Bio-medical Ontologies Maintenance and Change Management

48 E. De Francesco et al.
Fig. 6. Result formats
represent data in a tabular format, separating attributes and records by special
characters (e.g., commas and tabulations). The latter ones (supported for
example by BioCyc [4], EcoCyc [11] and HumanCyc [18]) organize data as
pairs .
In other cases, special formats have been explicitly conceived for biological
data. An example is the FASTA format [44], commonly used to represent
sequence data (it is exploited in all genomic databases, except for ColiBase
[9], PhotoList [21] and StreptoPneumoList [25]). Each entry of a FASTA
document consists in three components: a comment line, that is optional and
reports brief information about the sequence and the GenBank entry code;
the sequence, represented as a string on the alphabet {A, C, G, T} of the
nucleotide symbols, and a character denoting the end of the sequence.
More recently, in order to facilitate the spreading of information in heterogeneous
contexts, the XML format has been sometimes supported. The
main XML-based standards in the biological context are the System Biology
Markup Language (SBML) [36] and the Biological Pathway Exchange
(BioPAX) [26]. SMBL is used to export and exchange query results such
as pathways of cellular signals, gene regulation and so on. The main data
types here are derived from XML-Schema. Similarly, BioPAX has been designed
to integrate different pathways resources via a common data format.
BioPAX specifically consists of two parts: the BioPAX ontology, that provides
an abstract representation of concepts related to biological pathways, and