[InterMine Dev] biopax data visulization

Julie Sullivan julie at flymine.org
Mon Mar 19 09:01:07 GMT 2012


Hi Su

Have you loaded interactions from IntAct or BioGRID?  If so, adding the 
interactions displayer is easy.

1. add the entry for that displayer to your webconfig-model.xml file, as 
described here:

	http://intermine.org/wiki/ReportDisplayerGallery#Interactionnetwork

2. re-release your webapp and you should see the interaction displayer on gene 
report pages.

Regarding pathways, that's exactly what FlyMine does - links out to the data 
source.  To do that, take a look at flymine's web.properties file:

http://intermine.org/browser/trunk/flymine/webapp/resources/web.properties

I think these are the two entries you are interested in:

# KEGG
attributelink.KEGG.Pathway.*.identifier.url=http://www.genome.jp/dbget-bin/www_bget?map<<attributeValue>>
attributelink.KEGG.Pathway.*.identifier.text=KEGG: <<attributeValue>>
attributelink.KEGG.Pathway.*.identifier.imageName=KEGG_logo_mini.gif
attributelink.KEGG.Pathway.*.identifier.dataset=KEGG pathways data set

# REACTOME
attributelink.reactome.Pathway.*.identifier.url=http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_<<attributeValue>>
attributelink.reactome.Pathway.*.identifier.text=Reactome: <<attributeValue>>
attributelink.reactome.Pathway.*.identifier.imageName=Reactome_logo.png
attributelink.reactome.Pathway.*.identifier.dataset=Reactome data set

Here are the docs:

	http://intermine.org/wiki/WebProperties

Let us know if you have any problems!

Cheers
Julie

On 17/03/12 13:22, wang su wrote:
> I Think both interaction and pathway displayer I will be used in the future, so can you help me implement the interaction player first, and then for pathway displayer~~
> In addition, because the pathway biopax data are all public data which downloaded from Reactome, NCI and so on, these websites have a pathway displayer, so if I can have a link to these sites, that's also be OK!
>
> Thank you!
>
> Su



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