Beauheim Catherine C, Wymore Farrell, Nitzberg Michael, Zachariah Zachariah K, Jin Heng, Skene J H Pate, Ball Catherine A, Sherlock Gavin
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA.
BMC Bioinformatics. 2007 Sep 13;8:338. doi: 10.1186/1471-2105-8-338.
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.
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.
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/.
生物医学本体正被广泛用于以计算机可访问、一致且定义明确的方式注释生物数据。然而，由于其规模和复杂性，无论是专家还是非专家，使用本体中的适当术语注释数据通常都具有挑战性，因为几乎没有工具能让用户快速找到相关本体术语来轻松填充网页表单。
我们开发了一个工具OntologyWidget，它允许用户快速搜索和浏览本体术语。OntologyWidget可以轻松嵌入到其他基于网络的应用程序中。OntologyWidget是使用AJAX（异步JavaScript和XML）编写的，有两个相关元素。第一个是动态自动完成本体搜索功能。当用户在搜索框中输入字符时，会远程查询适当的本体以查找与输入文本匹配的术语，查询结果会在下拉列表中显示所有潜在匹配项。从列表中选择一个术语后，用户可以在一个通用的动态本体浏览器中定位该术语，这是该工具的第二个元素。本体浏览器显示从所选术语到根节点的路径以及父/子树层次结构。我们在斯坦福微阵列数据库（SMD）中实现了网络服务，该服务为OntologyWidget提供对来自开放生物本体（OBO）网站1的40多个本体的访问。每个本体每周更新一次。OntologyWidget的采用者可以使用SMD的网络服务，也可以选择依靠自己的服务。部署OntologyWidget可以通过三个简单步骤完成：（1）在自己的网络服务器上安装Apache Tomcat 2；（2）下载并安装提供对SMD本体网络服务访问的OntologyWidget servlet存根；（3）使用简单、定义明确的格式创建一个引用OntologyWidget的html（超文本标记语言）文件。
我们开发了OntologyWidget，这是一个易于使用的本体搜索和显示工具，通过创建一个简单的html描述即可在任何网页上使用。OntologyWidget提供了快速自动完成搜索功能以及交互式树状显示。我们开发了一个网络服务层，用于在网页界面和本体术语数据库之间进行通信。我们目前存储了来自OBO网站1的40个本体以及其他一些本体。这些本体每周自动更新。OntologyWidget可用于任何基于网络的应用程序，以利用我们通过网络服务提供的本体或其他以正确格式在其他地方提供的任何本体。OntologyWidget的JavaScript完整源代码和描述可从http://smd.stanford.edu/ontologyWidget/获取。
