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Chapter 4: The main window in Biblio-MetReS

You are now in the main window of the application (fFigure 6). This window provides you with various options that will let you use the application in different ways. On the top-most left of the window, you find a “Back to select organism” button that will take you back to the Select Organism window, in case you want to change the organism you are studying. On the top-most right of the window you will find the “Exit” button, which will allow you to properly exit the application.

figure 6Figure 6: The main window of the application

Then, just below the “Back to select organism” button we have three columns with check boxes (Figure 7). These columns let you choose the search engines and document databases that Biblio-MetReS will use to search for documents in which the genes you select are cited, and, in those documents, identify other genes from the same organism that are also mentioned.


Figure 7: The database options

The first column has a list of general web search engines, like Yahoo or Ask. When you select any of these engines, you are telling the application to use this search engine to look for documents to analyze. We strongly recommend that you think twice before selecting a search engine from this column. The reason for this is that in most of the cases, one of the top results will be a document containing the full genome, with all its genes. Given that we are using co-occurrence of genes in scientific literature as an indication of cooperation between the genes in a given biological function, finding these documents will completely defeat the purpose of the search. The last option in this column allows you to select all other options in the column simultaneously.

The second column has a list of Literature Databases. These databases contains a large corpus of scientific papers that grows every day. We recommend that you select options from this column. If you choose only Medline, you will only analyze abstracts from Medline. If you select any of the other options you will analyze the full documents contained in the different databases. The last option in this column allows you to select all other options in the column simultaneously.

The third column contains a list of scientific journals. These have been chosen because of their importance. If you select any of them you will search documents from those journals. Again, the last option in this column allows you to select all other options in the column simultaneously.

On the right-hand side of the main widow, there is another frame that contains several elements (Figure 8). The left-most element is a list of all genes from the organism under study. You can either scroll down and up to find the genes or gene you are interested in or write the name of the gene and the list will show it to you. You need to double click on your gene of interest in order to select it for analysis in the published literature. Each gene you select will appear on the right-most list within this frame. If you double click on a gene in the list of genes you have selected, you will remove that gene from the right-most list of genes.

figure 8

Figure 8: Gene selection options

In between the two lists, in the middle of the frame, you have a text field and a list. By typing in the text field, a list of genes whose names start with the letter you type are shown in the list bellow. If you double-click any of these genes, you will select it to the righ-most list of genes to analyze. This is especially useful for organisms with very large genomes to save you scrolling time.

Alternatively, you can select one or more genes from the left-most list and click the “Add>>” button to add them to the column of genes you will analyze. In a similar way, if you select a gene on the right-most list and click on the “<<Clear” button, you will remove it from the list of genes to be analyzed.

Once all options have been appropriately set and the genes of interest have been selected, the user should press the button “Start Bibliomics Analysis” (Figure 9). This button is located immediately below the “Previous Analysis” checkbox. This button will start the analysis of all selected sources, genes and processes. The Progress Bar below this button will show you the percentage of analyzed data. Once the analysis start, no option can be modified until the analysis is finished.


Figure 9: Starting the analysis

Please keep in mind that the analysis time will increase with the number of datasources you select. Analysis can take anywhere from a few second to more than 20 minutes, depending on the number of documents that are found, on the size of these documents and on the number of genes that are selected for at the beginning of the analysis.

While the program is performing the search you can still type in the search box shown in Figure 8, as well as add or delete genes from the right-most list of genes. however, these changes will only reflect in your next, not on the one that is being performed.

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