EUCLIS--an information system for circadian systems biology.
A major barrier to progress in systems biology is the absence of suitable infrastructure for data and software integration, which would enable working biologists to use and manipulate the techniques directly. We describe the incremental development of key components of such an infrastructure for a research community focused on a specific (but important) biological system. EUCLOCK combines the expertise of 34 chronobiology laboratories from 29 institutions in 11 European countries in a 5-year effort to understand how circadian clocks are synchronised to their specific cyclic environment (entrainment). We envision that the EUCLOCK Information System (EUCLIS) will subsequently evolve to support the worldwide chronobiology community. The architecture of EUCLIS integrates a database for circadian systems biology, containing modules for experimental data (Clock Experiments) and models (Clock Models) with a digital library (Clock KnowledgeBase) for the research community. The digital library paradigm is superior to the simple 'access' or 'mining' as well as the 'data warehouse' approaches currently used in other systems as it provides a flexible framework for community information needs and the potential to use emerging reference models and standards, which will enable easier integration with other systems in the future. The main Clock KnowledgeBase components for EUCLIS V1.0, Clock Genes and Clock Library, are described in detail. An important aspect this work will need to address in the future is the integration of the database and digital library management functions.
Batista
R T B
RT
Department of Computer Science, University of the Philippines, Diliman.
Ramirez
D B
DB
Santos
R D
RD
del Rosario
M C I
MC
Mendoza
E R
ER
D000818:Animals; D001683:Biological Clocks / Q000502:physiology*; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism*; D002940:Circadian Rhythm / Q000502:physiology*; D003628:Database Management Systems; D016208:Databases, Factual; D006801:Humans; D033181:Information Dissemination / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D015398:Signal Transduction / Q000502:physiology*; D049490:Systems Biology / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism
D018797:Cell Cycle Proteins; D014157:Transcription Factors