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Re: From strings to things: ClinicalTrials.gov

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Sun, 17 Feb 2013 13:48:44 -0500
Message-ID: <CAFKQJ8=MS418XdGPwnQ2VyGnh6icP8J9zZNsrifX8fp+5QozxQ@mail.gmail.com>
To: Oktie Hassanzadeh <oktie@cs.toronto.edu>
Cc: Kerstin Forsberg <kerstin.l.forsberg@gmail.com>, public-semweb-lifesci@w3.org, em@zepheira.com, cdsouthan@hotmail.com, brendan.kelleher@karmadata.com

One thing I think would be helpful is attending more to using human
readable labels for terms. For example, if we browse directly at
linkedct.org we see a lot of long strings of numbers. But for most of
these there is a reasonable label. For example, under outcomes, the
first element is printed as 92f8444723382d2b6f2c06f69f3fe6f8, but if
we browse to http://linkedct.org/resource/outcome/92f8444723382d2b6f2c06f69f3fe6f8/
we see the property measure "Graft vs tumor effect as measured by CT
scan at days 30, 60, and 100 following transplant", which in this case
is a reasonable label. Similarly on this page we see provenances as
http://clinicaltrials.gov/show/NCT00003553?displayxml=true, whereas:
"Clinicaltrials.org record for the study: Peripheral Stem Cell
Transplant in Treating Patients With Metastatic Kidney Cancer" is much
more inviting. That would link to the same place, but give the viewer
a reason to hit the link.

One thing that's happened when I've tried to engage clinical
colleagues with linkedct is that it is hard for them to get past this
(and frankly for me too).

Contact me off list if you want to understand the issue with the
licensing you've chosen.


On Sat, Feb 16, 2013 at 6:47 PM, Oktie Hassanzadeh <oktie@cs.toronto.edu> wrote:
> Dear Kerstin,,,
> LinkedCT provides many external links including the seeAlso links you have
> pointed out, so the data is clearly 5-star Linked Data.
> Regarding the type of the links, there were long discussions at some point
> on this same list I believe on whether or not we should use sameAs to link
> to other resources, and the conclusion was that it's safer to use seeAlso
> since stating that an intervention on LinkedCT is the same as a drug on
> DBpedia for example, may be inaccurate.
> Regarding the quality and the quantity of the external links, we clearly can
> do better (and that's what we are planning to do), but existing links have
> already proven useful in a couple of use cases that take advantage of the
> links to PubMed, DrugBank, and DBpedia. One example is the LinkedSPLs work
> lead by Rich Boyce:
> Dynamic enhancement of drug product labels to support drug safety, efficacy,
> and effectiveness R.D. Boyce et al. Journal of Biomedical Semantics 4(1), 5,
> BioMed Central Ltd, 2013
> Cheers,
> Oktie
> On Sat, Feb 16, 2013 at 11:36 AM, Kerstin Forsberg
> <kerstin.l.forsberg@gmail.com> wrote:
>> 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. WebDB 2011
>>> Oktie Hassanzadeh, Anastasios Kementsietsidis, Lipyeow Lim, Renée J.
>>> Miller, Min Wang: LinkedCT: A Linked Data Space for Clinical Trials. 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 Sunday, 17 February 2013 18:49:45 UTC

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