Dear David,

sorry for a bit late response.
By checking better CiTo and the examples on citations, sure we can get 
several ideas on how we may be able to include (as PubMan extension) 
these citations as list.
First to point, that PubMan focus is not on counting citations and 
providing these services. Our plan is to rely on external services for 
this purpose.
PubMan has a citation style manager service - its focus in on formatting 
bibliographic metadata in a specific citation style such as AJP, APA 
etc. - but has no handling of citations, counts and relation types as 
defined in the CiTo ontology.

I could see here basically two separate use cases where PubMan may 
provide some services:

a) export: i.e. users select items for citation list from PubMan that 
can be used as list of references in another publication. PubMan may 
provide the CiTo export format for selected publications such as:

 cito:cites pubMan-Item-ID;
    cito:inTextCitationFrequency [
      a cito:InTextCitationCount ;
      cito:inTextCountValue "XX"^^xsd:integer ;
      cito:inTextCitationTarget <http://dx.doi.org/10.1016/S0140-6736(99)80012-9> ;
    ] ; 
    cito:obtainsBackgroundFrom  pubMan-Item-ID ;
    cito:usesDataFrom pubMan-Item-Id;
    cito:confirms pubMan-Item-Id ;
    cito:extends pubMan-Item-id;      
    cito:sharesAuthorsWith pubMan-Item-Id;  


*(where PubMan-Item-Id is persistent identifier of the PubItem, either DOI - if exists, or Handle - assigned from PubMan)

In this case, users would have ready-made entry which they can actually modify to exact cito:inTextCountValue or 
may remove not needed relation-types such as e.g. cito:sharesAuthorsWith . This use-case does not require any handling of cito relations in PubMan. 

b) allowing manual or automatic (e.g. PDF extraction) creation of CiTo relations/tags for a publication item. 
This in fact is very interesting use case, and at the moment i can not see trouble for PubMan to implement such possibility.
In this case of course, PubMan would provide similar export snippet provided under a) but based on a publication and its cito relations.
In addition, by querying the semantic store component used by PubMan, we could think of some visualization services as well. 


Best,
Natasa 




David Shotton wrote:
> Dear Natasa,
>
> See the  preprint at http://imageweb.zoo.ox.ac.uk/pub/2008/ 
> publications/Shotton_ISMB_BioOntology_CiTO_preprint.pdf 
> <http://imageweb.zoo.ox.ac.uk/pub/2008/publications/Shotton_ISMB_BioOntology_CiTO_preprint.pdf>  
> for a description of CiTO, and see Figure 8 of  David Shotton, Katie 
> Portwin, Graham Klyne and Alistair Miles (2009) Adventures in semantic 
> publishing: exemplar semantic enhancements of a research article. 
> /PLoS Computational Biology/ *5* (4): e1000361./ 
> /http://www.ploscompbiol.org/doi/pcbi.1000361. for an example of its 
> use.  The ontology itself is available at  http://purl.org/net/cito/ - 
> this is very much a work in progress.
>
> David
>
>
>
> Natasa Bulatovic wrote:
>> Dear David,
>>
>> Was greatly surprised that you pay attention to our citation manager 
>> service.
>> Before providing you some proper answer, would like to check a bit on 
>> the CiTo ontology.
>> In general, the tool is very flexible and before we provide proper 
>> answer, will have actually to take a better look into the CiTo ontology.
>> Maybe you can also elaborate with some examples a bit what you mean?
>>
>> Best,
>> Natasa Bulatovic
>>
>>
>>
>>
>> David Shotton wrote:
>>> Dear Colleagues,
>>>
>>> I would like to bring to your attention three articles that I and my 
>>> research group have published in April 2009 on the subject of 
>>> semantic publishing, detailed at 
>>> http://imageweb.zoo.ox.ac.uk/pub/2008/publications/Shotton_Articles_on_Semantic_Publishing.pdf 
>>>
>>>
>>> An excellent critique of what we describe in the first of these 
>>> articles is given by Rod Page at 
>>> http://iphylo.blogspot.com/2009/04/semantic-publishing-towards-real.html, 
>>> in which, in essence, he correctly says we did not go far enough in 
>>> terms of making machine-readable data and metadata available, 
>>> thereby failing to contribute to an ecosystem of  *linked data* 
>>> (http://linkeddata.org/).
>>>
>>> The third article concerns our Citation Typing Ontology, which 
>>> provides a way to provide structured metadata concerning the nature 
>>> and purpose of bibliographic citations and of the cited works.  
>>> Those developing PubMan 
>>> (http://www.escidoc.org/JSPWiki/en/PublicationManagement) may be 
>>> able to comment on whether it might be possible to include a tool 
>>> within PubMan to type citations in this way using the CiTO ontology.
>>>
>>
>>> I hope you find these papers interesting and helpful.
>>>
>>> Kind regards,
>>>
>>> David
>>>
>>> -- 
>>>
>>> Dr David 
>>> Shotton                                                      
>>>  [log in to unmask] <mailto:mailto:[log in to unmask]>
>>> 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
>>>
>>
> -- 
>
> Dr David Shotton                                                      
>  [log in to unmask] <mailto:mailto:[log in to unmask]>
> 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
>

-- 
Natasa Bulatovic
Max Planck Digital Library (MPDL)
Amalienstrasse 33
80799 Munich, Germany
http://www.mpdl.mpg.de

e-Mail: [log in to unmask]
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