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Re: HCLS - visualization task force?

From: Jun Zhao <jun.zhao@zoo.ox.ac.uk>
Date: Tue, 13 Mar 2012 21:04:38 +0000
Message-ID: <4F5FB666.8000500@zoo.ox.ac.uk>
To: public-semweb-lifesci@w3.org
Dear all,

Apology that I missed today's presentation due to conflicting engagement.

I believe that we have had strong demonstration that LOD is right way to 
go for data sharing and open access. But for HCLS, we still have way to 
go to prove its efficiency for supporting data analysis kind of tasks. 
And effective data visualization is a must towards this goal!

Although I have also been one benefiting from reusing existing 
visualization tools for presenting SW data, I am also a strong believer 
on customized tools and presentations. A lot of existing tools could be 
too generic to be useful for HCLS data and use cases particularly.

I've been using various js libraries and Google APIs to build heatmap 
kind of visualizations for gene expression data, to assist biologist to 
identify tissue-specific genes [1]. Everything underneath is SW 
technology powered. This same framework has been used by the LODD task 
in 2009's triplication challenge.

I'll be happy to join force building useful visualizations of hcls data 
based on constructive use cases. So count me in!

[1] 
http://www.open-biomed.org.uk/flykit/src/app/gene-expression-by-gene-batch/

-- Jun



On 13/03/2012 19:38, Alexander Garcia Castro wrote:
> Hi all, it was indeed an interesting meeting. Definitely the topic is
> really interesting, here is a nice review paper about visualizing linked
> data:
>
> Semantic Web 2 (2011) 89124 89 DOI 10.3233/SW-2011-0037
> IOS Press
>
> Approaches to visualising Linked Data: A survey
>
> Editor(s): Krzysztof Janowicz, Pennsylvania State University, USA
> Solicited review(s): Anthony Robinson, Pennsylvania State University, USA;
> Sarven Capadisli, National University of Ireland, Ireland
>
> Aba-Sah Dadzie a,* and Matthew Rowe b
>
> I will circulate the use cases (over the weekend) and some other info that
> I have gathered; also, I have relfinder, visor and sig.ma (not sure about
> this last one because my server crashed a month ago and sig.ma is no longer
> available for the general community to download), I will share those links
> as well.
>
> Best.
>
>
>
> On Tue, Mar 13, 2012 at 7:55 PM, Michel Dumontier<
> michel.dumontier@gmail.com>  wrote:
>
>> Indeed, lots of exciting opportunities here :)
>>
>> I started a wiki page to capture the essence of a task force and relevant
>> resources
>>
>> http://www.w3.org/wiki/HCLSIG/Visualization
>>
>> you're more than welcome to contribute to this document (add your name
>> too), and we'll soon discuss meeting times etc
>>
>> m.
>>
>>
>> On Tue, Mar 13, 2012 at 11:37 AM, Helena Deus<helenadeus@gmail.com>wrote:
>>
>>> Hi all,
>>>
>>> During the telco today Eric mentioned  http://www.distilbio.com/ , which
>>> was apparently built on top of exhibit3, seems like a great way to start.
>>>
>>> I would propose not to limit ourselves to "ways to visualize RDF graphs",
>>> but to actually try to plug linked data into data visualization paradigms
>>> already widely adopted, like dendrograms, heatmaps, sunburst plots, etc
>>>
>>> Example of a heatmap built from a SPARQL query (medicines VS their
>>> classes):
>>> http://mathbiol-lena.googlecode.com/hg/dendroheat/dendroheat_cma.html
>>>
>>> Finally, in the same lime of thinking,  a TED talk by Jer Thorp (NYT)
>>> about visualization -
>>> http://www.youtube.com/watch?feature=player_embedded&v=Q9wcvFkWpsM
>>>
>>> There's lots of really REALLY cool js libraries that we could use for
>>> very quickly prototyping!
>>> Best,
>>> Lena
>>>
>>>
>>> On Tue, Mar 13, 2012 at 5:12 PM, Luciano, Joanne Sylvia<luciaj2@rpi.edu>wrote:
>>>
>>>> Michel,
>>>>
>>>> A task force on visualization is a great idea.  And it would make sense
>>>> to have it aimed at and work with helping each of the other task forces
>>>> utilize visualization capabilities.  It's something I've been thinking
>>>> about with respect to the work we did on the TMO/TMKB. How do we
>>>> demonstrate beyond sparql queries?
>>>>
>>>> cheers,
>>>> joanne
>>>>
>>>> On Mar 13, 2012, at 12:58 PM, Chris Baker wrote:
>>>>
>>>>> Related to this topic .....
>>>>>
>>>>> Changing the Equation on Scientific Data Visualization
>>>>> by: Peter Fox, James Hendler
>>>>> http://www.sciencemag.org/content/331/6018/705
>>>>>
>>>>> The changing face of visualisation in a world of data intensive
>>>> science.
>>>>> http://eresearchau.files.wordpress.com/2011/11/peter-fox.pdf
>>>>>
>>>>> On Tue, Mar 13, 2012 at 1:15 PM, Michel Dumontier
>>>>> <michel.dumontier@gmail.com>  wrote:
>>>>>>
>>>>>> Hi all,
>>>>>>    At today's HCLS Life Sciences Forum (see minutes [1]) we had Alex
>>>> Garcia present on the topic of RDF visualization, indeed important for the
>>>> whole of the HCLS community. In addition to a Semantic Web Journal review
>>>> article [2], is anybody aware of comprehensive lists of use-cases for human
>>>> computer interaction with semantic web data (e.g. browse, search, query,
>>>> discovery)?
>>>>>>
>>>>>>    Second, I would like to gauge the interest of our community in
>>>> visualization, and whether it would be worthwhile to set up a task force
>>>> around HCLS visualization (use cases, requirements, tools and technologies,
>>>> collaborative development, deployment, evaluation). Please reply indicating
>>>> your interest.
>>>>>>
>>>>>> Cheers!
>>>>>>
>>>>>> m.
>>>>>>
>>>>>> [1] http://www.w3.org/2012/03/13-HCLS-minutes.html
>>>>>> [2] http://iospress.metapress.com/content/2822p340453463g1
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Michel Dumontier
>>>>>> Associate Professor of Bioinformatics, Carleton University
>>>>>> Visiting Associate Professor, Stanford University
>>>>>> Chair, W3C Semantic Web for Health Care and the Life Sciences
>>>> Interest Group
>>>>>> http://dumontierlab.com
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Christopher J. O. Baker Ph. D.
>>>>> Associate Professor
>>>>> Dept. Computer Science and Applied Statistics
>>>>> University of New Brunswick, Canada
>>>>> http://ca.linkedin.com/in/christopherjobaker
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Helena F. Deus
>>> Post-Doctoral Researcher at DERI/NUIG
>>> http://lenadeus.info/
>>>
>>>
>>
>>
>> --
>> Michel Dumontier
>> Associate Professor of Bioinformatics, Carleton University
>> Visiting Associate Professor, Stanford University
>> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
>> Group
>> http://dumontierlab.com
>>
>>
>
>
Received on Tuesday, 13 March 2012 21:05:12 GMT

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