- 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) CONFIDENTIALITY NOTICE: This message is intended only for the addressee(s), may contain information that is considered to be sensitive or confidential and may not be forwarded or disclosed to any other party without the permission of the sender. 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