W3C home > Mailing lists > Public > public-lod@w3.org > January 2011

Re: best practice relation for linking to image/machine-opaque docs? biomedical use case

From: M. Scott Marshall <mscottmarshall@gmail.com>
Date: Mon, 10 Jan 2011 17:30:10 +0100
Message-ID: <AANLkTimJ4y1SFu6RETdV2ynrUZUWtWwWU6SmyzqkMiQT@mail.gmail.com>
To: HCLS <public-semweb-lifesci@w3.org>, public-lod@w3.org, Daniel Rubin <dlrubin@stanford.edu>, Tim Clark <tim_clark@harvard.edu>, John Madden <john.madden@duke.edu>
Cc: Vasiliy Faronov <vfaronov@gmail.com>, Toby Inkster <tai@g5n.co.uk>, Peter DeVries <pete.devries@gmail.com>, Tim Berners-Lee <timbl@w3.org>
[Scott dusts off old use case and pulls from the shelf. Adjusts
subject of thread. Was: best practice for referring to PDF]

In Health Care and Life Science domains, image data is a common form
of data under discussion so a best practice for referring to an image
or to an (extractable) feature *within* an image would cover a
fundamental need in biomedicine to point to 'raw' data as evidence (as
well as giving meaning to the raw data!).

A clinical example from breast cancer:
There is a scan that produces an image that contains features referred
to by the radiologist as 'microcalcifications', which can be
indicative of the presence of a tumor.

I can think of a few scenarios that would refer to the image data
(mammogram). There are probably more:
1) The radiology report (in RDF) asserts the presence of
microcalcifications and refers to the entire image as evidence.
2) The radiology report (in RDF) asserts the presence of
microcalcifications and refers to the entire image as evidence, along
with a image processing/feature extraction program that will highlight
the phenomenon in the image.
3) The radiology report (in RDF) asserts the presence of
microcalcifications and refers to a specific region in the image as
evidence using some function of a 2D coordinate system such as
polyline.

The question: How can we refer to the microcalcifications as an
indication of a certain type of tumor in each case 1, 2, and 3 in RDF?

I am especially interested in the 'structural' aspects: How do we
refer to the image document as containingEvidence ? How can we refer
to a *region* of the image in the document? How can we refer to the
software that will extract the relevant features with statistical
confidence, etc.?

Any ideas or pointers to existing practices would be appreciated. I'm
aware of some related work in multimedia to refer to temporal regions
but I am specifically interested in spatial regions.

Note that an analogous question of practice exists for textual
documents such as literature in PubMed that can be text-mined for
(evidence of) assertions.

* Note: 2D is a simplification that should come in handy in
implementations and often deemed necessary, such as thumbnails.

-Scott

-- 
M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
Leiden University Medical Center / University of Amsterdam
http://staff.science.uva.nl/~marshall

On Mon, Jan 10, 2011 at 4:01 PM, Tim Berners-Lee <timbl@w3.org> wrote:
> It is well to look at and make best practices for the things
> we have if we don't
>
> It was the FOAF folks who, initially, instead of using linked data,
> used an Inverse Functional Property to uniquely identify
> someone and then rdfs:seeAlso to find the data about them.
> So any FOAF browser has to look up the seeAlso  or they
> don't follow any links.
>
> So tabulator always when looking up x and finding x see:also y will
> load y.  So must any similar client or any crawler.
>
> So there is a lot of existing use we would throw away if we
> allowed rdfs:seeAlso for pointing to things which do not
> provide data. (It isn't the question of conneg or mime type,
> that is a red herring. it is whether there is machine-redable
> standards-based stuff about x).
>
> Further, we should not make any weaker properties like seeDocumentation
> subproperties of see:Also, or they would imply
> We maybe need a very weak top property like
>
> mayHaveSomeKindOfInfoAboutThis
>
> to be the superProperty of all the others.
>
> One things which could be stronger than seeAlso is definedBy if it
> is normally used for data, to point to the definitive ontology.
> That would then imply seeAlso.
>
> Tim
Received on Monday, 10 January 2011 16:31:00 UTC

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