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Re: Mashup browser compatibility - and use of Mashup for Mouse BIRN contribution to future demo

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Sat, 12 May 2007 23:54:27 -0600
Message-Id: <D98749CB-ED61-4AD2-A10A-19A28CF3FB1B@gmail.com>
Cc: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
To: William Bug <William.Bug@DrexelMed.edu>

On May 12, 2007, at 11:31 PM, William Bug wrote:

> Works for me now (MacTel running OS X v10.4.9 & Firefox v2.0.0.3  
> with a ridiculous number of plugins installed).
> This is great, Alan.
> So if I understand the changes you've made, we are now looking at a  
> side-by-side comparison of the pseudo-colored, gene-specific  
> immunohisto. sections from two different brains - (the brains 'gene  
> painted' for Kcnip3 & Kcnd1) - presenting the roughly equivalent  
> sagittal sections (Kcnip3@2850 and Kcnd1@2800) from those two brains?

Yes. Just to warn - I need to rerun the Allen translation. I've  
noticed at least two things 1) There are fewer genes that are in the  
KB currently than I though I had loaded - don't know what happened.  
And 2) I need to use the newest purl.org uri scheme and do a mapping  
to entrez gene, as I realized that wasn't in the initial mapping.   
Also, I want to merge the ABA ontology with the sciencecommons  
ontology, so there may be some changes in predicate and class names  
to conform with the style we finally settled on. I'll load this in to  
a new graph and then tell you when it is ready and what has changed.

I've also noticed the effects of the lack of spatial alignment  
between images. You can see it clearly in another version of the  
exhibit example. So high on my list when talking with them will be to  
get some spatial information.

The MBAT tools sounds cool. Do you think it should go into the sfn  


> Work has begun on the Mouse BIRN Atlasing Tool project to link this  
> into our framework.  The idea would be, when viewing atlas- 
> registered images or spatially-mapped gene expressions results  
> overlaid onto an MBAT atlas view, a user would be able to right  
> click on a an image and would be presented with a very simple way  
> to query against your neurocommons ABA RDF store.  If they click on  
> a spatially mapped gene-expression pattern, they'd be presented  
> with a very simple option:
> 	1) view Nissl & immuno-stain for the ABA brain stained for that  
> gene - constrained to the set of sections from that ABA brain known  
> to intersect with the selected brain region
> 	2) view this side-by-side comparison by providing a user the  
> ability to select from a list of other genes (preferably two lists  
> - one constrained to genes we can relate to the current expressed  
> gene pattern they just clicked on via www.genenetwork.org or via a  
> pathways ontology; the other way to select a gene would be through  
> a text query box - just give any string and we'd return all gene  
> names that match via a regex either to the full gene name or gene  
> name abbrev. tag)
> If they just click on an image with segmented brain regions (no  
> gene expression), they'd provided with a way to again act on those  
> two options above (Nissl + immuno for 1 ABA brain OR immuno  
> comparison view for 2 brains) - selecting genes based on some  
> combination of string matching and ontology constraints based on  
> gene networks, pathways, genes related to a specific GO MF or GO CC.
> The results from the SPARQL query would then dynamically populate  
> your Google Map HTML+JS template which would be presented in a  
> JFrame (MBAT is a Java app).  Our developers are also spec'ing out  
> how to add an additional "slicing" widget to the Google Map  
> widgets, so a user could process through one of these constrained  
> image sets (constrained based on their 'cutting' through a given  
> brain region) from a given ABA gene-painted brain.
> I don't see any reason why most of this functionality wouldn't be  
> ready to include in the SfN presentation (possibly even in alpha  
> for ISMB in July, pending our access to MBAT programmer resources  
> for whom this may not be the top priority).
> Cheers,
> Bill
> On May 13, 2007, at 12:45 AM, Alan Ruttenberg wrote:
>> Hi Don,
>> When you or someone else gets a chance, give a try again. I think  
>> it will work now, thanks to:
>> Brian Gilman (use a modern Ajax framework) and
>> Mike Travers( wrap parentheses around the expression to be  
>> evaluated).
>> Much appreciated!!
>> -Alan
>> On May 12, 2007, at 8:26 AM, Donald Doherty, Ph.D. wrote:
>>> Alan,
>>> I'm getting the same errors in Firefox 2.0 and IE 6.0 on the  
>>> Windows XP
>>> platform.
>>> Don
>>>> On the demo page there is a link to the Google Maps/Allen Brain
>>>> Institute/SPARQL mashup. It works properly on Safari. However it  
>>>> gets
>>>> an error in Firefox after retrieving the results and doesn't  
>>>> display
>>>> an image. In IE7, it retrieves the results but then doesn't seem to
>>>> to update the images shown properly. The firefox test is on the  
>>>> Mac,
>>>> the IE7 test is under XP.
>>>> I suspect that this has to do with details of the  
>>>> XMLHTTPRequest. If
>>>> there is someone knowledgeable about such issues I'd appreciate if
>>>> you could have a look and see if you can figure out what the  
>>>> problem
>>>> is. Also testing on other browsers/OS would be appreciated.
>>>> The URL to test is http://hcls1.csail.mit.edu:8890/map/
>>>> #Kcnip3@2850,Kcnd1@2800
>>>> Thanks!
>>>> -Alan
>>> -- 
>>> Donald Doherty, Ph.D.
>>> Brainstage Research, Inc.
>>> www.brainstage.com
>>> donald.doherty@brainstage.com
>>> 412-683-1410
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> Bill Bug
> Senior Research Analyst/Ontological Engineer
> Laboratory for Bioimaging  & Anatomical Informatics
> www.neuroterrain.org
> Department of Neurobiology & Anatomy
> Drexel University College of Medicine
> 2900 Queen Lane
> Philadelphia, PA    19129
> 215 991 8430 (ph)
> 610 457 0443 (mobile)
> 215 843 9367 (fax)
> Please Note: I now have a new email - William.Bug@DrexelMed.edu
Received on Sunday, 13 May 2007 05:52:33 UTC

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