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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