Bio-medical Ontologies Maintenance and Change Management

A Summary of Genomic Databases: Overview and Discussion 39
is a sequence of symbols on an alphabet of four characters, that are, A, T ,
C and G, representing the four nucleotides Adenine, Thymine, Cytosine and
Guanine. In genomic sequences, three kinds of subsequences can be distinguished:
i) genic subsequences, coding for protein expression; ii) regulatory
subsequences, placed upstream or downstream the gene of which they influence
the expression; iii) subsequences apparently not related to any function.
Each gene is associated to a functional result that, usually, is a protein.
Protein synthesis can be summarized in two main steps: transcription and
translation. During transcription, the DNA genic sequence is copied into a
Messenger Ribonucleic Acid (RNAm), delivering needed information to the
synthesis apparatus. During translation, the RNAm is translated into a protein,
that is, a sequence of symbols on an alphabet of 20 characters, each
denoting an amino acid and each corresponding to a nucleotide triplet. Therefore,
even changing one single nucleotide in a genic subsequence may cause a
change in the corresponding protein sequence. Proteins as, more in general,
macromolecules, are characterized by different levels of information, related
to the elementary units constituting them and to their spatial disposition.
Such levels are known as structures. In particular, the biological functions
of macromolecules also depend on their three-dimensional shapes, usually
named tertiary structures. Moreover, behind the information encoded in the
genomic sequence, additive knowledge about biological functions of genes and
molecules can be attained by experimental techniques of computational biology.
Such techniques are devoted, for example, to build detailed pathway
maps, that are, directed graphs representing metabolic reactions of cellular
signals [14].
1.2 Biological Database Classification
As pointed out in [31], all the biological databases may be classified, w.r.t.
their biological contents, in the following categories (see also Figure 1):
Macromolecular Databases: contain information related to the three main
macromolecules classes, that are, DNA, RNA and proteins.
– DNA Databases: describe DNA sequences.
– RNA Databases: describe RNA sequences.
– Protein Databases: store information on proteins under three different
points of view:
· Protein Sequence Databases: describe amino acid sequences.
· Protein Structure Databases: store information on protein structures,
that are, protein shapes, charges and chemical features, characterizing
their biological functions.
· Protein Motif and Domain Databases: store sequences and structures
of particular protein portions (motifs and domains) to which
specific functional meanings can be associated, grouped by biological
functions, cellular localizations, etc.