Bio-medical Ontologies Maintenance and Change Management

A Summary of Genomic Databases: Overview and Discussion 45
Fig. 3. Database schemas
based on the genolist schema are, for example, AureoList [2], LegioList
[19] and PyloriGene [22].
The Chado Schema [8]: this is a relational schema having an extensible
modular structure, and is used in some model organism databases such
as BeetleBase [3] and FlyBase [42].
The Pathway Tools Schema [39]: this is an object schema, used in Pathway/Genome
databases. It is based on an ontology defining a large set
of classes (there are about 1350 of them), attributes and relations to
model biological data, such as metabolic pathways, enzymatic functions,
genes, promoters and genic regulation mechanisms. Databases based on
this schema are BioCyc [4], EcoCyc [11] and HumanCyc [18].
Unspecific Schema refers to databases which do not correspond to any
of the specific groups illustrated above; in particular, most of them are
based on a relational schema, without any special adaptation to manage
biological data.
2.3 Query Types
In Figure 4, query types supported by the analyzed databases are illustrated.
By simple querying it is possible to recover data satisfying some standard
search parameters such as, e.g., gene names, functional categories and others.
Batch queries consist of bunches of simple queries that are simultaneously
processed. The answers to such queries result as a combination of the answers
obtained for the constituent simple queries. Analysis queries are more
complex and, somehow, more typical of the biological domain. They consist
in retrieving data based on similarities (similarity queries) and patterns
(pattern search queries). The former ones take in input a DNA or a protein
(sub)sequence, and return those sequences found in the database that are the
most similar to the input sequence. The latter ones take in input a pattern p
and a DNA sequence s and return those subsequences of s, whichturnoutto
be most strongly related to the input pattern p. Asanexample,considerthe
pattern TATA, that is, a pattern denoting a regulative sequence upstream