The emphasis in bioinformatics has so far been on structures, in a
wide sense of the word; (comparatively) easy to represent, store, analyse.
- The genomes
- Protein 3D structure/function
- Transcriptome, proteome, metabolome
- Pathways (wiring diagrams)
Biology = structures + processes
Biology deals with processes, but, so far, bioinformatics has not been
able to formalize and handle biological processes nearly as
successfully as biological structures.
To make biology computable, there is a need for a formalization of
biological processes. Databases will be requried where the data models
contain time is a fundamental coordinate.
- The microarray time-series experiments contain both complete
structural data, as well as temporal data.
- The 'Gene Ontology' project contains a Biological Process
concept, albeit without any description of the dynamics.
- Systems Biology, simulation engines: temporal data will be
required as constraints and tests.
- The various pathways and interactions databases rarely have the
concept of time.
- Specialised databases in developmental biology (mouse, C elegans)
contains some temporal data.
$Date: 2001/04/17 16:52:14 $