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Re: linking a symbol with a dataset

From: Michel Dumontier <michel.dumontier@gmail.com>
Date: Thu, 11 Dec 2014 11:33:16 -0800
Message-ID: <CALcEXf4GJkgZXrrRan8kXEaDcp2NgrJed_TY_PFr8+_qpvkomw@mail.gmail.com>
To: Anders Riutta <anders.riutta@gladstone.ucsf.edu>
Cc: snachimuthu@mmm.com, Vladimir Mironov <vladimir.n.mironov@gmail.com>, w3c semweb hcls <public-semweb-lifesci@w3.org>
Thanks for this suggestion Anders. I'm somewhat concerned about the
semantics of schema.org, but it's clear that there could be a mapping
from something more precise to schema.org.

m.
Michel Dumontier
Associate Professor of Medicine (Biomedical Informatics), Stanford University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com


On Wed, Dec 10, 2014 at 5:55 PM, Anders Riutta
<anders.riutta@gladstone.ucsf.edu> wrote:
> The property "hasPart" for schema:Dataset [1] doesn't have the problem with disjoint type, as long as you consider a protein a "CreativeWork".
>
> Anders Riutta
>
> [1] http://schema.org/Dataset
>
> ----- Original Message -----
>> From: snachimuthu@mmm.com
>> To: "Vladimir Mironov" <vladimir.n.mironov@gmail.com>
>> Cc: "Michel Dumontier" <michel.dumontier@gmail.com>, "w3c semweb hcls" <public-semweb-lifesci@w3.org>
>> Sent: Tuesday, December 9, 2014 2:36:10 PM
>> Subject: Re: linking a symbol with a dataset
>>
>> We use "has member" to relate arbitrary groups and their members. Our
>> implementation is for binary relationships in a relational database, and
>> so this should work for RDF too.
>>
>> Senthil.
>>
>>
>> Senthil K. Nachimuthu, MD, PhD | Medical Informaticist
>> 3M Health Information Systems, Inc.
>> 575 W Murray Blvd, Murray, UT 84123, USA
>> Office: +1 801 265 4636
>> snachimuthu@mmm.com | www.3mtcs.com
>>
>>
>>
>>
>> From:   Vladimir Mironov <vladimir.n.mironov@gmail.com>
>> To:     Michel Dumontier <michel.dumontier@gmail.com>
>> Cc:     w3c semweb hcls <public-semweb-lifesci@w3.org>
>> Date:   12/09/2014 03:20 PM
>> Subject:        Re: linking a symbol with a dataset
>>
>>
>>
>> Hi Michel,
>>
>> as everybody knows, atomic means 'indivisible'. In the world of Nature, of
>> course, there is nothing atomic.
>> However, in the world of RDF subject, predicate, and object are atomic -
>> there are no other concepts these three could be subdivided into.
>> I haven't seen such a property so far in vocabularies, I proposed it
>> because  you guys could not find anything suitable for the task.
>> I feel it serves the purpose and nothing may prevent you from introducing
>> a new property in want of appropriate ones. This one should be, of course,
>> a subProperty of 'partOf'.
>>
>> Cheers
>>
>> On 9 December 2014 at 19:36, Michel Dumontier <michel.dumontier@gmail.com>
>> wrote:
>> Hi Vladimir,
>>   Can  you elaborate with a definition for 'isAtomicPartOf'?  Is this
>> already defined in a vocabulary?
>>
>> m.
>> Michel Dumontier
>> Associate Professor of Medicine (Biomedical Informatics), Stanford
>> University
>> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
>> Group
>> http://dumontierlab.com
>>
>>
>> On Tue, Dec 9, 2014 at 12:33 AM, Vladimir Mironov
>> <vladimir.n.mironov@gmail.com> wrote:
>> > Hi,
>> >
>> > how about 'isAtomicPartOf'?
>> >
>> > Vladimir
>> >
>> > On 8 December 2014 at 18:04, Michel Dumontier <
>> michel.dumontier@gmail.com>
>> > wrote:
>> >>
>> >> Hi all,
>> >>   On the call today we discussed the issue [1] of linking a symbol in
>> >> a triple (e.g. a subject, a predicate, *or* an object) to a dataset.
>> >> The use case for this is twofold : to provide a direct link between
>> >> data items and their datasets in a Linked Data manner, and to survey
>> >> the use of data items across datasets. While we agreed that using a
>> >> relation such as dc:isPartOf is fairly natural to link the triple
>> >> itself to the dataset, it is much less clear for linking the
>> >> components to the dataset. In Bio2RDF we used void:inDataset, but the
>> >> domain of this relation is a foaf:Document, so it muddies the
>> >> semantics by entailing a possible disjoint type with whatever the
>> >> subject has been typed with (e.g. protein, disease, etc).
>> >>
>> >> We discussed the suitability of existing vocabularies, but none, to
>> >> our knowledge, clearly fit the situation. For instance, can
>> >> dc:isPartOf (http://purl.org/dc/terms/isPartOf) be used as a logical
>> >> partition of the dataset with the data item? or is SIO's refers to
>> >> (http://semanticscience.org/resource/refers-to) potential suitable, if
>> >> not somewhat vague?
>> >>
>> >> We welcome your thoughts on the matter. Do you know of a suitable
>> >> relation? Should we consider some new relation such as utilizes /
>> >> is-utilized-in or is-data-item-in / has-data-item?
>> >>
>> >> Cheers!
>> >>
>> >> m.
>> >>
>> >> [1] https://github.com/joejimbo/HCLSDatasetDescriptions/issues/90
>> >>
>> >> Michel Dumontier
>> >> Associate Professor of Medicine (Biomedical Informatics), Stanford
>> >> University
>> >> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
>> >> Group
>> >> http://dumontierlab.com
>> >>
>> >
>>
>>
Received on Thursday, 11 December 2014 19:34:04 UTC

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