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Re: About FaBiO and CiTO

From: Silvio Peroni <silvio.peroni@unibo.it>
Date: Fri, 15 Jan 2016 07:57:25 +0100
CC: Eric Stephan <ericphb@gmail.com>, <public-dwbp-comments@w3.org>
Message-ID: <3CDBE7B7-D787-4EA4-B7AE-9AD58C228E3C@unibo.it>
To: Bernadette Farias Lóscio <bfl@cin.ufpe.br>
Hi Bernardette, all,

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

Thanks, it’s been my pleasure.

> 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

That’s what I was thinking about when I wrote that email to you indeed.

> -  the object property cito:hasCitingEntity was included to connect cito:CitationAct and frbr:Work 

I would suggest a slightly small modification here. 

In the FRBR spec, the part/partOf relations are possible only with entities of the same type: work with work, expression with expression, manifestation with manifestation, and item with item. Now, a biro:BibliographicReference is indeed a piece of text within a larger document, and clearly refers to the FRBR expression level (which is the one responsible for the actual content of a document). Thus, the frbr:part relation in the diagram at [1] should be from a FRBR expression to the biro:BibliographicReference.

In addition to that, since the whole DUV W3C spec is about data citation, I also would suggest to adopt fabio:Expression instead of frbr:Expression, since the former class has been appropriately developed for the scholarly domain and includes the restrictions I’ve mentioned above for frbr:part/frbr:partOf, which are not present in the original FRBR RDFS vocab in [2]. If you go to the fabio:Expression documentation [3], you can also see the several subclasses it has, that basically address the main part of the scholarly publication types.

Thus, to my personal view, the modification should become:

- the object property cito:hasCitingEntity was included to connect cito:CitationAct and fabio:Expression 

What do you think?

Thanks again for involving me in this.
Have a nice day :-)

S.

[1] - https://drive.google.com/file/d/0BxTZf3B9yQ3oNDJoUFBvRHR5cUU/view?usp=sharing <https://drive.google.com/file/d/0BxTZf3B9yQ3oNDJoUFBvRHR5cUU/view?usp=sharing> 
[2] - http://vocab.org/frbr/core <http://vocab.org/frbr/core> 
[3] - http://www.essepuntato.it/lode/http://purl.org/spar/fabio#http://purl.org/spar/fabio/Expression <http://www.essepuntato.it/lode/http://purl.org/spar/fabio#http://purl.org/spar/fabio/Expression> 

> 
> The current diagram is available here [1]. Please feel free to make comments and suggestions. 
> 
> Many thanks again!
> Bernadette
> 
> 
> 
> 
> 
> 
> 
> 2015-12-29 4:11 GMT-03:00 Eric Stephan <ericphb@gmail.com <mailto: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 <http://libguides.lib.msu.edu/citedata> 
> [2] http://einstein.library.emory.edu/citations_general.html <http://einstein.library.emory.edu/citations_general.html>
> [3] http://www.icpsr.umich.edu/icpsrweb/content/datamanagement/citations.html <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 <mailto: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/ <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 <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/ <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/ <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 <tel:%2B39%20051%202094871>
> E-mail: silvio.peroni@unibo.it <mailto:silvio.peroni@unibo.it>
> Web: http://www.essepuntato.it <http://www.essepuntato.it/>
> Twitter: essepuntato
> 
> 
> 
> 
> 
> -- 
> Bernadette Farias Lóscio
> Centro de Informática
> Universidade Federal de Pernambuco - UFPE, Brazil
> ----------------------------------------------------------------------------



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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
Received on Friday, 15 January 2016 07:01:50 UTC

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