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Re: About FaBiO and CiTO

From: Bernadette Farias Lóscio <bfl@cin.ufpe.br>
Date: Thu, 14 Jan 2016 18:05:53 -0300
Message-ID: <CANx1Pzzx+oyBr5MtfGySHh=mAaGDuV7zvPAohxABf-fV2VN0XA@mail.gmail.com>
To: Eric Stephan <ericphb@gmail.com>
Cc: Silvio Peroni <silvio.peroni@unibo.it>, public-dwbp-comments@w3.org
Hello Dr. Peroni,

I am one of the DUV co-authors and I'd like to say that we really
appreciate your feedback.

We have discussed some of your questions about the meaning of the
duv:DataCitation class and  our idea was to use duv:dataCitation as a
"bibliographic reference contained in an entity, e.g., a paper (i.e., the
citing paper), to a particular dataset". So, considering the example that
you gave, we made the following changes:

-  the class duv:DataCitation was replaced by the class
biro:BibliographicReference
-  the object property cito:hasCitingEntity was included to connect
cito:CitationAct and frbr:Work

The current diagram is available here [1]. Please feel free to make
comments and suggestions.

Many thanks again!
Bernadette

[1]
https://drive.google.com/file/d/0BxTZf3B9yQ3oNDJoUFBvRHR5cUU/view?usp=sharing





2015-12-29 4:11 GMT-03:00 Eric Stephan <ericphb@gmail.com>:

