Bio-medical Ontologies Maintenance and Change Management

50 E. De Francesco et al.
In Figure 7, an example of the synthetic description we adopted is illustrated.
In particular, a form is exploited where both the acronym and
the full name of the database under analysis are showed. We consider the
CryptoDB [35] (Cryptosporidium Genome Resources) database, that is, the
genome database of the AIDS-related apicomplexan-parasite, as reported in
the brief description below the full name in the form. Also the web-link to
the considered database is provided, along with its database features. In
particular, CryptoDB is a relational DBMS based on the Genomic Unified
Schema (illustrated above, in Section 2.2). All features corresponding to the
other analysis criteria are reported. In detail, we highlight that CryptoDB
contains information on genes, clone/contig sequences, polymorphism and
motifs, and that it stores physical maps, pathways and bibliographic references
as well. It supports simple queries and also analysis queries based on
similarity search, and allows graphical interaction and sequence based query
methods. Additional information are contained in the form about the search
criteria supported by each database. In particular, CryptoDB can be queried
by using both keywords and map positions as search parameters (map positions
require the specification of the positions of chromosomic regions). The
result formats supported by CryptoDB are HTML (as all the other genomic
databases), FASTA and tab-separated files. It allows the user to download
data stored in its repository, but not to submit new data, as specified in the
last two field (“submit” and “download”) of the form.
3 Concluding Remarks
In this chapter we presented the main results of an analysis we have conducted
on 74 genomic databases. Such an analysis has been done mainly focusing
on a database technology point of view, by choosing five specific criteria
under which all the considered databases have been investigated. Thus, the
considered databases have been classified according to such criteria and their
synthetic descriptions are given, with the aim of providing a preliminary
instrument to access and manage more easily the enormous amount of data
coming from the biological repositories.
References
1. ArkDB, http://www.thearkdb.org/arkdb//index.jsp
2. AureoList, http://genolist.pasteur.fr/AureoList
3. BeetleBase, http://www.bioinformatics.ksu.edu/BeetleBase
4. Biocyc website, http://biocyc.org
5. Bovilist world-wide web server, http://genolist.pasteur.fr/BoviList
6. Candidadb: Database dedicated to the analysis of the genome of the human
fungal pathogen, candida albicans, http://genolist.pasteur.fr/CandidaDB
7. Central aspergilus data repository, www.cadre.man.ac.uk
8. Chado: The gmod database schema, http://www.gmod.org/chado