Bio-medical Ontologies Maintenance and Change Management

46 E. De Francesco et al.
Fig. 4. Query types
the genic sequence of every organism: filling the pattern search query form
with it on a database such as CandidaDB [6], and allowing at most one
mismatch, 311 genic subsequences extracted from the Candida (a fungus)
DNA and containing the TATA box in evidence are returned. Both sequence
similarity and pattern search queries exploit heuristic search algorithms such
as BLAST [29].
2.4 Query Methods
A further analysis criterium we considered is related to methods used to
query available databases, as illustrated in Figure 5. We distinguished four
main classes of query methods: text based methods, graphical interaction based
methods, sequence based methods and query language based methods.
The most common methods are the text based ones, further grouped in
two categories: free text and forms. In both cases, the query can be formulated
specifying some keywords. With the free text methods, the user can specify
Fig. 5. Query methods