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Re: linking a symbol with a dataset

From: Anders Riutta <anders.riutta@gladstone.ucsf.edu>
Date: Mon, 22 Dec 2014 11:24:51 -0800 (PST)
To: w3c semweb hcls <public-semweb-lifesci@w3.org>
Message-ID: <245679035.9641614.1419276291530.JavaMail.zimbra@gladstone.ucsf.edu>
To follow up, it appears the decision reached regarding linking a symbol with a dataset is to add two new terms to SIO: 

    * http://semanticscience.org/resource/has-data-item 
    * http://semanticscience.org/resource/is-data-item-in 
Anders Riutta 

----- Original Message -----

> From: "Jim McCusker" <mccusj@rpi.edu>
> To: "Michel Dumontier" <michel.dumontier@gmail.com>, "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>
> Sent: Thursday, December 11, 2014 11:48:14 AM
> Subject: Re: linking a symbol with a dataset

> FRBR has a partOf relation: http://vocab.org/frbr/core#partOf

> It's domain and range are Endeavour, which is defined as "A class whose
> members are any of the products of artistic or creative endeavour."

> An RDF graph definitely counts (I would use Expression to talk about an
> abstract graph, see
> http://rd.springer.com/chapter/10.1007%2F978-3-642-34222-6_5#page-1 or
> http://tw.rpi.edu/web/doc/mccusker2012ipaw ) and a triple should also count
> (especially if it's considered a subgraph).

> Jim

> On Thu Dec 11 2014 at 2:35:47 PM Michel Dumontier <
> michel.dumontier@gmail.com > wrote:

> > 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 Monday, 22 December 2014 19:25:16 UTC

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