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Re: inDataset (was Notes from today's meeting)

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Tue, 4 Jun 2013 15:05:08 +0200
Message-ID: <CALcEXf4AXYR-g_EK01wMKU0UxQ-eUcpZYBOM+w0wzGiYnS4zDQ@mail.gmail.com>
To: Jerven Bolleman <me@jerven.eu>
Cc: Alasdair J G Gray <Alasdair.Gray@manchester.ac.uk>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>
On Tue, Jun 4, 2013 at 2:40 PM, Jerven Bolleman <me@jerven.eu> wrote:

>
>
>
> On Tue, Jun 4, 2013 at 11:36 AM, Alasdair J G Gray <
> Alasdair.Gray@manchester.ac.uk> wrote:
>
>>
>> On 3 Jun 2013, at 17:51, Michel Dumontier <michel.dumontier@gmail.com>
>> wrote:
>>
>> About void:inDataset I personally don't like it. I suspect it would cost
>>> me a 13% growth in triple size for negligible benefits. This also means
>>> that the dataset description starts to affect the data. Although I could
>>> only present this in the rest / linked data interface and not in the sparql
>>> endpoint. I am worried that I can not put it into the FTP data dump rdf. As
>>> the data item concept does not map 1:1 on a set of triples that are atomic.
>>>
>>>
>> i'm not sure that i completely understand your objection. the primary use
>> of void:inDataset is to link data items to the dataset description, and as
>> such supports linked data applications without looking at the graph for a
>> potential, but un-guaranteed provenance description. Using void:inDataset
>> is normal practice in the RDF / linked data community. It would be strange
>> to not include it in any RDF dataset if you have the dataset description.
>>
>> http://www.w3.org/TR/void/#backlinks
>>
>>
>>
>>> e.g. someone can use just the UniProtKB sequences. Once they did that is
>>> it still the same dataset that I published it as? I don't think so. Which
>>> means uniprot end users need to be careful to remove more triples. Which
>>> why I disagree with alasdair's call for MUST.
>>>
>>>
>> if one wanted to know which version/issue of uniprot that the sequences
>> came from, it would be necessary to provide access to the dataset
>> description. if the void:inDataset predicate is used, the user need not
>> even retrieve that to store locally, as you should provide resolution
>> services to those dataset descriptions.
>>
>>
>> I also do not follow your objection. If you have created a file that
>> contains a subset of the data, then you can declare this to be a subset of
>> the parent-versioned-formatted dataset, ideally with some way of
>> distinguishing the content of the dataset.
>>
> I will try to explain my objections. The fist is the dataset is a set of
> triples while the void:inDataset is a predicate on a single
> resource/entity/subject.
> So as I have 1.4 billion entities I would add 1.4 billion void:inDataset
> triples. Which to me seems like the incorrect thing to do.
>

 we would like to know the provenance of every data item. if you define 1.4
billion entities, then you should provide 1.4 billion links to their
provenance.


>  Well you say you should only add them to the "important" resources and
> then we are down to a 100 million of these statements.
> Yet for users who use slices of our data these void:inDataset triples are
> annoying/misleading especially if they merge them with their own sources.
>
> e.g.
>
> uniref:UniRef100_ up:sequenceFor uniprot:P12345 .
> uniprot:P12345 a up:Protein ;
>                        void:inDataset dataset:uniprot .
> dataset:uniprot dcterms:licence cc:by-sa-v3 .
> uniprot:P12345 .roche:activatedBy secretdrugchemical:1000  .
> secretdrugchemical:1000 void:inDataset top:secret .
>
> Given these triples what is the license for knowledge about
> secretdrugchemical:1000 activating uniprot:P12345?
>
> The dataset description is about a set of data, not single triples so
> single back links seem to me to be the incorrect solution?
>
>
the focus on the assertion(s) is perfectly fine. several mechanisms have
now been proposed; nanopublications [1], micropublications [2] and ovopubs
[3]

[1]
http://www.w3.org/wiki/images/c/c0/HCLSIG$$SWANSIOC$$Actions$$RhetoricalStructure$$meetings$$20100215$cwa-anatomy-nanopub-v3.pdf
[2]http://arxiv.org/abs/1305.3506
[3]http://arxiv.org/abs/1305.6800



>
>
>> From all the scenarios I have encountered, scientists (not just in the
>> healthcare and life sciences) care about where their data has come from and
>> what version it is. As such, we need some way to allow for the linking of
>> data back to the description of the data.
>>
> Of course I don't disagree with the usecase. I disagree with the chosen
> solution because it is on the wrong level of granularity.
>
>
it's not wrong, it's just at a level that you don't want to provide.  We do
it in Bio2RDF, and now each of our data items from Release 2 are linked
accordingly.

m.


>
>> Alasdair
>>
>> Dr Alasdair J G Gray
>> Research Associate
>> Alasdair.Gray@manchester.ac.uk
>> +44 161 275 0145
>>
>> http://www.cs.man.ac.uk/~graya/
>>
>> Please consider the environment before printing this email.
>>
>>
>
>
> --
> Jerven Bolleman
> me@jerven.eu
>



-- 
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com
Received on Tuesday, 4 June 2013 13:05:56 UTC

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