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BotDB

What is BotDB?


Literature

What is botXminer?

What is the advantage offered by botXminer in comparison to Entrez-PubMed?

How should I cite botXminer?

The reference article (Mudunuri et al., 2006) mentioned 'Search' option which I don't see on botXminer page. Why?

In batch search, for publication date, neither did I enter anything in the text box nor choose any year from the range provided. Why am I still getting results?

In batch search, what happens if I enter year(s) in the text box and also select years from the provided range?


Why is the graphical view link not displayed for my 'Group Articles' search?

Why am I not able to see the image when I click on the SVG link in the results page of 'Group Articles' query with graphical view?

Where can I get more information on browser support for SVG?


Protein Analysis

Why am I getting a blank result page when I try to run the DSSP Analysis program?


Sequence Analysis

Why am I getting a blank results page when I try to run one of the Sequence Analysis programs: Blast/PSI-Blast/ClustalW/SWAT?

Why is an error being displayed instead of the results while trying to run one of the Sequence Analysis programs: Blast/PSI-Blast/ClustalW/SWAT?

Why does it say 'no hits found' while running Blast?

Why is it that it only prints one line after running SWAT/ClustalW?

General

I am getting an error not addressed in the FAQ's or in the Help section, what should I do?



What is BotDB?
BotDB is a database designed in an effort to provide easy access to the available information on clostridial neurotoxins. We visualize it to grow into an interactive database where bot researchers can submit their findings and communicate with other members of the bot community.
It is part of a joint collaboration among USAMRIID, NCI, ABCC at SAIC-Frederick and Geo-Centers. It is sponsored by the U.S. Army Research Institute for Infectious Diseases and supported in parts by DARPA and DTRA.

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What is botXminer?
MEDLINE is a collection of more than 15 million biomedical literature articles maintained by the National Library of Medicine (NLM). These articles are distributed to licensees in an XML format.
We have loaded these citations inside Oracle XMLDB and then created a separate database for BotDB literature queries. The bot citations contain only those articles with either 'botulinum' or 'tetanus' anywhere in their text. The database is updated biweekly.
botXminer is an interface to the first successful implementation of storing complete MEDLINE XML files in an object relational schema.


What is the advantage offered by botXminer in comparison to Entrez-PubMed?
An advantage offered by botXminer is that it can generate quantitative results with certain queries that are not feasible through the Entrez-PubMed interface. The citation results can also be grouped and displayed as hyperlinked tabulated or graphic results.

How should I cite botXminer?
Please cite botXminer with its URL 'http://botdb.abcc.ncifcrf.gov/botXminer'.

The reference article (Mudunuri et al., 2006) mentioned 'Search' option which I don't see on botXminer page. Why?
The 'Search' option has been renamed to 'Simple Search'. They have the same functionalities.

In batch search, for publication date, neither did I enter anything in the text box nor choose any year from the range provided. Why am I still getting results?
When a publication date is neither entered nor chosen from the provided range, the search is done from the years of 1877 through 2009 automatically.

In batch search, what happens if I enter year(s) in the text box and also select years from the provided range?
The batch search will be done using the year(s) you have entered in the text box. The text box must be empty if you would like to use the years selected from the provided range.

Why is the graphical view link not displayed for my 'Group Articles' search?
Graphical view is not available with a 'Group Articles' query because
(i) you ran a query by selecting No for displaying graphical view (or)
(ii) the number of articles containing the search term are more than 500 (or)
(iii) there were more than 250 terms by which the articles could be grouped.


Why am I not able to see the image when I click on the SVG link in the results page of 'Group Articles' query with graphical view?
The SVG viewer plugin is required to view the SVG images. The plugin can be downloaded from
http://www.adobe.com/svg/viewer/install/main.html

Where can I get more information on browser support for SVG?
The graphical views in the literature section are created using
aiSee.
We recommend checking their FAQ section for more information on SVG images
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Why am I getting a blank result page when I try to run the DSSP Analysis program?
Your file format is not correct. To view an example of a DSSP file at the CMBI, click
here. You may download DSSP files from the Centre for Molecular and Biomolecular Informatics (CMBI) FTP site.
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Why am I getting a blank results page when I try to run one of the Sequence Analysis programs: Blast/PSI-Blast/ClustalW/SWAT?
Refreshing the page should display the results in the right format. Sometimes problems with the web page might not allow it to display the results correctly.

Why is an error being displayed instead of the results while trying to run one of the Sequence Analysis programs: Blast/PSI-Blast/ClustalW/SWAT?
Check to see that valid options are selected before running the sequence analysis. Also the parameters have to be in the specified format.

Why does it say 'no hits found' while running Blast?
This might occur when the correct program is not selected for running Blast. For nucleotide sequences valid values for the last program are blastn (nucleotide sequences against nucleotide databases) and blastx (nucleotide sequences against protein databases). The only valid program for protein sequences is blastp (protein sequences against protein databases).

Why is it that it only prints one line after running SWAT/ClustalW?
If you are trying to run ClustalW or SWAT and in the results page there is no valid information then please check to see that the sequences submitted are in FASTA format.
If the sequences are FASTA sequences then refreshing the page might help. Sometimes problems with the web page might not allow it to display the results correctly.

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I am getting an error not addressed in the FAQ's or in the Help section, what should I do?
This might be because we have forgotten to mention it in the FAQ or that you have discovered some bug in our website. Although we hope that it's not the latter, we would greatly appreciate it if you can contact us at botdb[AT]mail.nih.gov to report any of the problems you encounter with this website.
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Last updated on July 28 2009


Sponsored by U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID) in collaboration with the National Cancer Institute (NCI) and Advanced Biomedical Computing Center (ABCC).Support for this project was provided by the Defense Threat Reduction Agency Joint Science and Technology Office-Chemical Biological defense (DTRA JSTO-CBD) project 3.10043_07_RD_B and by the National Cancer Institute, National Institutes of Health, under contract No. HHSN261200800001E. a logo of the U.S. Army Medical Research Institute of Infectious Disease a logo of the National Cancer Institute, United States a logo of the Advanced Biomedical Computing Center, Advanced Technology Program
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