OAT - The Ontology Annotation Tree browser tool

1. (a) (b) treesetup.cgi OATdb (c) (d) treebrowser.cgi QSdb (e) (f) (g) (h) report.cgi (j) (i) annotationReport.cgi (k) geneReport.cgi OAT - The Ontology Annotation Tree browser tool Motivation for OAT 1. Submit probe sets Technical Components The microarray technique has gained enormous popularity both amongthe 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 informationof microarray analysis is of such magni-tude that it is difficultto get an overview of the data.The need of condensing the information of an analysis istherefore evident. In order to address this challenge we havedeveloped the Ontology Annotation Tree browser tool (OAT-tool).The OAT-tool utilizes the two ontologies of Medical SubjectHeadings (MeSH) andGene Ontology (GO) to represent the information. 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 Significance of the Annotation Number of probe set annotated with this term MeSH is the National Library of Medicine's controlled vo-cabulary thesaurus. Thesauri are carefully constructed sets of terms often connected by broader-than, narrower-than, Number of probe set below Number of annotations below Link to MeSH description 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 3. Make a report The goal of the Gene OntologyTM Consort-ium is to produce a dynamic controlled vocabulary that can be applied to allorgan- At the home page of OAT (a) a link to the query form isfound.(b) The probe sets and the tree option issent to thetree setup script. The relevant information of the query is(c) extracted fromOATdb and (d) stored in QSdb.The tree browser script (e) reads data from QSdb and (f) visualisesit as a web page. For each modification of thetree visualisation(g) the tree browser script isreloaded with the new data. By markingterms and clicking on the submit button (h) the reportinformationis sent to (i) a redirection script. The report scripts, one eachfor the sorting of data in terms of genes or term strings, (j) reads datafrom QSdb and (k) generates a report web page. Work flow of the OAT-tool Link to Affymetrix DB isms.The terms are structured in three ontologies: Molecular Function, Biological Process and Cellular Componet. 1 Link to MeSH DB For each query of probe sets we extract a subsetof the ontologyand assign the annotated genes to the different terms in the ontology. The user browse the ontology in a hierarchical way from thetop-level terms and down to the more detailed ones. When a satisfyinglevel of detail is reached the user have the ability of summarizing theinformation in a report which could be used for further studies. Link to MEDLINE 2 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). 3 A more detailed description of the work is given in Interpretion of microarray expression data using ontology browsing, amaster thesis report (LiTH-IDA-Ex-02/75) from Linköpings Universitet by Anders Bresell. • Anders Bresell1, Bo Servenius2 • Department of Computer and Information Science, Linköpings Universitet, Linköping, Sweden. • Department of Molecular Sciences, AstraZeneca R&D Lund, Lund Sweden. • URL: http://bioinfo.selu.astrazeneca.net/~ext_abl/html/atb/