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

From: Maryann Martone <maryann@ncmir.ucsd.edu>
Date: Mon, 10 Jan 2011 13:10:47 -0800
Cc: Michael Miller <mmiller@systemsbiology.org>, "M. Scott Marshall" <mscottmarshall@gmail.com>, HCLS <public-semweb-lifesci@w3.org>, public-lod@w3.org, Daniel Rubin <dlrubin@stanford.edu>, "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>, Steve Lamont <spl@ncmir.ucsd.edu>, Willy WaiHo Wong <wawong@sdsc.edu>, Paolo Ciccarese <paolo.ciccarese@gmail.com>, Anita de Waard <A.dewaard@elsevier.com>
Message-Id: <7E8EBAEF-AD31-4736-A36C-6F0BEB5A6F2C@ncmir.ucsd.edu>
To: Tim Clark <tim_clark@harvard.edu>
We have also been working on semantic tagging of image parts, from the  
microscopy realm.  We have been working in this area with our Web  
Image Browser.  This system is designed for annotation of extrememly  
large images coming from light and electron microscopy.  A demo can be  
seen at:

http://ccdb-portal.crbs.ucsd.edu/WebImageBrowser/cgi-bin/start.pl?imagePath=http://ccdb-portal.crbs.ucsd.edu:8081/ZoomifyDataServer/data/MP_23_rec

The annotation creates a simple model of EQ (entity quality) drawing  
on the NIF ontologies through an autocomplete function.  In the "View  
xml" function, you can see the xml that we use to relate the  
annotations to the geometry.  The next step will be to specify these  
geometries in brain coordinates if the data are registered to our  
Whole Brain Catalog (http://wholebraincatalog.org) or some other  
coordinate system.

Maryann


On Jan 10, 2011, at 12:48 PM, Tim Clark wrote:

> Hi Michael,
>
> The default is assumed to be pixels.  Thanks very much for the  
> suggestion regarding GeIML.
>
> Subclasses of AO's Selector class have been worked through in some  
> detail for annotating text, but have not received comparably  
> detailed attention for images.
>
> This is something we are hoping to do in the future, particularly  
> for biomedical imaging.  Collaborators interested in working with us  
> on this topic are welcome.
>
> Kind regards,
>
> Tim
>
>
> On Jan 10, 2011, at 3:28 PM, Michael Miller wrote:
>
>> hi tim and scott,
>>
>> in looking at the ImageSelector, i'm surprised there are no units
>> specifically specified, either as a default or as a property.  are  
>> they
>> assumed to be pixels?
>>
>> also, you might want to take a look at GelML
>> (http://psidev.info/index.php?q=node/448) for a bit more  
>> sophisticated way
>> to specify a position.  the specification allows four different  
>> types of
>> basic shapes: BoundaryChain, BoundaryPointSet, Circle, and Rectangle.
>> altho it's an XML Schema spec, it should be easy enough to  
>> translate to
>> RDF.
>>
>> cheers,
>> michael
>>
>>
>>> -----Original Message-----
>>> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-
>>> lifesci-request@w3.org] On Behalf Of Tim Clark
>>> 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
>>>>
>>>> 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
>>>>
>>>>
>>>
>>
>>
>




Maryann Martone
Professor-In-Residence
Dept of Neurosciences
University of California, San Diego
San Diego, CA  92093-0446
Tel:  858 822 0745
Fax:  858 822 3610
Received on Monday, 10 January 2011 21:12:33 UTC

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