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Pete,<br>
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.<br>
<br>
Steve<br>
<br>
Peter DeVries wrote:
<blockquote
cite="mid:AANLkTi=TvwDOYh+kFXXBjOpWsokmG5dtLyMXQT5EXgz2@mail.gmail.com"
type="cite">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.
<div><br>
</div>
<div>A number of these kinds of issues have been discussed elsewhere.<br>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Whether it is the appropriate use of rdfs:seeAlso or other
existing widely used vocabularies. Note below a separate Annotations
vocabulary.</div>
<div><br>
</div>
<div>Respectfully,</div>
<div><br>
</div>
<div>- Pete<br>
<br>
<div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Tim Clark</b> <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:tim_clark@harvard.edu">tim_clark@harvard.edu</a>></span><br>
Date: Mon, Jan 10, 2011 at 1:34 PM<br>
Subject: Re: best practice relation for linking to image/machine-opaque
docs? biomedical use case<br>
To: "M. Scott Marshall" <<a moz-do-not-send="true"
href="mailto:mscottmarshall@gmail.com">mscottmarshall@gmail.com</a>><br>
Cc: HCLS IG <<a moz-do-not-send="true"
href="mailto:public-semweb-lifesci@w3.org">public-semweb-lifesci@w3.org</a>>,
<a moz-do-not-send="true" href="mailto:public-lod@w3.org">public-lod@w3.org</a>,
Daniel Rubin <<a moz-do-not-send="true"
href="mailto:dlrubin@stanford.edu">dlrubin@stanford.edu</a>>, "John
F. Madden" <<a moz-do-not-send="true"
href="mailto:john.madden@duke.edu">john.madden@duke.edu</a>>,
Vasiliy Faronov <<a moz-do-not-send="true"
href="mailto:vfaronov@gmail.com">vfaronov@gmail.com</a>>, Toby
Inkster <<a moz-do-not-send="true" href="mailto:tai@g5n.co.uk">tai@g5n.co.uk</a>>,
Peter DeVries <<a moz-do-not-send="true"
href="mailto:pete.devries@gmail.com">pete.devries@gmail.com</a>>,
Tim Berners-Lee <<a moz-do-not-send="true" href="mailto:timbl@w3.org">timbl@w3.org</a>>,
Paolo Ciccarese <<a moz-do-not-send="true"
href="mailto:paolo.ciccarese@gmail.com">paolo.ciccarese@gmail.com</a>>,
Anita de Waard <<a moz-do-not-send="true"
href="mailto:A.dewaard@elsevier.com">A.dewaard@elsevier.com</a>>,
Maryann Martone <<a moz-do-not-send="true"
href="mailto:maryann@ncmir.ucsd.edu">maryann@ncmir.ucsd.edu</a>><br>
<br>
<br>
Hi Scott,<br>
<br>
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.<br>
<br>
AO, Annotation ontology, here: <a moz-do-not-send="true"
href="http://code.google.com/p/annotation-ontology/" target="_blank">http://code.google.com/p/annotation-ontology/</a>,
presented at Bio Ontologies 2010, and full-length paper in press at BMC
Bioinformatics.<br>
<br>
Bio Ontologies 2010 slides here: <a moz-do-not-send="true"
href="http://www.slideshare.net/paolociccarese/ao-annotation-ontology-for-science-on-the-web"
target="_blank">http://www.slideshare.net/paolociccarese/ao-annotation-ontology-for-science-on-the-web</a><br>
<br>
AO uses a special subclass of Selector to specify the part of the
document (image) being referred to.<br>
<br>
see here for Selectors: <a moz-do-not-send="true"
href="http://code.google.com/p/annotation-ontology/wiki/Selectors"
target="_blank">http://code.google.com/p/annotation-ontology/wiki/Selectors</a><br>
<br>
and here for an example of image annotation: <a moz-do-not-send="true"
href="http://code.google.com/p/annotation-ontology/wiki/AnnotationTypes"
target="_blank">http://code.google.com/p/annotation-ontology/wiki/AnnotationTypes</a><br>
<br>
Best<br>
<font color="#888888"><br>
Tim<br>
</font>
<div>
<div class="h5"><br>
On Jan 10, 2011, at 11:30 AM, M. Scott Marshall wrote:<br>
<br>
> [Scott dusts off old use case and pulls from the shelf. Adjusts<br>
> subject of thread. Was: best practice for referring to PDF]<br>
><br>
> In Health Care and Life Science domains, image data is a common
form<br>
> of data under discussion so a best practice for referring to an
image<br>
> or to an (extractable) feature *within* an image would cover a<br>
> fundamental need in biomedicine to point to 'raw' data as evidence
(as<br>
> well as giving meaning to the raw data!).<br>
><br>
> A clinical example from breast cancer:<br>
> There is a scan that produces an image that contains features
referred<br>
> to by the radiologist as 'microcalcifications', which can be<br>
> indicative of the presence of a tumor.<br>
><br>
> I can think of a few scenarios that would refer to the image data<br>
> (mammogram). There are probably more:<br>
> 1) The radiology report (in RDF) asserts the presence of<br>
> microcalcifications and refers to the entire image as evidence.<br>
> 2) The radiology report (in RDF) asserts the presence of<br>
> microcalcifications and refers to the entire image as evidence,
along<br>
> with a image processing/feature extraction program that will
highlight<br>
> the phenomenon in the image.<br>
> 3) The radiology report (in RDF) asserts the presence of<br>
> microcalcifications and refers to a specific region in the image as<br>
> evidence using some function of a 2D coordinate system such as<br>
> polyline.<br>
><br>
> The question: How can we refer to the microcalcifications as an<br>
> indication of a certain type of tumor in each case 1, 2, and 3 in
RDF?<br>
><br>
> I am especially interested in the 'structural' aspects: How do we<br>
> refer to the image document as containingEvidence ? How can we
refer<br>
> to a *region* of the image in the document? How can we refer to the<br>
> software that will extract the relevant features with statistical<br>
> confidence, etc.?<br>
><br>
> Any ideas or pointers to existing practices would be appreciated.
