[tdwg-content] Fwd: Annotation Ontology best practice relation for linking to image/machine-opaque docs? biomedical use case

Steve Baskauf steve.baskauf at vanderbilt.edu
Sat Jan 15 04:46:31 CET 2011

I think that what you need to remember is that a lot of people on this 
list just don't know as much about the Linked Data world as you do.  For 
example, I think I was the guilty party for suggesting an incorrect use 
of rdfs:seeAlso .  That was based on a faulty memory of something I read 
six months ago.  So what seems to be resistance in many cases may just 
be ignorance or misinformation.  The other part of it is that to some 
extent we are in the process of cramming a square peg in a round hole in 
trying to make existing biodiversity informatics terms, databases, 
systems, etc. work in the LOD world.  Those things weren't necessarily 
designed to work with LOD and it's going to take some time and education 
to figure out how to round off the corners enough to make them fit.  A 
lot of people have invested a lot of time, effort, and money in square 
pegs and they are not going to be willing or even able to just throw 
them all away and suddenly buy all new round pegs.  I think that there 
are a significant number of people in this community who are willing to 
give Linked Data a shot, but it's going to take some time and 
education.  You might know that certain predicates are widely used, but 
since I'm not spending much of my time immersed in the LOD world, I 
won't necessarily know those predicates - to a large extent I'm getting 
my education from this list.  I'm not really following what is being 
discussed elsewhere - not enough time.


Peter DeVries wrote:
> This discussion of what specific meanings to assign to various widely 
> used predicates reminds me how often this list seems to prefer 
> operating only within itself.
> A number of these kinds of issues have been discussed elsewhere.
> The argument has always been made that we should use standards but 
> when those standards are not those proposed on this list they seem to 
> be ignored.
> Whether it is the appropriate use of rdfs:seeAlso or other existing 
> widely used vocabularies. Note below a separate Annotations vocabulary.
> Respectfully,
> - Pete
> ---------- Forwarded message ----------
> From: *Tim Clark* <tim_clark at harvard.edu <mailto:tim_clark at harvard.edu>>
> Date: Mon, Jan 10, 2011 at 1:34 PM
> Subject: Re: best practice relation for linking to 
> image/machine-opaque docs? biomedical use case
> To: "M. Scott Marshall" <mscottmarshall at gmail.com 
> <mailto:mscottmarshall at gmail.com>>
> Cc: HCLS IG <public-semweb-lifesci at w3.org 
> <mailto:public-semweb-lifesci at w3.org>>, public-lod at w3.org 
> <mailto:public-lod at w3.org>, Daniel Rubin <dlrubin at stanford.edu 
> <mailto:dlrubin at stanford.edu>>, "John F. Madden" <john.madden at duke.edu 
> <mailto:john.madden at duke.edu>>, Vasiliy Faronov <vfaronov at gmail.com 
> <mailto:vfaronov at gmail.com>>, Toby Inkster <tai at g5n.co.uk 
> <mailto:tai at g5n.co.uk>>, Peter DeVries <pete.devries at gmail.com 
> <mailto:pete.devries at gmail.com>>, Tim Berners-Lee <timbl at w3.org 
> <mailto:timbl at w3.org>>, Paolo Ciccarese <paolo.ciccarese at gmail.com 
> <mailto:paolo.ciccarese at gmail.com>>, Anita de Waard 
> <A.dewaard at elsevier.com <mailto:A.dewaard at elsevier.com>>, Maryann 
> Martone <maryann at ncmir.ucsd.edu <mailto:maryann at ncmir.ucsd.edu>>
> 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 at w3.org 
> <mailto:timbl at 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
> >
> >
> -- 
> ---------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / 
> GeoSpecies Knowledge Base <http://lod.geospecies.org/>
> About the GeoSpecies Knowledge Base <http://about.geospecies.org/>
> ------------------------------------------------------------

Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

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