SerbGO is a web-based application designed to (i) facilitate researchers the task of determining which of the existing tools are appropriate for their needs and (ii) to enable a comparison between some of the available tools.
- The input needed to select those tools with the desired set of capabilities is a list of functionalities from the Standard Functionalities Set.
- The input needed to compare several tools is the list of programs to be compared.
Both actions can be performed interactively using the Query Form or the Compare Tools menu options ().
Figure 1. SerbGO workflow. (A) First page of the Query Form shows the Standard functionalities for the following sections: TOOL FOR, TYPE OF EXPERIMENT, INTERFACE and AVAILABILITY. (B) After the first validation a user selects the SUPPORTED SPECIES required and (more ...)
The Query Form menu option at the top of the page allows the user to select different functionalities and to get the most appropriate tools to provide them. This form contains the Standard Functionalities Set arranged in nine sections () and spread out over six pages.
Number of standard functionalities per section
To find the ‘right tool’ a user selects the desired functionalities by checking the appropriate fields at the specific sections (A–C). Once the choices have been made for a page it is required to validate the query by clicking on the ‘Next’ button at the bottom of the page, which allows the user to move on the following one. The next page will show the new sections and the remaining tools will appear at the top-right corner. At the last selection page a ‘Find’ button will appear instead of ‘Next’ button. This new button allows users to move on to the outputs after validation.
Nonavailable features are shown as shaded colors. They can be activated by switching the corresponding radio button. In such cases, the user could have access to this option by switching on the previous radio button.
Queries are implemented with the logical operator AND. That is, the more capabilities are selected, the less tools will be available.
During the process of navigation over the pages, and at any time, it is possible to start a new query if the user clicks on the Query Form menu option at the top of the page.
By checking any of the tools in the Compare Tools form, a list of their capabilities according to the Standard Functionalities Set can be obtained (F).
The output for the Query Form is a table with an alphabetically sorted list of the tools performing the functionalities demanded, the name of the developer and the name of the tool linked to its corresponding site (D). The programs shown can be compared by clicking the Find button at the bottom of the results page (E).
The output page for the Compare Tools form shows a table where rows contain the categorized functionalities and columns contain the GO tools names, which are linked to their respective sites (E).
To illustrate the concept of how to determine which GO tools for gene-expression analysis provide the features required by a potential user the following example can be considered.
A potential SerbGO user has a list of Drosophila melanogaster genes. He/she would like to know which tools are available to (i) do a GO enrichment analysis (ii) that allow FlyBase Ids and (iii) correction for multiple testing for hypergeometric distribution tests. In such a situation, the user should click on the Query Form menu option and selects ‘Exploration’ at the TOOLS FOR section (A). After that, move on the next page and selects ‘Drosophila melanogaster’ option (B). When validation is made, there are 19 tools available. In DATA section, the user checks ‘FlyBase ID’ identifiers. He/she has to follow until the STATISTICAL ANALYSIS section, where will select ‘Enrichment of GO Terms’, ‘Hypergeometric’ test and ‘Correction for Multiple Tests’. When the user gets the last query page, after clicking on the Find button the outputs are shown (C). The researcher can see that there are two tools implementing the capabilities desired: GENECODIS and GeneMerge (D). Now, if he/she wishes to compare the tools, it can be done by simply clicking on the new ‘Find’ button. This comparison will show a cross-tabulation of the capabilities available in GENECODIS and GeneMerge (E).