D440 Nucleic Acids Research, 2007, Vol. 35, Database issue of genes and the large number of paralogs that could consequently be identiﬁed, make Paramecium an outstanding model for studying the evolutionary consequences of whole genome duplication. PARAMECIUMDB ARCHITECTURE ParameciumDB was built using components of the Generic Model Organism Database (GMOD, http://www.gmod.org) toolkit. GMOD is an open source project initiated in 2002 with the objective of providing generic software so that a small community with limited informatics infrastructure can build a new model organism database. We provide a brief description of the GMOD core components used to build ParameciumDB. Chado is a modular relational database schema developed at FlyBase. ParameciumDB implements the Chado schema using the PostgreSQL open source relational database man- agement system. The Chado schema includes a genetic mod- ule, and we have added a stock sub-module to the genetic module. Chado implements data classes using controlled, structured vocabularies known as ontologies. Ontologies cap- ture knowledge in a way that can be understood by humans and processed by machines, and represent an important step toward bioinformatics data integration. The GMOD standard implementation of Chado integrates the widely used Sequence (15), Gene (16) and Relationship (17) Ontologies. We have begun to develop Paramecium Anatomy Ontology, largely orthogonal to Gene Ontology (GO), for use in modeling phenotypes. Turnkey is a generic framework that autogenerates a web interface from a database schema (http://turnkey.sourceforge. net). Turnkey relies on the Perl module SQL::Translator to do this and the only input is an SQL ﬁle describing the data- base tables and relationships. Turnkey builds the interface code into an Apache/mod_perl web server. For each data table in the database, Turnkey generates a template for a web page that contains all the values in the table and shows all the relation- ships to other tables in the database. Customization of the web pages is achieved by modiﬁcation of the templates. The Generic Genome Browser (GBrowse) is a mature, widely used standard for viewing genome annotations via the web (18). GBrowse is an integral part of the web interface generated by Turnkey. Software that allows the GBrowse CGI script to communicate with a Chado database is provided by the GMOD project. PARAMECIUMDB CONTENTS ParameciumDB contains genome sequence data and annota- tions from the Paramecium genome sequencing project (EMBL/GenBank/DDBJ accession nos CT867985– CT868681) and genetic data including the Gif Paramecium stock collection and RNA interference experiments (Table 1). We have begun to model phenotypes in ParameciumDB using a schema proposed for the description of mouse pheno- types (19), involving ﬁve classes of ontology: organism, entity, attribute, value and assay. For example, the Parame- cium mutant sm19-1 (20) has a phenotype: entity cell with attribute size returning value small by a visual inspection Table 1. Data in ParameciumDB (August 2006) 39 642 85 212 45 072 4 978 982 185 29 59 57 Gene models UniProt protein matches (19 035 gene models have at least 1 match) InterPro domains (20 767 predicted proteins have at least 1 domain) Best Reciprocal Hits to Tetrahymena thermophila gene predictions Stocks Mutant alleles (35 alleles are linked to sequences) Genotypes characterized by non-Mendelian heredity RNAi experiments Phenotypes assay. The entity in this case can be found in GO. The attributes and values we have used to describe Paramecium phenotypes come from the Phenotype Attribute Ontology (PATO, http://obo.sourceforge.net/). We have begun to develop a Paramecium Anatomy Ontology, since we need more granular ‘cellular component’ and ‘biological process’ terms than presently available in GO to describe some species- or phylum-speciﬁc traits (nuclear dimorphism; cyto- logical features such as a cell cortex that is organized as several thousand repeating unit territories around the ciliary basal bodies; regulated secretion of very elaborate defensive organelles; swimming behavior in response to external stimuli mediated by ion channels and receptors, etc.). We have also begun to develop a Paramecium Assay Ontology that could perhaps be integrated into a more general ontology of assays (20). USING PARAMECIUMDB Overview Every page of ParameciumDB contains a top row of naviga- tion tabs (Home, Search, Gbrowse, Blast, Tools, Help) and a sidebar. The sidebar on the home page (and some information pages) contains internal and external links for community news, downloads and information about speciﬁc topics such as the genome sequencing project, the stock collection, Paramecium mitochondrial and ribosomal DNA. The Help page provides some explanation of how data is organized in ParameciumDB and strategies for ﬁnding data using the Search page. The Search page contains help buttons that bring up windows with additional tips and/or examples. The Search page features three boxes. The ﬁrst two allow the user to query Sequence and Genetic data (an example, showing integration of sequence and genetic data, is provided in Gene page and Allele page sections). The third box makes it possible to browse some of the tables in the database. Browsing tables using the third box on the Search page is particularly useful for genetic data. For example, each row in the Phenotype table is linked to a page for the Phenotype, showing how it has been modeled with ontology terms and providing links to all related mutant alleles and RNAi reagents. Stock and allele tables can also be browsed, although a more direct approach would be to use the genetic query box to search for a stock, or to use the sequence query box to search for an allele.