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Re: ClinicalTrial Schema

From: Nolan Nichols <nichols.nolan@gene.com>
Date: Sun, 24 Mar 2019 13:41:40 -0700
Message-ID: <CAFmLkxU+FRR9OyB=yG8VgYaYTrt73S7Nf3ZoLCnmdFxS1TgXuw@mail.gmail.com>
To: Marc <twamarc@gmail.com>
Cc: paoladimaio10@googlemail.com, "schema.org Mailing List" <public-schemaorg@w3.org>
Hi Paola and Marc,

Thank you for your responses and interest in this topic.

Paola: WRT Research Protocols, these are indeed one aspect of the Clinical
Trial schema I have in mind, but trial protocols get complex very quickly
and I would like to start simple by capturing some basic protocol
information (e.g., patient population, primary/secondary outcomes,
eligibility criteria, etc.). I'd be interested to hear more about what you
are working on and see if it makes sense to collaborate. Feel free to reach
out to me directly or point me to where I can find more info!

Marc: Thanks for the pointer to schemed, I'll post some followup thoughts
over at public-schemed@w3.org and try to keep the ball rolling.

Cheers,

Nolan

On Sun, Mar 24, 2019 at 7:16 AM Marc <twamarc@gmail.com> wrote:

> Hi Nolan,
> Hi all,
> Nice raising topic here....
> I support this from the beginning, ... in the past there was a idea in
> this sense but not enough community support and no clear support from
> clinicaltrial.gov
> If now we have a real interest and use cases.... please take a lead and we
> will organize a discussion through https://www.w3.org/community/schemed/
>
> Regards,
>
> Best regards
>
> Marc Twagirumukiza
>
> ~ScheMed W3C Group
>
>
>
>
>
> Le dim. 24 mars 2019 à 11:20, Paola Di Maio <paola.dimaio@gmail.com> a
> écrit :
>
>> Dear Nolan
>> Thanks for sharing. I am working on Research Protocols, and feel the same
>> I wonder if you would consider a research protocol ( biomed research
>> protocol, but there  I wonder if we should generalize ) a similar enough
>> case to a clinical trial and should we join forces, or
>> not . Let me know what you think
>> PDM
>>
>> On Sun, Mar 24, 2019 at 8:57 AM Nolan Nichols <nichols.nolan@gene.com>
>> wrote:
>>
>>> Hi All,
>>>
>>> I've started looking into creating a schema of clinical trial metadata
>>> using schema.org and mapping instances from public repositories (e.g.,
>>> clinicaltrials.gov), to a clinical trial schema that could then be
>>> published to datacommons.org.
>>>
>>> From what I see, it looks like a good starting point would be to build
>>> on what has already been defined in the health-lifesci group with
>>> schema.org:MedicalTrial <https://health-lifesci.schema.org/MedicalTrial>
>>> .
>>>
>>> There are a handful of attempts at doing something similar elsewhere,
>>> such as:
>>>
>>> - Wikidata ClinicalTrial
>>> <https://www.wikidata.org/wiki/Wikidata:WikiProject_Medicine/Data_models/Trials>
>>> - Clinical Trial Data as RDF
>>> <https://github.com/phuse-org/CTDasRDF/blob/master/doc/HandsOnCreateTriplesFromOWL.md#more-ts-mapping>
>>>
>>> - Open Trials <https://opentrials.net/>
>>> - Linked CT <http://linkedct.org/> - broken ;-(
>>>
>>> While those efforts capture semantics, others provide a pretty clean
>>> tabular representation of clinical trial metadata like the AACT database
>>> <https://aact.ctti-clinicaltrials.org/>.
>>>
>>> I'd love to start a conversation about how we can create a schema for
>>> clinical trials that fits into the schema.org vision and can publish
>>> useful information like what is in the AACT database as linked data.
>>>
>>> I took the humble approach of defining a few terms that would extend the
>>> schema of datacommons.org to capture just a single attribute of a trial
>>> (i.e., phase). I submitted this as a PR
>>> <https://github.com/google/datacommons/pull/41>.
>>>
>>> I would love to get feedback on how I can move this idea forward and
>>> work with this community to define a schema that could be used to publish
>>> information about clinical trials.
>>>
>>> Cheers,
>>>
>>> Nolan
>>>
>>> --
>>> Nolan Nichols, PhD
>>> Bioinformatics & Computational Biology
>>> Genentech, Inc.
>>> nichols.nolan@gene.com
>>> https://orcid.org/0000-0003-1099-3328
>>>
>>>
Received on Sunday, 24 March 2019 20:42:41 UTC

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