Supporting Genome Information Processing by MetaCommander
Yasuhiko Kitamura 1
kitamura@info.eng.osaka-cu.ac.jp
Shoji Tatsumi 1
tatsumi@info.eng.osaka-cu.ac.jp

Tetsuya Nozaki 1
noz@kdel.info.eng.osaka-cu.ac.jp
Akira Tanigami 2
atanigam@gan2.res.ncc.go.jp

1

Department of Information and Communication Engineering,
Faculty of Engineering, Osaka City University
3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558 Japan
2
Radiobiology Division, National Cancer Center Research Institute5-1-1, Tsukiji, Chuo-ku, Tokyo 104, Japan
Abstract
MetaCommander is developed as a generic tool to retrieve and integrate information from WWW
servers by interpreting a script. By using MetaCommander, we can support genome information
processing on WWW browsers in various ways.

1MetaCommanderWith the advance of genome informatics and Internet technologies, an overwhelming large amountof genome data has been stored in a number of databases which are distributed over the world, andnowadays it is accessible through the WWW system. As the number and size of genome databases increase, we have more demands to retrieve and collect a large amount of data through WWW browsers,
but to meet the demands we have tiresome operations such as repeating similar operations many times
and inputting various combinations of parameters.
We developed MetaCommander[1, 2] as a remedy for this problem. By preparing a script, MetaCommander can automates many of tiresome operations on the WWW. Figure 1 show the overview ofMetaCommander system. A user gives commands to MetaCommander by writing a MetaCommander(MC) script. MetaCommnader interprets the script and executes the commands. It gets access toWWW servers through the Internet by talking HTTP (Hyper Text Transfer Protocol) and is also able
to read and write local data files. It rearranges retrieved data and outputs the result as an HTMLfile, so the user can read it by using a WWW browser.
MetaCommander is a public domain software which is written in Java language, so it runs on mostof platforms such as Macintosh, Windows95, and UNIX. It is available by down-loading the code from
our MetaCommander homepage (http://www.kdel.info.eng.osaka-cu.ac.jp/MetaCommander/).

WWW
Browser

HTMLText

MCScript

Data

MetaCommanderInternetFigure 1: Overview of MetaCommander.

2

MetaCommander Scripts
1: set( url, "http://www.genome.ad.jp/htbin/www_bfind_sub" ) /* URL of Genome Net */2: set( dbkey, "genbank" ) /* database name */3: set( mode, "bfind" ) /* data retrieve method */4: set( max_hit, 10 ) /* max number of data hits */5: set( keywords, "hiv human mRNA") /* search keywords */6: getURL( $url, "dbkey"=$dbkey,"keywords"=$keywords, "mode"=$mode,"max_hit"=$max_hit) { /* get access to genbank with parameters *7:
getAnchor($max_hit) { /* get each of hyperlinks from index page */8:
print /* print the hyperlink */9:tag("BR") /* break the line */10:
getURL($_) { /* follow the hyperlink and retrieve the page */11:
cutString("REFERENCE","FEATURES") {/* cut data between REFERENCE and FEATURES */12:tag("PRE") { /* print the data as a plain text */13:
print }}}}}

Figure 2: An example of script.
Figure 2 shows an example of MetaCommander script. This script is for collecting reference dataconcerning keywords “hiv human mRNA” from GenBank and integrating them as an HTML text. We
have made a number of MetaCommander scripts for supporting genome data processing as follows,
and some of them are available through the script library of our MetaCommander homepage.
• Automating parameter inputting for BLAST1 , GDB Insert Amplimer2 , Grail3, and Hexon4 .
• Integrating reference data from GenBank5 and abstracts from Medline6 .
• Integrating Grail3 and Hexon4 for better gene prediction.
• Extracting updated data from Genbank-upd7 into a personalized database.

Acknowledgements
The authors would like thank Toru Ishida, Teruhisa Miura, Hideyuki Nakanishi, Minoru Kanehisa,Shinsei Minoshima, and Katsuhiko Murakami for their helpful comments. This work was supported inpart by a Grant-in-Aid for Scientific Research on Priority Areas “Genome Science” from The Ministryof Education, Science, Sports and Culture of Japan.

References[1] Y. Kitamura, et al., “MetaViewer and MetaCommander: Applying WWW Tools to Genome
Informatics,” Proceedings of the Seventh Workshop on Genome Informatics, 137-146, 1996.
[2] Y. Kitamura, et al., “A Script-based WWW Information Integration Support System and Its
Application to Genome Databases,” Proceedings of IEICE Symposium on Software Agents andTheir Applications, 87-92, 1997.
1

http://www.genome.ad.jp/SIT/BLAST.html
http://gdbwww.gdb.org/gdb-bin/genera/restrict/genera/hgd/Amplimer?!action=insertform3
http://avalon.epm.ornl.gov/Grail-bin/EmptyGrailForm
4
http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html
5
http://www.genome.ad.jp/htbin/www bfind?genbank-today
6
http://www.genome.ad.jp/dbget-bin/www bfind?medline
7
http://www.genome.ad.jp/htbin/www bfind?genbank-upd
2