botXminer Examples
The three different options of botXminer are demonstrated below.(I) Search Example
(II) Batch Search Example
(III)Group Articles (Advanced Search) Example
(I) Search Example
1) Click on Search of botXminer portal page.2) Choose your search fields which could be one or a combination of the following fields: PMID, author, title, abstract, MeSH, journal, volume or publication date.
3) For the following example, enter "kinetics AND botulinum toxin" in Abstract contains text box.
4) Select Publication Date range from "2005" to "2009". Note that if you choose not to select publication range, the search will be done from the years 1877 through 2009.
5) Click Submit.
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(II)Batch Search Examples
There are two types of batch searches: Batch Search (basic mode) and Batch Search (matrix mode).Example 1: Batch Search (basic mode)
1) Click on Batch Search.
2) In the Search term text area, enter six search terms in different lines:
"kinetics"
"botulinum toxin"
"kinetics AND botulinum toxin"
"kinetics OR botulinum toxin"
"botulinum"
and "toxin".
Note: Each line is treated as a different query and there is no limit in the number of characters per query line or the number of terms you enter.
3) Select Publication Date range from "2007" to "2009". Note that if you choose not to select publication range, the search will be done from the years 1877 through 2009.
4) Click Submit.
5) Clicking on the number "37" under "Citations" on the result table takes us to all the citations which had the search term in one of the search fields.
6) Clicking on the number "154" under "Authors" on the result table takes us to the list of citations grouped by authors.
7) Clicking on the number "31" under "Journals" on the result table takes us to the list of citations grouped by journals.
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Example 2: Batch Search (matrix mode)
1) Click on Batch Search (matrix mode) on the interface of Batch Search (basic mode).
2) In the First term(s) text area, enter ten search terms in different lines:
"olfactory"
"optic"
"oculomotor"
"trochlear"
"trigeminal"
"abducens"
"facial"
"vestibulocochlear"
"glossopharyngeal"
"vagus"
"accessory"
"hypoglossal"
Note: This list can be obtained from Sample Files under Cranial Nerve List.
3) In the Second term(s) text area, enter four search terms in different lines:
"botulinum neurotoxin"
"BoNT"
"bot"
"botox"
4) For this search, the publication date is not selected which means the search will be done from 1877 through 2009.
5) Click Submit.
(III)Group Articles (Advanced Search) Example
Note that the following example is for Advanced Search. However, the regular Group Articles functions very similar to the Advanced Search feature.1) Click on Advanced search on Group Articles page or go to http://botdb.abcc.ncifcrf.gov/botXminer/groupArticlesAdv.jsp.
2) A search term can be as simple as "botulinum" or as complex as "near ((snare, interact%), 5".
For this example, enter "near ((snare, interact%), 5)" in Search term box.
Note: This search was designed to locate the search words 'snare' and 'interact%' (or interacts, interacting, etc.) that are separated by no more than five words.
3) Select "Abstract" for Search Field.
4) Select "AND" for Connect Term.
5) Check on "chemical" for Group by.
6) Select "Yes" for Graphical View.
7) Click Submit.
Note: This search was conducted to find potential interactions between the SNARE proteins (three of which are substrates for the proteolytic botulinum neurotoxins) and other proteins. The substrates of interest [syntaxin-1A, synaptobrevin (VAMP) and SNAP-25] are intimately involved in the evoked release of neurotransmitter from synaptic vesicles. The retrieved citations for SNARE protein-protein interactions may, thus, help to predict what other cellular functions might be affected in addition to the toxin-induced blockade of neurotransmission.
8) The result page displays a tabulated listing of 83 Group (chemical) terms that appeared in 19 MEDLINE XML files. The graphical outputs are available in three formats: SVG, PNG, and HTML. Results can be sorted by clicking on the sort icon located near 'Groupby Term' or 'Number of Articles'. Values for the 'Number of Articles' for a given term are hyperlinked to a second table that lists citations associated with the selected term.
9) To sort by the "Number of articles", click on the Sort (
) icon twice. Similarly, sorting may be done using "Groupby Term". 
10) Clicking on the highlighted value of '19' produces a list of all the retrieved citations.
The PMID numbers are hyperlinked to their corresponding MEDLINE pages, which are presented in a modified format, while article titles in this table are hyperlinked to their PubMed abstracts.
11) To visualize these data is in a network graph format, click on SVG, PNG, or HTML hyperlinks.
Note: In this example, there are 83 Group terms (chemical names) and 849 connections (circles) between these terms. All pairs of chemical terms are connected by color-coded lines and circles that show the relative 'Number of Articles' for two co-occurring chemical terms. Each rectangle is hyperlinked to a list of citations containing the Group (chemical) term, whereas each circle is hyperlinked to a list of citations that contain the pair of terms associated with that connection.
12) Focus on and recognize patterns for the most frequent co-occurring terms by zooming in (accessed through the drop-down menu with the right-hand mouse button) that is used with SVG. It is recommended that SVG be viewed in Microsoft Internet Explorer for zooming capabilities.
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Please feel free to contact us for any comments/suggestions/questions at botdb[AT]mail.nih.gov.