I'm<br>
> aware of some related work in multimedia to refer to temporal
regions<br>
> but I am specifically interested in spatial regions.<br>
><br>
> Note that an analogous question of practice exists for textual<br>
> documents such as literature in PubMed that can be text-mined for<br>
> (evidence of) assertions.<br>
><br>
> * Note: 2D is a simplification that should come in handy in<br>
> implementations and often deemed necessary, such as thumbnails.<br>
><br>
> -Scott<br>
><br>
> --<br>
> M. Scott Marshall, W3C HCLS IG co-chair, <a moz-do-not-send="true"
href="http://www.w3.org/blog/hcls" target="_blank">http://www.w3.org/blog/hcls</a><br>
> Leiden University Medical Center / University of Amsterdam<br>
> <a moz-do-not-send="true"
href="http://staff.science.uva.nl/%7Emarshall" target="_blank">http://staff.science.uva.nl/~marshall</a><br>
><br>
> On Mon, Jan 10, 2011 at 4:01 PM, Tim Berners-Lee <<a
moz-do-not-send="true" href="mailto:timbl@w3.org">timbl@w3.org</a>>
wrote:<br>
>> It is well to look at and make best practices for the things<br>
>> we have if we don't<br>
>><br>
>> It was the FOAF folks who, initially, instead of using linked
data,<br>
>> used an Inverse Functional Property to uniquely identify<br>
>> someone and then rdfs:seeAlso to find the data about them.<br>
>> So any FOAF browser has to look up the seeAlso or they<br>
>> don't follow any links.<br>
>><br>
>> So tabulator always when looking up x and finding x see:also y
will<br>
>> load y. So must any similar client or any crawler.<br>
>><br>
>> So there is a lot of existing use we would throw away if we<br>
>> allowed rdfs:seeAlso for pointing to things which do not<br>
>> provide data. (It isn't the question of conneg or mime type,<br>
>> that is a red herring. it is whether there is machine-redable<br>
>> standards-based stuff about x).<br>
>><br>
>> Further, we should not make any weaker properties like
seeDocumentation<br>
>> subproperties of see:Also, or they would imply<br>
>> We maybe need a very weak top property like<br>
>><br>
>> mayHaveSomeKindOfInfoAboutThis<br>
>><br>
>> to be the superProperty of all the others.<br>
>><br>
>> One things which could be stronger than seeAlso is definedBy
if it<br>
>> is normally used for data, to point to the definitive ontology.<br>
>> That would then imply seeAlso.<br>
>><br>
>> Tim<br>
><br>
><br>
<br>
</div>
</div>
</div>
<br>
<br clear="all">
<br>
-- <br>
---------------------------------------------------------------<br>
Pete DeVries<br>
Department of Entomology<br>
University of Wisconsin - Madison<br>
445 Russell Laboratories<br>
1630 Linden Drive<br>
Madison, WI 53706<br>
<a moz-do-not-send="true" href="http://www.taxonconcept.org/"
target="_blank">TaxonConcept Knowledge Base</a> / <a
moz-do-not-send="true" href="http://lod.geospecies.org/"
target="_blank">GeoSpecies Knowledge Base</a><br>
<a moz-do-not-send="true" href="http://about.geospecies.org/"
target="_blank">About the GeoSpecies Knowledge Base</a><br>
------------------------------------------------------------<br>
</div>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
VU Station B 351634
Nashville, TN 37235-1634, U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 343-6707
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
</pre>
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