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Re: From strings to things: ClinicalTrials.gov

From: Kerstin Forsberg <kerstin.l.forsberg@gmail.com>
Date: Sat, 16 Feb 2013 17:36:29 +0100
Message-ID: <CAKi6PjUESMf81s4x849kQ5oO4GWOk81u7EeQ5Nb5C5Vx68NB6g@mail.gmail.com>
To: Oktie Hassanzadeh <oktie@cs.toronto.edu>
Cc: public-semweb-lifesci@w3.org, em@zepheira.com, cdsouthan@hotmail.com, brendan.kelleher@karmadata.com
Dear Oktie,

Yes, and I'm also pointing colleagues to this great dataset part of LODD (
http://linkedct.org).

Two reflections:
1) My understanding is that colleagues are more comfortable with going
directly to the source and use the XML download (
http://clinicaltrials.gov/ct2/resources/download )
2) I meant 5-star linked data in terms of linking outwards to existing
identifiers instead of "internal" URIs like
http://linkedct.org/resource/intervention/a0e0900a02a9fa5501b51b95c281e3f9/for
Atorvastatin (Intervention).

Looks like you do a good job with your See also links, e.g.
http://dbpedia.org/resource/Atorvastatin and
http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB01076) However,
my understanding is that some of the types of things are quite challenging,
see for example Drug Identification Links: Connecting Up,
http://www.citeulike.org/user/cdsouthan/article/10423875

Kerstin


2013/2/16 Oktie Hassanzadeh <oktie@cs.toronto.edu>

> 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_trials and
>> 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
>>
>
>
Received on Saturday, 16 February 2013 16:36:57 GMT

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