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Java Web Start based GO browser

ungsik ungsik at kribb.re.kr
Tue May 21 02:10:40 PDT 2002


I have written a Java web start based GO browser.
Pleas try the program and send me bug reports, suggestions, enhancement
requests ... .

You can try the program at the following address.
    http://neon.kribb.re.kr/javaws/index.html.

You need to install the Sun JRE 1.4.0 or later.
JRE can be downloaded from SUN,
    http://java.sun.com/j2se/1.4/download.html.

Searching:
   Term: GO term name/definition/synonym search
   GO id : GO id search
   Gene Product : gene product symbol and full name search
   Gene Product Accesskey search : DB access key such as SWISS-PROT
        access key O43623 or INTERPRO IPR000335
Expression search :
   For Term and Gene Product search, Java style regular
        expression is used.
   For GO id search : For single GO id, selected GO id is highlighted
       on the Full Gene Ontology Tree. For multiple GO id search, new
       tree is built.
List search : only exact match is used.
   GO id can be specified as GO:0003674 or just 3674.
   You can specify many search items. Space, tab, CR, newline can be
   used as a separator. You can paste search terms from window
   application into the search list input area using ctrl-c and crtl-p.

For tree like information, to see further information, first select
   a term using "Left" mouse and then click "Right" mouse button. Popup
menu appears.

For tabular information, first select one or more lines/columns/... and
then click "Right" mouse button. You can paste the selected region of
the table to Window applications such as Excel/Word.
You can sort the table according to the one column by selecting an
appropriate column heading. Column width of the table can be adjusted.
Entire column can be moved to another column position by dragging
the column header.

When multiple terms are selected, there is a number after the GO
definition. It is the count of the unique selected term for itself and
all of its decendents. It can be used for the categorization of gene
products or DNA chip data analysis.

The data is taken from the DB dump of the GO database.
The GO directed acyclic graph is converted as a tree.
Some(many) external resource access links are not checked/verified.
When too many terms are selected, error might occur.

After testing and publish, I plan to submit it to the GO consortium
and/or biojava.

Sincerely yours,
Ungsik

=====================================================
Ungsik Yu, Ph.D. Bioinformatics, Principal Researcher
ungsik at kribb.re.kr   Tel:42-866-7188  Fax:42-860-4409
Genome Research Center, KRIBB
52, Oun, Yusong, Daejeon, 305-333, KOREA


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