Nucleic Acids Research, 2003, Vol. 31, No. 13 3727-3728
© 2003 Oxford University Press
AHMII: Agent to Help Microbial Information Integration
Hideaki Sugawara*,1,2 and
Satoru Miyazaki1
1 Center for Information Biology and DDBJ, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
2 SOKENDAI, Department of Genetics, Hayama, Kanagawa 240-0193, Japan
*To whom correspondence should be addressed at Center for Information Biology and DDBJ, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan. Tel: +81 55 981 6895; Fax: +81 55 981 6896; Email: hsugawar{at}genes.nig.ac.jp
Received February 12, 2003; Revised and Accepted March 17, 2003
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ABSTRACT
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Reproducibility is the key to science. Therefore, the fidelity
of organisms, particularly type strains, used in molecular biology
must be authenticated before embarking on a series of experiments.
In the case of microbes the authentic strain can be obtained
from a culture collection. However, tracking down a culture
collection that possesses the strain can be an arduous task.
With this in mind we have developed a one-stop search engine
for bacteria, fungi, yeasts and cell lines that indicates which
collections carry the strain of interest. The search agent is
named Agent to Help Microbial Information Integration (AHMII)
and the URL address is
http://www.wdcm.org/AHMII/ahmii.html.
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INTRODUCTION
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One of the central dogmas of science is that experiments should
be reproducible by other researchers. To achieve this reproducibility
attention must be paid to the quality and purity of chemical
and biological agents used in experiments. To ensure purity
of microbial agents (particularly in the case of wild-type strains)
these should be obtained from type culture collections. Often
strains that bear the same scientific name have diverse biological
characteristics. Consequently, researchers should also refer
to the accession number assigned to the strain by the culture
collection in their manuscripts just as they would the accession
number of a nucleic acid sequence deposited in a public database.
According to the statistics prepared in 2002 by WFCC-MIRCEN World Data Center for Microorganisms (http://www.wdcm.org), 62 countries are home to at least 468 culture collections that collect, evaluate, maintain and distribute microbial strains and cell lines. However, an individual culture collection does not maintain the entire set of microbial strains that have a given scientific name. Unfortunately, finding a specific strain, particularly if it is obscure, may be tedious and time consuming as it may involve searching many individual collections before the strain is found. The tool we have devised, AHMII, removes this burden by simultaneously searching the web sites of multiple collections for the desired strain.
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MATERIAL AND METHOD
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AHMII was first developed in 1996 by using Perl and has been
upgraded by the use of Java. The throughput of the current AHMII
is very high due to the function of threading and Servlet technologies
of Java. The scheme of the AHMII search engine is simple and
can be viewed at the home page of the site;
http://www.wdcm.org/AHMII/ahmii.html.
The search engine accepts a query (an organism name for bacteria,
fungi and yeasts, and key word(s) for cell lines) from a web
browser and dispatches it to multiple web sites distributed
on the Internet. The engine displays results of each search
in an HTML file on a first-come first-displayed basis.
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LOOK AND FEEL
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To carry out a search, one of three search engines for bacteria,
fungi and yeast or cell lines is chosen. Each of these categories
lists a different set of sites that will be searched for the
requested strain. Figure
1 shows a screen dump of the web page
for searching the bacterial category in which up to 17 web servers
may be simultaneously queried by selecting ‘Select-All’.
Alternatively, individual or groups of servers can be queried.
A search field is provided into which the species name is typed,
however, you may also choose to query with using only a genus
name or a sub-species name.
It should be noted that you can search the taxonomy file prepared
by the International Nucleotide Sequence Databases (INSD,
http://www.ddbj.nig.ac.jp/intro-e.html).
INSD is composed of the DNA Data Bank of Japan (DDBJ), the EMBL
bank at the European Bioinformatics Institute (EBI) and GenBank
at the National Center for Biotechnology Information (NCBI).
These three data banks control the scientific name in the data
submitted by use of the taxonomy file. This ensures consistency
of the scientific names in the INSD. You can check the scientific
name that you used with a complete lineage from the taxonomy
file. In Figure
2, the results from the taxonomy file are shown
together with results from the World Directory and some of the
culture collections.
View larger version (44K):
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Figure 2. The results of a search are displayed in an HTML file, although the contents and format of output varies from site to site: the lineage from the INSD, the list of culture collections from WDCM and the result from two culture collections of JCM and DSMZ.
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CONCLUSION
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After submitting a query the results will be returned from all
the servers specified in AHMII in a few seconds. In the case
of the bacterial search the queried sites were recently expanded
from seven to 17. Nevertheless, the response time apparently
remains as short as before expansion. This suggests that the
search engine processes the query and search results in parallel.
This will allow us to expand AHMII to cover 468 culture collections
if all of them disclose their culture collection databases by
web server. Even in its current less expansive form AHMII will
assist researchers in tracking down microbiological strains
with the minimum amount of time and effort by querying multiple
strain collection databases for a strain of their choice.
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ACKNOWLEDGEMENTS
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The authors would like to express their sincere thanks to Dr
Chris Mackenzie, University of Texas Health Science Center at
Houston, for his comments. They would also like to extend their
thanks to Mr Yasumasa Shigemoto and Mr Masashi Matsuo, Fujitsu,
for their support in developing AHMII.
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