Re: From strings to things: ClinicalTrials.gov

Dear Kerstin,

Have you ever looked at http://linkedct.org ?

LinkedCT uses a complex process to turn ClinicalTrials.gov into
high-quality 5-start Linked Data. And yes it does provide HTTP URIs for all
the "things" on ClinicalTrials.gov, provides HTML or RDF, SPARQL endpoint,
etc.

Please take a look at http://linkedct.org , http://linkedct.org/stats/ ,
and http://linkedct.org/faq/ , and the following articles for any questions
you might have.

Oktie Hassanzadeh, Soheil Hassas Yeganeh, Renée J. Miller: Linking
Semistructured Data on the
Web<http://webdb2011.rutgers.edu/papers/Paper%2027/paper27-camera-ready.pdf>.
WebDB 2011
Oktie Hassanzadeh, Anastasios Kementsietsidis, Lipyeow Lim, Renée J.
Miller, Min Wang: LinkedCT: A Linked Data Space for Clinical
Trials<http://arxiv.org/abs/0908.0567>.
CoRR abs/0908.0567 2009


Cheers,
Oktie

========================
Oktie Hassanzadeh
oktie@cs.toronto.edu
http://www.cs.toronto.edu/~oktie


On Sat, Feb 16, 2013 at 7:58 AM, Kerstin Forsberg <
kerstin.l.forsberg@gmail.com> wrote:

> Hi,
> a couple of tweets, blog post comments 1) and email exchanges during the
> week on moving ClinicalTrials.gov "from strings to things" made me think
> this could be a topic for discussion at the upcoming CSHALS. As I'll not be
> able to be there in person I'm using this email list to hear your thoughts.
>
> Background:
> We see many nice examples of curated/standardized feeds of CT.gov data,
> such as http://linkedct.org, http://www.patientslikeme.com/clinical_trialsand
> http://www.clinicalcollections.org/trials/ etc.. Most of them do a good
> job in turning “strings into things” and a few of them apply the Linked
> Data principles. However, I don’t think any of them use http-based URIs to
> identify things such as sponsor organization, clinical sites, clinical
> investigators, geography, disease, drug, and time.
>
> I argue that we as a community caring for clinical trials data should push
> back to FDA and NLM to get an official, standardized, linked data interface
> directly to the CT.gov at source. And yes, also for FDA and NLM to push
> back to pharma companies to provide standardized data about our trials with
> URIs to identify things instead of all these text strings. And also if
> pharma company websites such as http://www.gsk-clinicalstudyregister.com/and
> http://www.astrazenecaclinicaltrials.com/ did the same.
>
> Given the current movement for clinical trial data transparency 2) I may
> think the timing is good. But, potentially challenging both for FDA, NLM
> and for the pharma companies. They (we) will all look for practical advice
> on what URIs to use for things such as drugs and organizations.
>
> Thoughts?
> Kerstin
>
>
> 1)
> http://blog.karmadata.com/2013/02/11/loading-clinical-trials-data-in-ten-minutes-flat/comment-page-1/#comment-20
> 2)
> http://www.placebocontrol.com/2013/02/our-new-glass-house-gsks-commitment-to.html
>