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Re: [linkedlifew3cnote] Re: Linkset Provenance

From: Claus Stie Kallesøe <clausstiekallesoe@gmail.com>
Date: Thu, 16 Jun 2011 18:40:05 +0200
To: linkedlifedatapracticesnote@googlegroups.com, Helena Deus <helenadeus@gmail.com>
Cc: Claus Stie Kallesøe <CSH@lundbeck.com>, HCLS <public-semweb-lifesci@w3.org>, Anja Jentzsch <anja@anjeve.de>
Message-Id: <1308242405.3983.5.camel@Nokia-N900-51-1>
Thanks lena, very helpful

claus
----- Original meddelelse -----
> Hi Claus, all
> 
> Lately I have been preferring the second option, for
> provenance/attribution issues   - I want to be able to separate my list
> of instances of a class from the list of instances defined somewhere
> else. A neat way to do that is to say that
> < "drugX" rdf:type myshema:drug > and then somewhere else state that
> < myschema:drug owl:sameAs someother:drug >.
> 
> A triple store with inference like owlim is able to return "drugX" either
> when I ask for ?drug rdf:tpe myschema:drug OR ?drug rdf:type
> someother:drug
> 
> Best
> Lena
> 
> 
> 
> On Thu, Jun 16, 2011 at 3:18 PM, M. Scott Marshall
> <mscottmarshall@gmail.com
> > wrote:
> 
> > Hi Claus,
> > [bouncing this to the list because I think this is of general interest
> > and there is plenty of expertise there]
> > 
> > This is where many get stuck. Happily, you are not the first one
> > looking for specific classes/terms that match your data although there
> > are plenty of areas of ontological usage that still need clarification
> > and improvement.
> > 
> > In TMO, we selected from a number of existing ontologies as much as we
> > could and filled in where we couldn't find the right fit. See the
> > attached image for an overview of the structure. TMO is also available
> > from Bioportal.
> > 
> > See also, the NCBO Ontology Recommender as a place to get started.
> > 
> > http://www.bioontology.org/ontology-recommender
> > 
> > http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Client_Examples
> > 
> > -Scott
> > 
> > --
> > M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
> > http://staff.science.uva.nl/~marshall
> > 
> > On Thu, Jun 16, 2011 at 3:35 PM, Claus Stie Kallesøe
> > <CSH@lundbeck.com>wrote:
> > 
> > > Ok, now I am ready.
> > > 
> > > I will try to follow your steps so starting by creating an ontology
> > > for LudnebckResearch (compound, batch, assay, project, scientist
> > > etc).
> > > 
> > > I will use TopBraid composer. Its comprehensive (protege seems even
> > > harder) but I think I have worked out what parts I need and from the
> > > neologism site I found this - which is actually really helpful in
> > > order to understand what it is and what it is not!:
> > > 
> > > ----
> > > Neologism is no ontology editor. If you want to build large and
> > > complex domain ontologies, if you need the full power of OWL, or if
> > > you need sophisticated reasoning services, consider applications
> > > such as TopBraid Composer, Protégé, or the NeOn Toolkit. Neologism
> > > is designed for the simpler space of RDF vocabularies. OWL
> > > ontologies tend to be about modelling a domain with the formal
> > > language of logics; RDF vocabularies thend to be about exchanging
> > > and integrating data between systems and on the Web.
> > > 
> > > ----
> > > 
> > > So when building an ontology i am thinking of something like
> > > lundbeck:compound; lundbeck:scientist etc. As an overall research
> > > ontology. I will then link these to the specifics in the relational
> > > databases like lundbeck:compound SKOS:narrowmatch/OWL:sameAs
> > > ddis:compound (ddis being one of the databases I have mapped with
> > > D2R). This is all the Phil approach.
> > > 
> > > But as many of the concepts are known outside lundbeck (and we migth
> > > want to link to that later) should I instead use something like this:
> > > http://bioportal.bioontology.org/ontologies/45788 as "chemical
> > > entities of biologicalinterest" is what I have? Or should I create
> > > my own and then later do lundbeck:compound OWL:sameAS chebi:compound
> > > or similar?
> > > 
> > > Remember the best practices paper several times mentioned always to
> > > reuse....
> > > 
> > > Ok, my last question for today.
> > > 
> > > claus
> > > 
> > > 
> > > 
> > > -----Original Message-----
> > > From: Anja Jentzsch [mailto:anja@anjeve.de]
> > > Sent: Thursday, June 16, 2011 12:51 PM
> > > To: Claus Stie Kallesøe
> > > Cc: M. Scott Marshall
> > > Subject: Re: Linkset Provenance
> > > 
> > > > I had a look here:
> > > > http://www4.wiwiss.fu-berlin.de/latc/toollibrary/example.php
> > > > 
> > > > That might actually be some of the things I have been looking for.
> > > > What tools to use for what, in what order and how to put it
> > > > together. Anja, this also describes what to do with the link
> > > > descriptions from Silk ;-)
> > > 
> > > I wrote this tutorial and it is exactly what I described yesterday ;)
> > > Probably I didn't put it specific enough.
> > > 
> > > Anja
> > > 
> > > > I will try to set something like this up to play
> > > > 
> > > > c
> > > > 
> > > > -----Original Message-----
> > > > From: Anja Jentzsch [mailto:anja@anjeve.de]
> > > > Sent: Wednesday, June 15, 2011 6:02 PM
> > > > To: Claus Stie Kallesøe
> > > > Cc: M. Scott Marshall
> > > > Subject: Linkset Provenance
> > > > 
> > > > I just put this on IRC but you're already gone:
> > > > 
> > > > 17:00 Anja       I wonder if it makes sense to have provenance data
> > > > on the
> > > linksets provided via D2R as a plugin as well
> > > > 17:00 Anja       this would cover the concerns Scott was talking about
> > > 
> > > 
> > 
> > 
> > --
> > M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
> > http://staff.science.uva.nl/~marshall
> > 
> > 
> 
> 
> -- 
> Helena F. Deus
> Post-Doctoral Researcher at DERI/NUIG
> http://lenadeus.info/
Received on Thursday, 16 June 2011 16:40:42 UTC

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