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PathBinderH

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Using PathBinderH: a Sample Query One Step at a Time

The following sequence of steps will result in sentences from PubMed which contain the terms "embryo" and "development," and which are in abstracts mentioning the name of any plant taxon.

1) Access the PathBinderH Web site by using a Web browser to go to site www.plantgenomics.iastate.edu/PathBinderH. You should see a screen as show in Figure 1.



Figure 1

2) The two major operations that must be done are to specify the taxonomic filter and to specify the query terms. Start setting the taxonomy filter by clicking on the link Set species filter. The result will be a screen like shown in Figure 2.



Figure 2

3) Click the BROWSE link. This should bring up a page like shown in Figure 3.



Figure 3

4) Step a. is optional; step b. is required:

a. Click directly on the term Chlorophyta (not the funnel icon next to it). This brings up a screen showing more details of the taxonomy below chlorophyta. However, since we are interested in all green plants, not just chlorophyta, click the back button on your Web browser to return to the screen just shown in step 3.

b. Click on the funnel icon ("") in the line Viridiplantae (Green plants) . This should bring up a screen like shown in Figure4.



Figure 4

Note the small but significant difference between this screen shot and the preceding one:

now shows that you have identified viridiplantae as the filtering taxon (multiple taxa can be selected, but there is no point in doing so in this case because all plant taxa are covered by viridiplantae).

5) PathBinderH must now be asked to apply the identified taxon to filter abstracts in PubMed. To do so, simply click the

button. As the screen states below that button, it may be necessary to wait in some cases, though not in this one. After clicking this button, a screen will be displayed that may look like the next screen shot shown in Figure 5. If it does not look like that, try scrolling it all the way down, because the bottom section of the page is what is shown in Figure 5.



Figure 5

6) This displays the current filter list and also provides a button for clearing the filter list to start over, labeled "Clear filter list." In the same box labeled Keyword search you will find different options for selecting your first query term. These currently allow you to get a listing of possible query terms that begin with, or contain somewhere (not necessarily at the beginning), the string you will type in during the next step.

7) In the "Keyword Search" box you can type a term in the typein box labeled "Search the list for". For illustration, let us do it that way. Type embryo in the typein box labeled "Search the list for." To get all "E" terms beginning with "embryo," leave the small circular button labeled "Starting with" activated, as it is by default. You can also click on the button next to it labeled "Containing." This will list all terms that contain "embryo" in them. For this exercise, click the small circular button labeled "Starting with ." Then click the rectangular grey button labeled "Search." This results in the page as shown in Figure 6.



Figure 6

Alternative way: You can also reach this page through "Browse by index" by clicking on E (for "embryo") in the alphabetical index.
Notice that the result screen states there are 24 pages of terms starting with "E." The first of these pages is shown. You can go to the next page by clicking the "Next>>" link, the last of the 24 pages by clicking the "Last>>" lk, or to pages 2, 3, 4, or 5 by clicking one of those numbers. You can also type a page number in the typein box labeled "Jump to page" to go to that page number. Finally, you can type a term in the keyword search as mentioned above.

8) Click the "embryo" entry in the list shown on the screen. This will result in the screen shown in Figure 7.



Figure 7

9) Notice that this screen contains the line "Pages (91): [1] [2] [3] [4] [5] [Next»] [Last»|]" which states that there are no less than 91 pages of terms that occur in the same sentence as the term "embryo." To avoid hunting through these pages for the desired 2nd query term, type this term, "development", in the typein box labeled "Search the list for," and then click the grey "Search" button. This results in the screen shown in Figure 8.



Figure 8

10) Click on the term "development" in the list of three terms shown. This results in the screen shown in Figure 9.



Figure 9

11) The screen you now see lists sentences containing the terms "embryo" and "development" which are in PubMed abstracts containing the taxonomic term "plant," "viridiplantae," or some other synonym, or which contain the name or synonym of any subtaxon of viridiplantae, such as the name of a particular species of plant or a plant family. Each sentence is shown along with the year of publication of the abstract and the PubMed ID (PMID) of the PubMed abstract containing it. Note that the second sentence in the table appears to be about zebrafish. Nevertheless, somewhere in the abstract containing that sentence, is a plant term.

12) To see the complete PubMed entry containing a sentence listed in the table by PathBinderH, simply click on its PMID. This will take your browser to the PubMed Web site run by the US National Library of Medicine and bring up the PubMed entry whose PMID was clicked. For example, if you clicked the PMID of the first sentence, you would see the screen as shown in Figure 10.



Figure 10

13) The screen shown overlays the PathBinderH screen that you just clicked. You can bring it to the foreground, or destroy the PubMed screen by clicking the "X" button in its top right corner to see the PathBinderH sentence display again.

14) You can start over with your next query by clicking on the "home" link in the top menu bar of the PathBinderH screen.

Happy Browsing,
The PathBinderH team.