Example of use of XplorMed - Page 1

Example of use of XplorMed

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Through these pages we are going to show the application of XplorMed with an example that illustrates how you can progressively focuse on more and more specific subjects.

Several features of the analysis process are shown at different stages, including the filtering of information, computation of keywords, analysis of the relations for particular words and sentence extraction.

Assume that a researcher is interested in papers dealing with the relation between heparin and the Alzheimer disease. One possibility is to search MEDLINE for papers containing the words `alzheimer' and `heparin'.

There are two ways in starting the analysis of your own query in XplorMed. The simplest is to type it directly in the default entry page:

Figure 1a. Direct entry for XplorMed
Figure 1. Direct entry page for XplorMed. Notice that an identifier ('example') was given to the session. Very large queries are truncated to 500 abstracts.

... and click on the NEXT ACTION buttom.

The second way starting is to perform the query at NCBI and to store it in your own disk. The name of that file will be next provided to XplorMed. To generate the query file you have to go to NCBI's Entrez server and make the query. Then choose 'MEDLINE' format in the 'Display' menu and 'File' in the 'Send to' menu. Next click on 'Send to':

Figure 1a. Entry page for the NCBI's Entrez server
Figure 2. Entry page for the NCBI's Entrez server. Notice the link to "Limits" under the query window. You may use it in order to limit our search and produce a number of abstracts that can be handled by the server.

The resulting file is basically a flat file text that contains different information about each selected paper, such as title, authors, journal, abstract (if any), MeSH terms, etc. If you are a Mac user, make sure that it is saved as DOS text.

Now, go to XplorMed and choose the 'green entry'. You can provide the name of the just saved file to XplorMed writing down it in the box or by clicking in the 'Browse...' buttom (Figure 3a):

Figure 3a. Starting with your own set of abstracts.
Figure 3a. Starting with your own set of abstracts. As you will see the current size limitation for the query is 500 abstracts. Nevertheless, bigger queries are accepted at this stage, since there can be suitable filtered by the user in the next step.

Now, you can carry on with the first step by hitting the "Sort abstracts according to MeSH category" button. MeSH stands for Medical Subject Headings. Each MEDLINE entry is indexed with a set of terms (MeSH terms compiled at the National Library of Medicine) grouped in eight main categories. To know more about the MeSH terms, you can visit the MeSH page at the National Library of Medicine.

Finally, by choosing the 'pink option' it is also possible to analyse the set of literature references linked to any entry of the following databases: SwissProt, SpTrembl, OMIM and SMART (Figure 3b).

Figure 3b. Starting from an entry of a database.
Figure 3b. Analysis of the literature concerning SAM domains.

For example, if you are interested in the SAM domains, you should select 'SMART' in the box, and type 'SAM' in the window. An XplorMed session will start over the papers that are linked to the SAM entry in the SMART database (see Figure 3c).

Figure 3c. Smart literature concerning SAM domains.