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Re: Scientific Discourse - Call for comments on IG notes

From: Tim Clark <twclark@nmr.mgh.harvard.edu>
Date: Fri, 11 Sep 2009 15:26:17 -0400
Cc: Alexandre Passant <alexandre.passant@deri.org>, HCLS IG <public-semweb-lifesci@w3.org>, Paolo Ciccarese <paolo.ciccarese@gmail.com>, Anita de Waard <a.dewaard@elsevier.com>
Message-Id: <170D7F40-5E10-4B6D-BE21-D6BEABCFC4EE@nmr.mgh.harvard.edu>
To: David Shotton <david.shotton@zoo.ox.ac.uk>
Hi David,

Thanks very much for your helpful and thoughtful comments.

I look forward to seeing you at ISWC and discussing your ideas for  



On Sep 11, 2009, at 1:43 PM, David Shotton wrote:

> Alexandre Passant wrote:
>> Dear HCLS IG members,
>> On behalf of the Scientific Discourse Task Force [1], we are  
>> pleased to announce three notes on the topic of scientific  
>> discourse in HCLS.
>> Hence, we'd like to solicit your comments on the following documents:
>> - SIOC, SIOC Types and Health Care and Life Sciences : http://www.w3.org/2001/sw/hcls/notes/sioc/
>> - Semantic Web Applications in Neuromedicine (SWAN) Ontology : http://www.w3.org/2001/sw/hcls/notes/swan/
>> - SWAN/SIOC: Alignment Between the SWAN and SIOC Ontologies : http://www.w3.org/2001/sw/hcls/notes/swansioc/
>> We'd be glad if you can provide feedback - if any - by replying to  
>> this e-mail before the 15th of September (i.e. two weeks from now).
>> Thanks a lot,
>> Regards
>> Alex. and Paolo
> Dear Alex and Paolo,
> Greetings (since I have not met either of you to date).  Please find  
> below my feedback on your excellent work.
> A: Changes to the documents themselves
> SIOC, SIOC Types and Health Care and Life Sciences and SWAN/SIOC:  
> Alignment Between the SWAN and SIOC Ontologies
> No comments, other than that both documents read well.
> Semantic Web Applications in Neuromedicine (SWAN) Ontology
> Most of this document reads well and is clearly intelligible.   
> However, the English falls apart in a few places.  I attach a Word  
> document (if you will forgive me!) using Track Changes to show  
> proposed corrections.
> B: Issues for further consideration
> Semantic Web Applications in Neuromedicine (SWAN) Ontology - Section  
> 4:
> "citations: it covers the requirements of the SWAN applictions but  
> could be swapped with another ontology for representing  
> bibliographic records such as the Bibliographic Ontology [BIBO]. "
> Yes, indeed.  Your "citations" have many overlaps with BIBO classes,  
> and need to be harmonized.  However, what you describe as  
> "citations" are what I describe as "cited works".  Para 1.1 from my  
> paper on CiTO, the Citation Typing Ontology (attached), reads:
> What is meant by a citation
> In the context of the Citation Typing Ontology, a bibliographic  
> citation is a reference within a particular citing work of another  
> publication (e.g. a journal article, a book chapter or a web page)  
> termed the cited work. This use of the word ‘citation’ should be  
> distinguished from the common related use of this word to indicate  
> the cited work itself. Within CiTO, ‘cite’ and 'citation' denote the  
> performative act of citation itself, not the target of the citation.
> Is it possible for you to change SWAN to refer to "cited works"  
> rather than "citations"?
> SWAN/SIOC: Alignment Between the SWAN and SIOC Ontologies - Section  
> 2.1. Alignment between properties
> "In addition to the previous classes, mappings have been defined  
> between different properties of the SWAN Scientific Discourse Module  
> and the SIOC Core Ontology."
> The SWAN Scientific Discourse Module has considerable overlap with  
> the Citation Typing Ontology (CiTO; http://purl.org/net/cito/),  
> although their purposes are subtly different.  Tim Clark, Alan  
> Ruttenberg and I have agreed that we all need to get our heads  
> together over this.  I apologise that over the last several weeks I  
> have been preoccupied with planning and running last week's  
> Standardization Workshop for MIIDI, a Minimal Information standard  
> for reporting an Infectious Disease Investigation (for rough pre- 
> release information about that see http://imageweb.zoo.ox.ac.uk/wiki/index.php/MIIDI 
> ).  However, from now on I should have more time to devote to  
> harmonizing CiTO and the SWAN Scientific Discourse Module.  Perhaps  
> we can start this conversation at the upcoming Workshop on Semantic  
> Web Applications in Scientific Discourse at ISWC2009.
> One final point:  Both BIBO and SWAN do not adopt the FRBR  
> (Functional Requirements for Bibliographic Records; http://www.ifla.org/VII/s13/frbr/frbr1.htm 
> ) classification of Work, Expression and Manifestation that I have  
> adopted for CiTO.  As I say  in my CiTO paper:
> CiTO makes a clear distinction between the Work, the Expression of  
> the work, and the Manifestation of that expression, distinctions  
> that are not made by BIBO and SWAN. Despite the clumsiness of this  
> FRBR nomenclature, and the occasional seemingly redundant  
> terminology that results from its use (e.g. Work: Report;  
> Expression: ReportDocument), this level of granularity avoids  
> ambiguities of meaning present in these other ontologies.
> For example, you have the class swansioc:OnlineJournal, which  
> conflated these concepts.  Whether that really matters is something  
> we need to discuss.
> Unfortunately I am at yet another conference on Friday September  
> 18th, so will sadly be unable to participate in the next scientific  
> discourse conference call.  However, please put SWAN-CiTO  
> harmonization on the agenda of work for 2009-10!
> Hope all this is helpful.
> Kind regards to everyone,
> David
> -- 
> Dr David  
> Shotton                                                       david.shotton@zoo.ox.ac.uk
> Reader in Image Bioinformatics
> Image Bioinformatics Research Group                                 http://ibrg.zoo.ox.ac.uk
> Department of Zoology, University of Oxford                  tel:  
> +44-(0)1865-271193
> South Parks Road, Oxford OX1 3PS, UK                    fax: +44-(0) 
> 1865-310447
> <Suggested changes to SWAN working  
> draft.doc><Shotton_ISMB_BioOntology_CiTO_final_postprint.pdf>

Received on Friday, 11 September 2009 19:27:08 UTC

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