The following sections provide a quick overview of how to use the PubCrawler web service. More details are available through an online tutorial at http://pubcrawler.gen.tcd.ie/tutorial
Upon registration, users choose their own account name and password, which protects their personal results page from others. Additionally, a contact email address is required for the alerts when relevant new database entries appear. Specification of a schedule allows queries to be triggered at certain time points. In addition to the daily and weekly range, we have, upon user request, also added a monthly option. All submitted data are treated with the strictest confidence. Nevertheless, the transparency of the Internet should caution users not to provide sensitive passwords or addresses.
One of the strong points of PubCrawler is the user-friendly configuration of even complex queries through the Configurator, which provides pull-down menus for search fields and Boolean operators. For both PubMed and GenBank queries, there is no restriction on the size or number of queries that can be constructed, which allows very comprehensive searches to be carried out. An interesting feature provided by Entrez lies in the ability to carry out neighbourhood searches within their databases. This is also integrated into PubCrawler and provides notification of new entries related to one's favourite articles or sequences.
Users can access their results any time on a personal web page on the PubCrawler server, or they can have them sent by email. The latter method aids in keeping copies of results from different time points, since the web pages are overwritten every time the queries are carried out. Another option consists of a short notification that is sent to users, alerting them of new updates on their results page.
Figure 1 A sample output from a PubCrawler results page. An index at the top provides a quick overview of how many new results were retrieved for each query. Aliases can be used to provide descriptive handles for them. Numbers are reported for the total amount (more ...)