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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!).


> -----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
> 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 UTC

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