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OAT - The Ontology Annotation Tree browser tool Motivation for OAT 1. Submit probe sets The microarray technique has gained enormous popularity both among the major pharmaceutical companies and academic institutions. Even though all the benefits of the technique, we have to face the problems of that the amount of resulting information of microarray analysis is of such magnitude that it is difficult to get an overview of the data. The need of condensing the information of an analysis is therefore evident. In order to address this challenge we have developed the Ontology Annotation Tree browser tool (OAT-tool). The OAT-tool utilizes the two ontologies of Medical Subject Headings (MeSH) and Gene Ontology (GO) to represent the information. Technical Components The OAT-tool runs from a web server. It is written in Perl and CGI. All data are stored in the OAT database (OATdb) and for each query a Query Specific database (QSdb) is generated. The information flow of OAT’s three main scripts is outlined below to the right. 2. Browse the Ontology The information flow of OAT Checkbox for terms which are to be included in the report (b) Significance of the Annotation The source of information The gene information is collected from AffymeterixTM-files. Ontology information is collected from MeSH and GO. Annotations is collected from EMBL/MEDLINE and Gene Ontology Annotation Campaign (GOAC). OATdb treesetup.cgi (c) (d) (e) QSdb Number of probe set annotated with this term MeSH is the National Library of Medicine's controlled vocabulary thesaurus. Thesauri are carefully constructed sets of terms often connected by broader-than, narrower-than, and related links. These links show the relationships between related terms and provide a hierarchical structure that permits searching at various levels of specificity from narrower to broader. There are more than 19,000 terms in MeSH The goal of the Gene OntologyTM Consortium is to produce a dynamic controlled vocabulary that can be applied to all organisms. The terms are structured in three ontologies: Molecular Function, Biological Process and Cellular Componet. (a) (g) treebrowser.cgi (f) Number of probe set below Number of annotations below Link to MeSH description 3. Make a report Work flow of the OAT-tool 1 For each query of probe sets we extract a subset of the ontology and assign the annotated genes to the different terms in the ontology. 2 3 The user browse the ontology in a hierarchical way from the top-level terms and down to the more detailed ones. When a satisfying level of detail is reached the user have the ability of summarizing the information in a report which could be used for further studies. Anders Bresell1, Bo Servenius2 1. Department of Computer and Information Science, Linköpings Universitet, Linköping, Sweden. 2. Department of Molecular Sciences, AstraZeneca R&D Lund, Lund Sweden. URL: http://bioinfo.selu.astrazeneca.net/~ext_abl/html/atb/ Link to Affymetrix DB Link to MeSH DB Link to MEDLINE report.cgi (h) (j) (i) annotationReport.cgi (k) geneReport.cgi At the home page of OAT (a) a link to the query form is found. (b) The probe sets and the tree option is sent to the tree setup script. The relevant information of the query is (c) extracted from OATdb and (d) stored in QSdb. The tree browser script (e) reads data from QSdb and (f) visualises it as a web page. For each modification of the tree visualisation (g) the tree browser script is reloaded with the new data. By marking terms and clicking on the submit button (h) the report information is sent to (i) a redirection script. The report scripts, one each for the sorting of data in terms of genes or term strings, (j) reads data from QSdb and (k) generates a report web page. A more detailed description of the work is given in Interpretion of microarray expression data using ontology browsing, a master thesis report (LiTH-IDA-Ex-02/75) from Linköpings Universitet by Anders Bresell.