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RE: [COI] Clinical data RDF examples?

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Wed, 20 Feb 2013 06:19:54 -0800
Message-ID: <12b4686149d2aae74eee185c653871b7@mail.gmail.com>
To: "M. Scott Marshall" <mscottmarshall@gmail.com>
Cc: HCLS <public-semweb-lifesci@w3.org>, conor dowling <conor-dowling@caregraf.com>, "Pathak, Jyotishman, Ph.D." <Pathak.Jyotishman@mayo.edu>, Alan Ruttenberg <alanruttenberg@gmail.com>, Kerstin Forsberg <kerstin.l.forsberg@gmail.com>, "Eric Prud'hommeaux" <eric@w3.org>, Guoqian Jiang <jiang.guoqian@mayo.edu>, Charlie Mead <charliem22@yahoo.com>, Sajjad Hussain <sajjad.hussain@crc.jussieu.fr>
hi scott,

although it is in XML, it might be worthwhile to consider translating the
TCGA clinical and sample information on the patients into RDF (if it
hasn't been done already!).

cheers,
michael

> -----Original Message-----
> From: M. Scott Marshall [mailto:mscottmarshall@gmail.com]
> Sent: Wednesday, February 20, 2013 5:52 AM
> To: conor dowling; Pathak, Jyotishman, Ph.D.; Alan Ruttenberg; Kerstin
> Forsberg; Eric Prud'hommeaux; Guoqian Jiang; Charlie Mead; Sajjad
Hussain
> Cc: HCLS
> Subject: [COI] Clinical data RDF examples?
>
> Hello Conor, All,
>
> [I started send this request to Jyoti, Conor, and Alan but realize
> that this is probably interesting to others in HCLS such as Eric and
> Charlie so now CCing the mailing list. In a sense, this relates to
> Kerstin's efforts to create OWL/RDF versions of CDISC standards, which
> should also involve representations of patient information, but I
> suppose that my request is more oriented at the EHR level. Ideally,
> however, there should be identical triples for certain data, e.g.
> [patient hasAge Age] that can be used to match a patient with the
> eligibility criteria of a trial.  ]
>
> Just a quick question: I am hoping that you could share some of your
> OWL/RDF choices (schema) with me that you made with your OWLization of
> XXX (e.g. OpenVISTA).  So, I am looking for some choices of
> namespaces, coding systems (NCI vs. SNOMED etc.), predicates (patient
> hasDisease <disease>), etc. Even just a paste of some RDF for one
> patient record that contains (non-identifying) demographics, type of
> cancer, TNM status, etc. would be helpful, especially of an example
> cancer patient. Could you send something like that? I would appreciate
> any form of input, on or 'off list'.
>
> SWAT4LS this year fed in to a few interesting developments/connections
> related to clinical care and clinical research, among them:
>
> 1) SWAT4LS Paris Nov 2012:
> http://www.w3.org/wiki/HCLS/SWAT4LS2012/Hackathon
>
> http://www.w3.org/wiki/HCLS/SWAT4LS2012/Hackathon#CDA_and_Clinical
> _Trial_Protocols_to_RDF
>
> 2) EHR4CR hosted a meeting in Paris on Jan. 22:
> http://www.w3.org/wiki/HCLS/ClinicalObservationsInteroperability/Conver
> gence
>
> The EHR4CR convergence meeting (2 above) will be followed up with
> discussions in COI teleconferences which I hope that you can also
> attend (Eric has kindly agreed to take us under his wing in COI).
> Charlie, who was present at 2, also enthusiastically supports
> continued discussion in this area. There will be an even larger
> convergence meeting held in March, organized by a EURECA colleague
> from EuroRec. Eventually (soon?), a merged summary report of the
> Convergence meeting will be shared on the wiki.
>
> Kind regards,
> Scott
>
> --
> M. Scott Marshall, PhD
> MAASTRO clinic, http://www.maastro.nl/en/1/
> http://eurecaproject.eu/
> https://plus.google.com/u/0/114642613065018821852/posts
> http://www.linkedin.com/pub/m-scott-marshall/5/464/a22
Received on Wednesday, 20 February 2013 14:20:33 GMT

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