The Stanford Microarray Database: implementation of new analysis tools and open source release of software

The Stanford Microarray Database (SMD; ) is a research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. The primary mission of SMD is to be a research tool that supports researchers from the point of data generation to data publication and dissemination, but it also provides unrestricted access to analysis tools and public data from 300 publications. In addition to supporting ongoing research, SMD makes its source code fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD. In this article, we describe several data analysis tools implemented in SMD and we discuss features of our software release

OntologyWidget – a reusable, embeddable widget for easily locating ontology terms

Abstract Background Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. Results We have produced a tool, OntologyWidget, which allows users to rapidly search for and browse ontology terms. OntologyWidget can easily be embedded in other web-based applications. OntologyWidget is written using AJAX (Asynchronous JavaScript and XML) and has two related elements. The first is a dynamic auto-complete ontology search feature. As a user enters characters into the search box, the appropriate ontology is queried remotely for terms that match the typed-in text, and the query results populate a drop-down list with all potential matches. Upon selection of a term from the list, the user can locate this term within a generic and dynamic ontology browser, which comprises the second element of the tool. The ontology browser shows the paths from a selected term to the root as well as parent/child tree hierarchies. We have implemented web services at the Stanford Microarray Database (SMD), which provide the OntologyWidget with access to over 40 ontologies from the Open Biological Ontology (OBO) website 1. Each ontology is updated weekly. Adopters of the OntologyWidget can either use SMD's web services, or elect to rely on their own. Deploying the OntologyWidget can be accomplished in three simple steps: (1) install Apache Tomcat 2 on one's web server, (2) download and install the OntologyWidget servlet stub that provides access to the SMD ontology web services, and (3) create an html (HyperText Markup Language) file that refers to the OntologyWidget using a simple, well-defined format. Conclusion We have developed OntologyWidget, an easy-to-use ontology search and display tool that can be used on any web page by creating a simple html description. OntologyWidget provides a rapid auto-complete search function paired with an interactive tree display. We have developed a web service layer that communicates between the web page interface and a database of ontology terms. We currently store 40 of the ontologies from the OBO website 1, as well as a several others. These ontologies are automatically updated on a weekly basis. OntologyWidget can be used in any web-based application to take advantage of the ontologies we provide via web services or any other ontology that is provided elsewhere in the correct format. The full source code for the JavaScript and description of the OntologyWidget is available from http://smd.stanford.edu/ontologyWidget/.</p

OntologyWidget – a reusable, embeddable widget for easily locating ontology terms-2

<p><b>Copyright information:</b></p><p>Taken from "OntologyWidget – a reusable, embeddable widget for easily locating ontology terms"</p><p>http://www.biomedcentral.com/1471-2105/8/338</p><p>BMC Bioinformatics 2007;8():338-338.</p><p>Published online 13 Sep 2007</p><p>PMCID:PMC2080642.</p><p></p>aths from the selected term ("cellular metabolic process") to the root of the ontology ("Biological Process") are shown. Instances of the search term are highlighted as a visual aid. Selection of a more or less specific term from the ontology browser will populate the text box with that term

OntologyWidget – a reusable, embeddable widget for easily locating ontology terms-6

<p><b>Copyright information:</b></p><p>Taken from "OntologyWidget – a reusable, embeddable widget for easily locating ontology terms"</p><p>http://www.biomedcentral.com/1471-2105/8/338</p><p>BMC Bioinformatics 2007;8():338-338.</p><p>Published online 13 Sep 2007</p><p>PMCID:PMC2080642.</p><p></p>aths from the selected term ("cellular metabolic process") to the root of the ontology ("Biological Process") are shown. Instances of the search term are highlighted as a visual aid. Selection of a more or less specific term from the ontology browser will populate the text box with that term

OntologyWidget – a reusable, embeddable widget for easily locating ontology terms-4

<p><b>Copyright information:</b></p><p>Taken from "OntologyWidget – a reusable, embeddable widget for easily locating ontology terms"</p><p>http://www.biomedcentral.com/1471-2105/8/338</p><p>BMC Bioinformatics 2007;8():338-338.</p><p>Published online 13 Sep 2007</p><p>PMCID:PMC2080642.</p><p></p>ontains both an autocomplete box, into which text can be typed, and an ontology browser, which can either be browsed from the top level, or can be opened at a selected node, based on the entered term. Each instance of the widget is connected to a different ontology