[Biojava-l] Java Webstart based GO browser

[ungsik]

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 searched.
   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. Resulting tree information can be copied to
system clipboard. You can change the depth of exported tree info by
collapsing/expanding the tree.

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 a 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 descendants. It can be used for the classification of gene
products or DNA chip data analysis.

The data is taken from the DB dump of the GO database.
I wrote a program which read GO db dump file and build data structure.
It also has some access methods which might be useful for other kind
of GO bio java programming.

The GO directed acyclic graph is converted as a tree.
Some(many) external resource access links are not checked/verified.
The message before external webpage browing is some kind of debugging
message and it will be removed after external resouce pages are verified.

After testing, enhancement 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@kribb.re.kr   Tel:42-866-7188  Fax:42-860-4409
Genome Research Center, KRIBB
52, Oun, Yusong, Daejeon, 305-333, KOREA