dictybase ( ) is the model organism database ( mod ) for the social amoeba dictyostelium discoideum . like other mods such as flybase ( 1 ) , wormbase ( 2,3 ) , mouse genome informatics ( 4 ) and the saccharomyces genome database ( sgd ) ( 5 ) , dictybase ( 6 ) uses the organism 's genome sequence to organize the biological knowledge resulting from experimental studies using dictyostelium . an amoeba during most of its life , starvation induces a very interesting developmental program during which individual cells stream together by chemotaxis to form a multicellular tissue ( 7 ) . a morphogenetic process involving cell migration and cellular morphogenesis transforms a simple mound of cells into a slug or pseudoplasmodium establishing a relatively simple developmental pattern . this structure then develops into a fruiting body consisting of multiple cell types including spores and terminally differentiated stalk cells . these features together with the efficient genetic manipulation by gene targeting and replacement as well as insertional mutagenesis and suppressor screens have made dictyostelium a popular experimental system . research using dictyostelium has been critical in understanding fundamental processes such as cell migration ( 8) , cell signaling ( 9,10 ) , phagocytosis and morphogenesis . recently dictyostelium has also been used to help establish the mechanisms of action of medically important drugs such as cisplatin ( 1114 ) , used to treat various cancers , and lithium and valproic acid ( 15 ) , used to treat depressive disorders . the recently completed dictyostelium genome sequence is housed at dictybase and has been integrated with other experimental data to provide investigators with a rich new resource that will facilitate future studies using dictyostelium experimentally and for comparative genomics . in may 2005 the sequence of the complete genome of dictyostelium was reported ( 16 ) . the a + t rich genome ( 77.6% ) consists of 34 million bases of dna sequence that are predicted to encode 13  573 genes  a number of genes comparable with drosophila . dictybase houses and maintains the genome sequence produced by the international sequencing consortium . as the first free living protozoan to be completely sequenced , the predicted proteome supports the hypothesis that dictyostelium represents an early branch in the eukaryotic tree of life that diverged after the split between animals , plants and fungi , with dictyostelium and other amoebae more closely related to animals . many dictyostelium proteins are more similar to human orthologs than are those of saccharomyces cerevisiae . the abundance of short sequence repeats produces unusual runs of amino acids , such as polyasparagine and polyglutamine tracts of 20 residues or more . the genome also contains a surprisingly large number of polyketide synthases , which may produce a previously unanticipated large complement of natural products . consistent with this apparently large secondary metabolism , the genome contains many abc transporters that may be involved in export of these natural products . also encoded are a large number of proteins containing multiple egf repeats that have been postulated to play roles in adhesion or cell recognition . these fascinating genomic features together with the unique biology of dictyostelium and the rich body of dictyostelium literature ( nearly 8000 publications ) provide a valuable opportunity to annotate many of the genes with functional information that will widen the spectrum of characterized proteins in public databases . this emphasizes the need for a well - curated database for dictyostelium  a need .that dictybase strives to fulfill . as the mod for d.discoideum , dictybase provides highly curated information that facilitates research by providing a searchable , structured repository of dictyostelium experimental results . in addition to the complete genome sequence , groups performing high - throughput experiments such as large - scale mutagenesis and microarray - based gene expression studies are depositing their data in dictybase for integration and distribution to the research community . dictybase uses the genomic dna sequence as a scaffold on which to organize and display the biological knowledge and experimental evidence derived from dictyostelium research . dictybase is the most comprehensive source of information regarding dictyostelium , and the database presents the highest quality annotations of dictyostelium genes . nearly all of the data in dictybase is available for bulk download through our download center ( ) . a gene page is available for each gene that has been shown or predicted to exist in the genome . the gene page collects and organizes all of the available information related to that gene into several sections . a general information section provides the official gene name together with any other names that have been used to refer to that gene . this assures that a search of the database will allow retrieval of a gene using any name that has been used to refer to that gene . scientific curators verify published and proposed gene names to encourage use of the dictyostelium nomenclature guidelines ( ) and to ensure that names are not duplicated . also in this section , gene product names and a brief description of the gene product are presented , as is the unique dictybaseid . next , the chromosomal coordinates section presents a graphical view of the gene and associated sequences such as expressed sequence tags ( ests ) , cdnas and other genbank entries . an associated sequences section provides links to sequences corresponding to each of the sequence features known for that gene , including gene predictions as well as ests , cdnas and genomic sequences submitted by individual researchers to other public databases . the protein information section contains the size , molecular weight and protein domains of the predicted protein . functional information is presented in sections for gene ontology ( go ) annotations and phenotypes whenever this information is available . phenotypic data is represented using a restricted vocabulary that describes the consequences of mutations reported for that gene . the gene ontology section lists terms from each of the function , process and component ontologies associated with the gene ( 17,18 ) . following links in each of these sections display additional details for these annotations . clicking on a go term or the expression section leads to developmental profiles for the gene that have been generated by large - scale microarray based studies performed at the baylor college of medicine and the university of california , san diego . the links section on the gene page provides links to genbank , uniprot , genedb at the sanger institute and , where appropriate , to signaling pathways at the signal transduction knowledge environment at science ( 19,20 ) . this section also links to researchers in our colleague database who are investigating that gene or gene product . a literature section lists the most recent publications referring to the gene and a link to a literature guide that contains a complete listing of papers relevant to that gene . as of the fall of 2005 , > 500 gene pages had a summary paragraph written by a dictybase curator that contains the current knowledge regarding that gene . dictybase curators are in the process of manually reviewing all of the automated gene predictions in light of available data such as ests and cdnas . dictybase curators have reviewed nearly 2500 genes , which corresponds to 20% of the total number of genes . dictybase also serves as a clearinghouse for resource materials for students , researchers and educators using dictyostelium in a wide range of classroom and laboratory settings . we maintain archives of the dictynews , a weekly electronic newsletter that presents abstracts of papers available upon acceptance for publication , as well as a growing collection of protocols for working with dictyostelium . this resource provides access to dictyostelium strains , including natural isolates , targeted mutants and gfp labeled strains . the collection also contains plasmids used to manipulate gene expression or create targeted gene disruptions . currently the dsc has > 700 strains and > 150 plasmids all available to researchers . a shopping cart system allows stock center users to add strains and proceed to a checkout system familiar to any user of online ordering systems . for users who are also registered as colleagues in the dictybase colleagues database , addresses for delivery and contact information dictybase holds all of the stock center data and provides the informatics support for the dsc . dictybase was initially established as a clone of the software developed and generously provided by sgd . these include the gbrowse tool for chromosome and map displays and , most recently , the chado database schema for storing sequence and sequence feature information . this entailed porting of the chado schema to oracle since both dictybase and sgd are implemented in oracle . dictybase has developed new code that separates communication with the database from code that generates the html interfaces . this object layer facilitated adoption of the chado schema without significant impact on the presentation interface and enables good software practices such as unit testing . dictybase strives to present a comprehensive , reliable , carefully curated dataset that integrates sequences , functional annotation , phenotypes , expression data and the research literature , while retaining the flexibility to integrate new data types as they become available . our goal is to assure that the information in dictybase is accessible in an effective and intuitive interface useful for biologists , while also maximizing its utility for the bioinformatics community to use computationally . our operating principles are to respond to users ' needs , to capitalize on the vast efforts of the dictyostelium research community , and to provide an important link in the network of mods . as additional amoebae genome sequences become available dictybase hopes to implement , and where necessary , develop interfaces and tools that facilitate comparative genomics of this diverse group of organisms . this sample gene page shows the types of information that are displayed on a dictybase gene page .