> Hi Dr Peroni,
>
> >>I’m just wondering right now… I don’t know what is the right meaning of
> the duv:DataCitation class, but I think two alternatives are possible:
>
> >> 1. it is a bibliographic reference contained in an entity, e.g., a
> paper (i.e., the citing paper), to a particular dataset, which is then
> characterised by a text that, in some way, refers to the actual cited
> dataset;
> >>2. it is the actual dataset that is cited by the citing entity.
>
> Thank you once again for your valuable feedback.  To help provide you with
> a better perspective or our rationale for the DataCitation class it was an
> attempt to ensure we had all of the essential citation information for
>  datasets based on common requirements[1][2][3] .  To me, properties of the
> DataCitation class could be capable of being expressed as a reference in a
> journal article or as a metadata record. The attempt was to support a dual
> purpose.
>
> From the helpful examples you provided below, I'm using this as guidance
> as to how we can achieve the above reusing the SPAR ontologies as you have
> illustrated.  I'll send an update to the vocabulary based on your feedback
> and send you an email so that you can review our latest updates.
>
>
> Many thanks again,
>
> Eric Stephan
>
> References
> [1] http://libguides.lib.msu.edu/citedata
> [2] http://einstein.library.emory.edu/citations_general.html
> [3]
> http://www.icpsr.umich.edu/icpsrweb/content/datamanagement/citations.html
>
>
> On Wed, Dec 23, 2015 at 2:24 PM, Silvio Peroni <silvio.peroni@unibo.it>
> wrote:
>
>> Dear Eric,
>>
>> Thank you so much for your kind response and very helpful guidance on the
>> use of SPAR ontologies.  Our citation model is very fluid at this point
>> where it is easy to make changes and I would prefer making changes based on
>> your recommendations prior to our request for comments in early January.
>>
>>
>> That’s great!
>>
>> We did look at biro:BibliographicRecord at one point but weren't sure
>> about its use.  I'll look over this, if we find additional properties that
>> are not in the scope of biro:BibliographicRecord I am wondering if our
>> additional properties could serve as requests for additional properties
>> within BIRO?  If we did use this I'd have to ask our other co-editors about
>> the use of FaBIO:work.
>>
>>
>> I’m just wondering right now… I don’t know what is the right meaning of
>> the duv:DataCitation class, but I think two alternatives are possible:
>>
>> 1. it is a bibliographic reference contained in an entity, e.g., a paper
>> (i.e., the citing paper), to a particular dataset, which is then
>> characterised by a text that, in some way, refers to the actual cited
>> dataset;
>> 2. it is the actual dataset that is cited by the citing entity.
>>
>> If 1) is true, then it seems quite odd to me that a reference has a title
>> and other attributes typically related with a proper bibliographic
>> resource: they are actually attributes of the referenced work. In SPAR,
>> that scenario could be modelled by means of the class
>> bibo:BibliographicReference and the classes fabio:Work and fabio:Expression
>> (or one of their subclasses). For instance, suppose that we have a paper A
>> citing a dataset B by using the following bibliographic reference:
>>
>> Doe, J. (2015). The example dataset to cite. Version 1, Sept 15, 2015.
>> DOI: 10.3456/4567.21
>>
>> Then, in SPAR, a good way for modelling this will be (I’m using Turtle
>> now):
>>
>> :dataset-b a fabio:Dataset , dcat:Dataset ;
>> dcterms:title "The example dataset to cite" ;
>> prism:doi "10.3456/4567.21" ;
>> dcterms:creator :j-doe ;
>> frbr:realization :dataset-b-v1 .
>>
>> :dataset-b-v1 a fabio:Expression ;
>> pav:version "Version 1" ;
>> prism:publicationDate "2015-09-15"^^xsd:date .
>>
>> :paper-a-work a fabio:ResearchPaper ;
>> frbr:realization :paper-a-expression .
>>
>> :paper-a-expression a fabio:JournalArticle ;
>> frbr:part :reference-to-dataset-b .
>>
>> :reference-to-dataset-b a biro:BibliographicReference, duv:DataCitation ;
>> dcterms:bibliographicCitation "Doe, J. (2015). The example dataset to
>> cite. Version 1, Sept 15, 2015. DOI: 10.3456/4567.21" ;
>> biro:references :dataset-b-2015-04-01 .
>>
>> :paper-a-cites-dataset-b a cito:CitationAct ;
>> cito:hasCitingEntity :paper-a-expression ;
>> cito:hasCitedEntity :dataset-b-v1 .
>>
>> As you can see, the title, the DOI, etc., are not attributes of the
>> bibliographic reference included in the citing paper, but are attributes of
>> the actual cited dataset. Note that I’ve used pav:version (
>> http://pav-ontology.github.io/pav/) for indicating the version number
>> here because dcterms:hasVersion actually relates two resources rather than
>> a resource with a literal. Note that here the duv:hasWork has been replaced
>> by frbr:part (in the other direction, but also frbr:partOf exist in case it
>> is needed).
>>
>> Another note: when we speak about citations, expressions (in terms of
>> FaBiO/FRBR ontological entities) should always exist, since they actually
>> define the actual content of a paper/dataset rather than its pure essence
>> (i.e., the FaBiO/FRBR work). Citations, in our scenarios, should exist only
>> when they are explicitly created by means of a text. That’s why I’ve used
>> fabio:Expression and fabio:JournalArticle (which is a subclass of
>> fabio:Expression) as proper entities linked to the related works (i.e.,
>> fabio:ResearchPaper and fabio:Dataset, that are subclasses of fabio:Work).
>>
>> On the other hand, if the alternative 2) is true, then, we can avoid the
>> explicit specification of such :reference-to-dataset-b, and consider our
>> duv:DataCitation as the dataset (actually, a particular version of a
>> dataset) cited. But then I’m not sure duv:DataCitation is actually a good
>> name, it may be just fabio:Expression.
>>
>> It might interest you as well that we are looking at several non-semantic
>> vocabularies expressed in XML (
>> https://www.force11.org/sites/default/files/d7/project/882/citing-data-in-jats-2015-06.pdf)
>>
>>
>>
>> I’ve done a bit of work on JATS to SPAR conversion (see [1] for more
>> details), and, while the mapping is always possible, it is not so direct as
>> one can guess. I didn’t know about this new spec from Debbie, but it seems
>> a very good XML spec to me, thanks.
>>
>> and JSON (e.g. http://okfnlabs.org/bibjson/) and the BFO/IBO/IAO
>> ontology suite .
>>
>>
>> I know them, but honestly not an expert yet.
>>
>>   I'd like to attempt map citation classes from the SPAR vocabularies to
>> these within the scope of DUV to get buy-in about our approach in other
>> metadata communities.  If you are aware of any work like this and can let
>> us know, please let me know.
>>
>>
>> Beside the JATS to SPAR work, I don’t have any. However, I would be
>> interested in working on the mapping between BibJSON and SPAR indeed…
>>
>> I hope it may help.
>> Have a nice day :-)
>>
>> S.
>>
>>
>> # Rererences
>> 1. Peroni, S., Lapeyre, D. A., Shotton, D. (2012). Mapping JATS to RDF
>> using the SPAR (Semantic Publishing and Referencing) Ontologies. In
>> Proceeding of the Journal Article Tag Suite Conference 2012 (JATS-Con
>> 2012). Bethesda, Maryland, USA: National Center for Biotechnology
>> Information. http://www.ncbi.nlm.nih.gov/books/NBK100491/
>>
>>
>>
>>
>> ----------------------------------------------------------------------------
>> Silvio Peroni, Ph.D.
>> Department of Computer Science and Engineering
>> University of Bologna, Bologna (Italy)
>> Tel: +39 051 2094871
>> E-mail: silvio.peroni@unibo.it
>> Web: http://www.essepuntato.it
>> Twitter: essepuntato
>>
>>
>


-- 
Bernadette Farias Lóscio
Centro de Informática
Universidade Federal de Pernambuco - UFPE, Brazil
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Received on Thursday, 14 January 2016 21:06:44 UTC

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