Dealing with Some Conceptual Data Model Requirements for Biological Domains

Knowledge representation in the biological domain suffers from two main difficulties that make it hard to apply traditional conceptual modeling tools: the inherent domain complexity and its constant evolution. The former requires complex types and associations, whereas the latter calls for an expressive language. We list in this paper a set of requirements for conceptual data modeling that should fulfil biologists' needs. We discuss these requirements by analyzing representation problems using traditional conceptual modeling languages. We claim that the biological domain deserves an ad-hoc modeling approach that would help with activities such as data integration and database design.

[1]  Christian S. Jensen,et al.  On the Ontological Expressiveness of Temporal Extensions to the Entity-Relationship Model , 1999, ER.

[2]  Wolfgang May,et al.  Nonmonotonic Inheritance in Object-Oriented Deductive Database Languages , 2001, J. Log. Comput..

[3]  Douglas Herrmann,et al.  A Taxonomy of Part-Whole Relations , 1987, Cogn. Sci..

[4]  Peter D. Karp,et al.  An ontology for biological function based on molecular interactions , 2000, Bioinform..

[5]  Martin Gogolla.  Unified Modeling Language , 2009, Encyclopedia of Database Systems.

[6]  Carole A. Goble,et al.  Conceptual modelling of genomic information , 2000, Bioinform..

[7]  Marijke Keet.  Conceptual Modelling for Applied Bioscience: The Bacteriocin Database , 2003 .

[8]  Martin Gogolla,et al.  Towards a semantic view of an extended entity-relationship model , 1991, TODS.

[9]  Functional Genomics Thickens the Biological Plot , 2005, PLoS biology.

[10]  I-Min A Chen,et al.  An Overview of the Object-Protocol Model (OPM) and OPM Data Management Tools , 1995, Inf. Syst..

[11]  S. Herrmann.  Orthogonality in Language Design – Why and how to fake it , 2003 .

[12]  R. Durbin,et al.  The Sequence Ontology: a tool for the unification of genome annotations , 2005, Genome Biology.

[13]  M. Crochemore,et al.  Motifs in Sequences: Localization and Extraction , 2004 .

[14]  Mark P. Styczynski,et al.  An extension and novel solution to the (l,d)-motif challenge problem. , 2004, Genome informatics. International Conference on Genome Informatics.

[15]  John V. Carlis,et al.  Genomic data modeling , 2003, Inf. Syst..

[16]  Kathleen R Ryan,et al.  Temporal and spatial regulation in prokaryotic cell cycle progression and development. , 2003, Annual review of biochemistry.

[17]  B. Kholodenko,et al.  Four-Dimensional Organization of Cellular Signal Transduction Cascades , 2001 .

[18]  Marie-France Sagot,et al.  Algorithms for Extracting Structured Motifs Using a Suffix Tree with an Application to Promoter and Regulatory Site Consensus Identification , 2000, J. Comput. Biol..