Bio-medical Ontologies Maintenance and Change Management

A Summary of Genomic Databases: Overview
and Discussion
Erika De Francesco 1 , Giuliana Di Santo 2 , Luigi Palopoli 2 ,
and Simona E. Rombo 2
1 Exeura, Via Pedro Alvares Cabrai, Edificio Manhattan,
87036 C.da Lecco, Rende (CS), Italy
erika.defrancesco@exeura.com
2 Università della Calabria, Via Pietro Bucci 41c, 87036 Rende, Italy
disanto@si.deis.unical.it, palopoli@deis.unical.it,
simona.rombo@deis.unical.it
Summary. In the last few years both the amount of electronically stored
biological data and the number of biological data repositories grew up significantly
(today, more than eight hundred can be counted thereof). In spite of
the enormous amount of available resources, a user may be disoriented when
he/she searches for specific data. Thus, the accurate analysis of biological
data and repositories turn out to be useful to obtain a systematic view of biological
database structures, tools and contents and, eventually, to facilitate
the access and recovery of such data. In this chapter, we propose an analysis
of genomic databases, which are databases of fundamental importance for
the research in bioinformatics. In particular, we provide a small catalog of 74
selected genomic databases, analyzed and classified by considering both their
biological contents and their technical features (e.g, how they may be queried,
the database schemas they are based on, the different data formats, etc.). We
think that such a work may be an useful guide and reference for everyone
needing to access and to retrieve information from genomic databases.
1 The Biological Databases Scenario
In such an evolving field like the biological one, having continuously new data
to store and to analyze seems natural. Thus, the amount of data stored in
biological databases is growing very quickly [12], and the number of relevant
biological data sources can be nowadays estimated in about 968 units [34].
The availability of so many data repositories is indisputably an important resource
but, on the other hand, opens new quests, as to effectively access and
retrieve available data. Indeed, the distributed nature of biological knowledge,
and the heterogeneity of biological data and sources, can often cause
trouble to the user trying specific demands. And, in fact, not only such data
sources are so numerous, but they use different kinds of representations, access
methods and various features and formats are offered.
A.S. Sidhu et al. (Eds.): Biomedical Data and Applications, SCI 224, pp. 37–54.
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