EntrezAJAX: direct web browser access to the Entrez Programming Utilities

Web applications for biology and medicine often need to integrate data from external data sources. Entrez, provided by the National Center for Biotechnology Information (NCBI) provides a searchable interface to important biological databases including PubMed, GenBank and GenPept [1]. Application developers may perform searches of Entrez directly by accessing the publically available Entrez Programming Utilities (Entrez eUtils) interface [2]. However, until now there has been no API available which allows web application ('webapp') developers to access Entrez eUtils directly from the browser. Developers are limited to accessing Entrez eUtils through software code running on the web "backend". This approach is less than ideal as it requires the call to Entrez eUtils to have been completed before each web page can be rendered. This means that that pages load slowly and may become blocked if the Entrez eUtils interface is unavailable for some reason (e.g. downtime, network congestion). It also means bandwidth required to provide the service may be increased due to the overhead of fetching the page from the backend and returning it to the user. This synchronous approach may also result in larger pages being generated, which also slow down page loading (Figure 1).The use of "Asynchronous JavaScript and XML" (AJAX) has transformed the usability and power of webapps over the past 5 years. These technologies have been instrumental in the development of rich web applications. Many popular web services, including Google, Twitter and Flickr permit direct programmatic access to their databases and services by offering AJAX APIs [2-4]. The availability of such APIs has given the ability to integrate multiple data sources within a web application without the need for backend server code. The ease-of-use of such approaches has driven the adoption of 'mash-up' applications which make it simple to integrate datasets from a diversity of sources. A typical example is the ability to lin