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Re: Scientific Discourse - Call for comments on IG notes

From: David Shotton <david.shotton@zoo.ox.ac.uk>
Date: Fri, 11 Sep 2009 18:43:55 +0100
Message-ID: <4AAA8C5B.7060307@zoo.ox.ac.uk>
To: Alexandre Passant <alexandre.passant@deri.org>
CC: HCLS IG <public-semweb-lifesci@w3.org>, Tim Clark <twclark@nmr.mgh.harvard.edu>, Paolo Ciccarese <paolo.ciccarese@gmail.com>, Anita de Waard <a.dewaard@elsevier.com>
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 
<http://www.w3.org/2001/sw/hcls/notes/swan/#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 
<http://swan.mindinformatics.org/spec/1.2/scientificdiscourse.html> 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,



Dr David Shotton                                                      
 david.shotton@zoo.ox.ac.uk <mailto:mailto:david.shotton@zoo.ox.ac.uk>
Reader in Image Bioinformatics

Image Bioinformatics Research Group                                 
Department of Zoology, University of Oxford                  tel: 
South Parks Road, Oxford OX1 3PS, UK                    fax: 

Received on Monday, 14 September 2009 08:51:34 UTC

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