RE: DSE TC, Friday May 25

Hi Stephen and Eric,
this looks very interesting and I also tried to to transform some files using Babel. However, I do have a lot on my plate the upcoming week, but would love to stay in the loop on how this stuff progress. Would be great if you could post the slightly updated files that Babel works on, the resulting JSON file and the Exhibit html.
 
Cheers
Kerstin

-----Original Message-----
From: Dobson, Stephen [mailto:Stephen.Dobson@pfizer.com]
Sent: 26 maj 2007 11:08
To: Eric Neumann; Forsberg, Kerstin L; public-hcls-dse@w3.org
Cc: dfhuynh@csail.mit.edu; karger@mit.edu
Subject: RE: DSE TC, Friday May 25



I love it.  

Yes it won't take the full set of data I'm just creating a smaller subpopulation to make it work.   Thanks for the dates thing, hadn't worked that out. 


Sure.  I can generate a SAS file with some metabolizing enzyme polymorphisms very easily and see if that can link in. 

 

I'd love some sort of quick hierarchical viewing mechanism if that's possible.   

Similar to how the NCBO's bioportal works.  It would be great for viewing things like the meddra hierarchy, organizational charts, multidimensional information.   I'm forever creating mindmaps to demo little bits of this type of hierarchical data.   

 

Cheers


Stephen.

 


  _____  


From: Eric Neumann [mailto:eneumann@teranode.com] 
Sent: Friday, May 25, 2007 4:44 PM
To: Dobson, Stephen; Forsberg, Kerstin L; public-hcls-dse@w3.org
Cc: dfhuynh@csail.mit.edu; karger@mit.edu
Subject: RE: DSE TC, Friday May 25

 

 

Stephen,

I was amazed how large the treament.xls file was, and so when I passed it to Babel with the other 3,  it choked... happy to hear you managed to make it work. Please append it to the DSE site.

Some Babel tips:

- make sure the main row item ID is in the first column, then babel will construct a URI for it (extra property).

- additional entity ID's (linker columns), need a URI to be generated manually (I believe), but will still use these local IDs as cross linkers if they have the same prop name in other files: e.g., AE_ID

- append a ':url' after a attribute (column) name if you wish it to be used as a URI

- other data types can be appended to column names to help Babel (like :item)

- object types can also be assigned (People, Events, etc) by adding a 'type' column

- dates should by in the ISO 8601 format (yyy-mm-dd)

If we can get all 4 files together correctly, building viewers should be easy.... should we try this also for some simple SAS tables?

I am working with the MIT researchers (David Karger and David Hyunh have been copied on this email;) to identify possible future features in Exhibit that we would find useful-- please pass along any general recommendations!

Eric



-----Original Message-----
From: Dobson, Stephen [ mailto:Stephen.Dobson@pfizer.com]
Sent: Fri 5/25/2007 4:18 PM
To: Forsberg, Kerstin L; Eric Neumann; public-hcls-dse@w3.org
Subject: FW: DSE TC, Friday May  25

Hi all,



The Exhibit system provides a great way of visualizing the tools.



Based on our conversation today am I right in thinking that this system
should "know" how to join data from multiple spreadsheets based on the
same URI's.  It looks like it has managed it for the AE's and demography
in the demonstration Eric provided.  Eric I assume you joined both these
datasets together simply by loading into bable?



I've managed to join treatment, demog and vitals together in the same
way.  It took me a while to work out you needed a unique record
identifier (e.g. vt_1, similar to Eric's AE_1) but after I discovered
that it works great.  I need to greatly reduce the spreadsheet to have
any hope of visualizing through the JSON file though.



I imagine we could eventually have applications where data could be
dragged and dropped and based on the URI's the system would know how to
join the data and what visualizations could be performed.   This would
be really nice.



Cheers

Stephen.





________________________________

From: public-hcls-dse-request@w3.org
[ mailto:public-hcls-dse-request@w3.org] On Behalf Of Forsberg, Kerstin L
Sent: Friday, May 25, 2007 8:15 AM
To: Eric Neumann; public-hcls-dse@w3.org
Subject: RE: DSE TC, Friday May 25



Hi Eric,

looks like we have a lot of interesting stuff to cover!



I have been playing around with the Exhibit viewer and JSON data. Great
stuff!!!



I would like us to have a discussions around what "web of data"
considerations that needs to made/applied to really make this the killer
app. That is, what we should consider in the process of taking data from
existing sources such as SAS/Excel datasets, rendering them as instances
of common entities (observations), enriching them by assigning URI:s and
annotating them using different ontologies, before making up the JSON
files



Talk to you soon

Cheers Kerstin

        -----Original Message-----
        From: public-hcls-dse-request@w3.org
[ mailto:public-hcls-dse-request@w3.org]On Behalf Of Eric Neumann
        Sent: 25 maj 2007 03:08
        To: public-hcls-dse@w3.org
        Subject: DSE TC, Friday May 25

        

        SW-HCLS(DSE) Friday, May 25, 8:30am-9:30am/13:30-14:30 UTC
        for a duration of 1 hour
        Zakim Bridge +1.617.761.6200 <tel:+1.617.761.6200> , conference
code
        3731 ("DSE1")
        Coordinator: Eric Neumann <eneumann@teranode.com>
       
        Agenda:
        a) Roll call, minutes review
       
        b) Propose next DSE call June 8, 2007
       
        c) 'Brief' review of CTO workshop meetings - take away messages?
           - On a related point, paper from Kerstin on 'informatics and
pharmacometrics': http://www.aapsj.org/view.asp?art=aapsj0901008
       
        d) Planning Preparation for DIA panel June 20
       
        e) SIMILE Exhibit viewing of SDTM data being constructed (see
attachments); will this be appropriate for a SDTM+biomarker RDF demo?
       
        f) BioONT DSE DCM discussion; see
http://esw.w3.org/topic/HCLS/OntologyTaskForce/BIONTDSEDCM
       
        g) (if we have time) DSE paper: goals, (journal), content, and
timing
       
       
        cheers,
        Eric

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