Bio-medical Ontologies Maintenance and Change Management

Towards Bioinformatics Resourceomes 15
bioinformatics simply offers the common daily tools. The suffix “omics” became
very famous up from the late 1990s to indicate the paradigm shift of
research: from the study of a single molecule (e.g. a gene, a protein) to the
study of the entire population of such molecules as a whole (e.g. the genome,
the proteome). Probably with the announcement of the completion of the
first draft of the human genome in the year 2000, bioinformatics reached the
status of “big science”, becoming popular in the media and to the common
people.
At the second level we can find the users which assemble resources. In the
decade around the year 2000, complex repetitive bioinformatics analyses were
automatized in form of programs written with script languages (e.g. Perl). Besides
being very compact and permitting rapid programs development, such
languages are mostly ideal also for performing sophisticated text analysis and
pattern matching. Some of them are even endowed with dedicated bioinformatics
libraries (e.g. Bioperl 3 ). Now, most of the bioinformatics programs as
well as database queries, can be invoked remotely as Web Services available
somewhere in the internet. Web pages with HTML form have been developed
for human beings, but being not standards and without any precise semantics
and syntax, they could not be tackled automatically by programs. Also the
affirmation of XML 4 as a standard for data interchange contributed firmly
to acquire a complete machine interoperability. Remote programs sparse over
the internet can talk - and understand - with each other using standard protocols.
Scripts to execute “in-silico” bioinformatics experiments have been
now substituted by workflows of Web Services, which can be composed in a
very simple visual manner. Therefore, also users without any programming
skill can easily assemble them.
At the higher level we pose the developers of resources. Either they could be
the computational biologists, which develop the algorithms, subsequently implemented
as stand alone programs or Web applications, accessible through
HTML forms or Web Services. Or they could be the database developers,
which expose their data or information, probably obtained also through complex
computations and filtering. Here still emerges the foundational binomial
of bioinformatics bioinformatics = database + computational biology. Thelatter
could in some way remember the notable algorithms + data structure =
programs [66].
To give an idea of the dynamicity of bioinformatics we do list the titles of
the articles in the “trends guide to bioinformatics” edited by Mark Boguski in
1998 [9]: Text-based database searching, Fundamentals of database searching,
Practical database searching, Computational genefinding, Multiple-alignment
and -sequence searches, Protein classification and functional assignment, Phylogenetic
analysis and comparative genomics, Databases of biological information,
Functional genomics. We can make a comparison with the categories
adopted from 2005 - only seven years later - by the journal Bioinformatics for
3 http://www.bioperl.org/
4 http://www.w3.org/XML/