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Re: About FaBiO and CiTO

From: Eric Stephan <ericphb@gmail.com>
Date: Thu, 14 Jan 2016 23:40:20 -0800
Message-ID: <CAMFz4jhtiEK_o8nGdSfYUgLQGHKZHJBiB_UkzLSVdX-qMVneOQ@mail.gmail.com>
To: Silvio Peroni <silvio.peroni@unibo.it>
Cc: Bernadette Farias Lóscio <bfl@cin.ufpe.br>, public-dwbp-comments@w3.org
Thank you again Dr Peroni for invaluable help.  Please look at the link to
model Bernadette provided earlier, I made updates based on your
recommendations.  I hope your guidance is captured accurately.


Eric S.

On Thu, Jan 14, 2016 at 10:57 PM, Silvio Peroni <silvio.peroni@unibo.it>
wrote:

> 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
>
> [2] - http://vocab.org/frbr/core
> [3] -
> 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>:
>
>> 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
>
> ----------------------------------------------------------------------------
>
>
>
>
>
> ----------------------------------------------------------------------------
> 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 07:40:48 UTC

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