natural history” to “Zebrafish anatomy and development”. In particular
in bioinformatics the role of ontologies has moved from a niche activity
to a mainstream one [8]. According to Bodenreider and Stevens the Gene
Ontology [20] has been phenomenally successfull. Starting from about 3500
terms in 1998 now it covers around 20000 terms and its controlled vocabulary
is adopted in more than 20 databases. Its success is due to the deep and continuous
involvement of the molecular biology community in the development
and maintenance of the ontology. Other important factors are its clear goals,
limited scope and simple structure.
The TAMBIS Ontology [2, 61], represents a remarkable attempt to semantically
organize bioinformatics concepts, including resources. The aim of
the TAMBIS project was that of providing transparent access to disparate
biological databases and analysis tools enabling users to utilize a wide range
of resources with the minimum effort. Proton [17] is a ontology prototype for
the classification of databases and algorithms for proteomics.
2.2 Web Services
Web Services, represent one of the most used middleware in distributed
programming. Thanks to the WSDL 11 descriptors (which characterize the
interface of the service) and the SOAP 12 messages (which make the communication
possible), Web Services are a great way to integrate distributed
10 http://obofoundry.org/
11 http://www.w3.org/TR/wsdl
12 http://www.w3.org/TR/soap