Bio-medical Ontologies Maintenance and Change Management

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40 E. De Francesco et al. Genomic Databases: contain data related to the genomic sequencing of different organisms, and gene annotations; – Human Genome Databases: include information on the human gene sequencing. – Model Organism Databases (MOD): store data coming from the sequencing projects of model organisms (such as, e.g., MATDB); they are also intended to support the Human Genome Project (HGP). – Other Organism Databases: store information derived from sequencing projects not related to HGP. – Organelle Databases: store genomic data of cellular organelles, such as mitochondria, having their own genome, distinct from the nuclear genome. – Virus Databases: store virus genomes. Experiment Databases: contain results of lab experiments; these can be grouped in three main classes: – Microarray Databases: store data deriving from microarray experiments, useful to assess the variability of the gene expression. – 2D PAGE Databases: contain data on proteins identified by twodimensional polyacrylamide gel electrophoresis (2-D PAGE), an experimental technique used to physically separate and distinguish proteins. – Other Experiment Databases: store results of specific experimental techniques, such as Quantitative PCR Primer Database [23]. Immunological Databases: store information associated to immunologic responses. Gene Databases: contain sequence data of DNA codifying subsequences, that are, the genes. Transcript Databases: store the set of transcribed genomic sequences of several organisms (that are, those genomic sequences characterizing organs’ and tissues’ cellular properties). Pathway Databases: contain information on metabolic reaction networks of cellular signals. Polymorphism and mutation Databases: report data on polymorphic variations and mutations. Meta-Database: store descriptions and links about (selected groups of) biological databases; Literature Databases: these are archives storing papers published on premier biological journals. Other Databases: store data related to specific application contexts, such as the DrugBank [10]. It is worth pointing out that the above classes in some cases overlap. As an example, EcoCyc [40] is to be looked at both as a genomic and as a pathway database. Note that this is intrinsic to the structure of the biological context. In fact, biological data sources contain data which can be classified under different perspectives, due to the various origins and goals of the associated repositories.
A Summary of Genomic Databases: Overview and Discussion 41 Biological database categories Macromolecular Databases Genomic Databases Experiment databases Immunological databases Gene databases Transcript databases Pathway databases Protein databases Polymorphism and mutation databases Meta Database (database of database) Literature databases Other databases DNA databases RNA databases Protein sequence databases Protein structure databases Protein motif and domine databases Human genome databases Model organism databases Other organism databases Organelle databases Virus genome databases Microarray databases 2D PAGE databases Other experiments databases Fig. 1. Biological database classification 2 Genomic Databases Analysis This section focuses on genomic databases, that represent one among the most important biological database categories. Differently from gene databases, containing only coding DNA sequences, genomic databases contain also non coding intergenic sequences. In the following, we discuss a selected subset of genomic repositories (74 units) and illustrate in detail their differences and common features according
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Bio-medical Ontologies Maintenance
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Extraction of Constraints from Biol
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Classifying Patterns in Bioinformat
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Mining Clinical, Immunological, and
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Substructure Analysis of Metabolic
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6 Conclusion Substructure Analysis
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Completing the Total Wellbeing Puzz
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Author Index Apiletti, Daniele 169
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Bio-medical Ontologies Maintenance and Change Management

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