Simplifying Class Management through EAV Design
When the number of instances of a class is expected to be numerous enough in a production schema, the standard Object Dictionary approach with class-specific tables holding object descriptions, as mentioned earlier is adequate. When it is not, we must consider alternative design approaches. One approach that is popular for modeling highly heterogeneous data is the Entity-Attribute-Value EAV approach. Some authors substitute Object for Entity. Attribute-Value pairs as a means of describing an...
A database of computational models of neuronal function ModelDB 5
that facilitates the creation and running of neuronal models over the Internet through a Web interface. The initial work, using the GENESIS neuronal simulator 6 was done by Bret Peterson. Subsequent work, described in 7 and done primarily by Jason Mirsky and Michael Hines, permits the use of an alternative simulator, NEURON 8 . NeuronDB 9 , a database of neuronal types, with associated receptors, neurotransmitters, canonical compartments, ion channels and relevant Iiterature citations. Such...
Limitations of the EAV model
The simplicity of EAV comes with a price, namely, a performance penalty. The physical representation of a class is quite different from its logical view as seen by the user. Assembling all the columns associated with a particular class object involves consulting the Class Attributes table and then gathering data from the appropriate EAV tables. More important, complex Boolean query of classes requires set operations as in the case of the general N-ary relationship structure described earlier ....
Conclusions
Our proposed database schema for managing heterogeneous data is a significant departure from conventional approaches. It is suitable only when the following conditions hold The number of classes of entity is numerous, while the number of actual instances in most classes is expected to be very modest. The number and nature of the axes describing an arbitrary fact as an N-ary association varies greatly. We believe that nervous system data is an appropriate problem domain to test such an approach.
Conclusions and Outlook
Being both comprehensive and fully integrated into the existing bioinformatics structures relevant to human genetics, HGMD has established itself as the central core database of inherited human gene mutations. Looking to the future, efforts will be made to improve the provision of flanking sequence data, to increase the number of cDNA and genomic reference sequences provided and to make the data collections on gross gene lesions and disease-relevant polymorphisms fully comprehensive. In order...
Karl Sirotkin
National Center for Biotechnology Information, National Library of Medicine, National lnstitutes of Health, Since 1992 the National Center for Biotechnology Information NCBI has provided integrated access to all public genetic sequence information and its associated annotation, as well as the citations and abstracts from the published literature referenced by the genetic sequence records. This chapter describes the main database that contains the genetic sequence data used by this integrated...
HOVERGEN Comparative Analysis of homologous
Laurent Duret, Guy Perri re and Manolo Gouy Laboratoire de Biom trie, G n tique et Biologie des Populations, UMR CNRS 5558, Universit Claude Bernard, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne cedex, Comparison of homologous sequences is an essential step for many studies related to molecular biology and evolution to predict the function of a new gene, to identify important regions in genomic sequences, to study evolution at the molecular level or to determine the phylogeny of species. The...
WITWIT2 Metabolic Reconstruction Systems
Ross Overbeek, Niels Larsen, Natalia Maltsev, Gordon D. Pusch, and Evgeni Selkov Argonne National Laboratory, Argonne, IL 60439 Introduction What Is Metabolic Reconstruction For the past few years, we have been developing metabolic reconstructions for organisms that have been sequenced, and we have made a number of these working models available. By the term metabolic reconstruction we mean the process of inferring the metabolism of an organism from its genetic sequence data supplemented by...