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