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

From: Daniel Rubin <dlrubin@stanford.edu>
Date: Mon, 10 Jan 2011 19:40:43 -0800
To: "'Paolo Ciccarese'" <paolo.ciccarese@gmail.com>
Cc: "'Tim Clark'" <tim_clark@harvard.edu>, "'M. Scott Marshall'" <mscottmarshall@gmail.com>, "'HCLS IG'" <public-semweb-lifesci@w3.org>, <public-lod@w3.org>, "'John F. Madden'" <john.madden@duke.edu>, "'Vasiliy Faronov'" <vfaronov@gmail.com>, "'Toby Inkster'" <tai@g5n.co.uk>, "'Peter DeVries'" <pete.devries@gmail.com>, "'Tim Berners-Lee'" <timbl@w3.org>, "'Anita de Waard'" <A.dewaard@elsevier.com>, "'Maryann Martone'" <maryann@ncmir.ucsd.edu>
Message-ID: <000101cbb141$53ad0670$fb071350$@stanford.edu>
Hi,

For example:

 

http://stanford.edu/~rubin/pubs/Rubin-IEEEIntelSys-2009.pdf

http://stanford.edu/~rubin/pubs/Channin-JDI-2009.pdf

 

or others there on Annotation and Image Markup..

 

Daniel

 

___________________________________

 Daniel L. Rubin, MD, MS                              Description:
Description: Description: Description: cid:image001.jpg@01CB4E1D.AC3DA3D0

            Assistant Professor

            Department of Radiology | Stanford University

            Richard M. Lucas Center | 1201 Welch Road, Office P285

            Stanford, CA 94305-5488

            Phone: 650-723-9495 | Fax: 650-723-5795

            Web:  <http://rubin.web.stanford.edu/>
http://rubin.web.stanford.edu/

 

From: Paolo Ciccarese [mailto:paolo.ciccarese@gmail.com] 
Sent: Monday, January 10, 2011 12:57 PM
To: Daniel Rubin
Cc: Tim Clark; M. Scott Marshall; HCLS IG; public-lod@w3.org; John F.
Madden; Vasiliy Faronov; Toby Inkster; Peter DeVries; Tim Berners-Lee; Anita
de Waard; Maryann Martone
Subject: Re: best practice relation for linking to image/machine-opaque
docs? biomedical use case

 

Dear Daniel,
I am very interested in revising the material you have related to image
fragments identification.

I just had a look of your website, could you help me in selecting the 2 or 3
papers that you consider most appropriate in this context?

Thank you
Paolo

On Mon, Jan 10, 2011 at 3:49 PM, Daniel Rubin <dlrubin@stanford.edu> wrote:

Interesting.
In case you weren't aware, we've done quite a bit on semantic image
annotation and creating and XML schema for specifying regions of images and
the ontology terms to describe them..
I have a number of papers on this on my web site if you're interested..

Daniel

___________________________________
       Daniel L. Rubin, MD, MS
       Assistant Professor
       Department of Radiology | Stanford University
       Richard M. Lucas Center | 1201 Welch Road, Office P285
       Stanford, CA 94305-5488
       Phone: 650-723-9495 | Fax: 650-723-5795
       Web: http://rubin.web.stanford.edu/



> -----Original Message-----
> From: Tim Clark [mailto:tim_clark@harvard.edu]
> Sent: Monday, January 10, 2011 11:35 AM
> To: M. Scott Marshall
> Cc: HCLS IG; public-lod@w3.org; Daniel Rubin; John F. Madden; Vasiliy
Faronov;
> Toby Inkster; Peter DeVries; Tim Berners-Lee; Paolo Ciccarese; Anita de
Waard;
> Maryann Martone
> Subject: Re: best practice relation for linking to image/machine-opaque
docs?
> biomedical use case
>

> Hi Scott,
>
> For referring to a portion of an image, let me point you to work in my
group done
> in collaboration with HCLS Scientific Discourse Task, UCSD, Elsevier, and
one of
> the major pharmas.  Paolo Ciccarese is the main author, and this work is
based on
> the earlier W3C project Annotea.
>
> AO, Annotation ontology, here:
http://code.google.com/p/annotation-ontology/,
> presented at Bio Ontologies 2010, and full-length paper in press at BMC
> Bioinformatics.
>
> Bio Ontologies 2010 slides here:
http://www.slideshare.net/paolociccarese/ao-
> annotation-ontology-for-science-on-the-web
>
> AO uses a special subclass of Selector to specify the part of the document
> (image) being referred to.
>
> see here for Selectors: http://code.google.com/p/annotation-
> ontology/wiki/Selectors
>
> and here for an example of image annotation:
> http://code.google.com/p/annotation-ontology/wiki/AnnotationTypes
>
> Best
>
> Tim
>
> On Jan 10, 2011, at 11:30 AM, M. Scott Marshall wrote:
>
> > [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
<http://staff.science.uva.nl/%7Emarshall> 
> >
> > 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
> >
> >




-- 
Dr. Paolo Ciccarese
Biomedical Informatics Research & Development
Instructor of Neurology at Harvard Medical School
Assistant in Neuroscience at Mass General Hospital
+1-857-366-1524 (mobile)   +1-617-768-8744 (office)

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Received on Tuesday, 11 January 2011 03:42:23 UTC

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