Re: Decision on decimal

[Oliver Ruebenacker]

 Hello,

  If you care about precision, why not give the standard error or a
confidence interval?

 Best, Oliver


On Tue, Aug 4, 2015 at 2:42 PM, Anthony Mallia 
wrote:

> Here is where I think we landed today on decimal
>
> fhir:decimal rdf:type owl:Class ;
>  rdfs:subClassOf fhir:Element ,
>  [ rdf:type owl:Restriction ;
>owl:onProperty fhir:fractionDigits ;
>owl:maxQualifiedCardinality
> "1"^^xsd:nonNegativeInteger ;
>owl:onDataRange xsd:nonNegativeInteger
>  ] ,
>  [ rdf:type owl:Restriction ;
>owl:onProperty fhir:fractionDigits ;
>owl:allValuesFrom xsd:nonNegativeInteger
>  ] ,
>  [ rdf:type owl:Restriction ;
>owl:onProperty fhir:value ;
>owl:maxQualifiedCardinality
> "1"^^xsd:nonNegativeInteger ;
>owl:onDataRange xsd:decimal
>  ] ,
>  [ rdf:type owl:Restriction ;
>owl:onProperty fhir:value ;
>owl:allValuesFrom xsd:decimal
>  ] ;
>
>  rdfs:comment "A rational number with defined precision" .
>
> Tony Mallia
>



-- 
Oliver Ruebenacker
Senior Software Engineer, Diabetes Portal
<http://www.type2diabetesgenetics.org/>, Broad Institute
<http://www.broadinstitute.org/>

Re: ACTION: Lloyd to ask James and Ewot about the underlying precision retention of xsd:decimal values

[Oliver Ruebenacker]

 Hello,

  "Java uses BigDecimal"? You mean, it is available in Java. More
relevantly, it is supported by some libs like Sesame (e.g. through
Literal.decimalValue).

 Best, Oliver

On Mon, Aug 3, 2015 at 11:55 PM, David Booth  wrote:

> Regarding the above action, and last week's discussion of xsd:decimal,
> Lloyd reports: "Java uses BigDecimal - so full retention of precision. C#
> uses decimal, which also retains precision."
>
> David Booth
>
>


-- 
Oliver Ruebenacker
Senior Software Engineer, Diabetes Portal
<http://www.type2diabetesgenetics.org/>, Broad Institute
<http://www.broadinstitute.org/>

Re: Good, up-to-date tutorial on OWL 2 and Protege for Biomedical domain?

[Oliver Ruebenacker]

 Hello,

  I tried Protege and TopBraid composer and found both unhelpful. I either
write Turtle with a text editor or write Scala code on top of Sesame that
creates the RDF I need, and I find that to be so much more efficient.
Banana RDF is worth looking into.

  The challenge of building ontologies is not technical, but
socio-political.

  I'd show them some real-world examples of ontologies like BioPAX, SBO,
GO, etc.

 Best, Oliver


On Sat, May 2, 2015 at 5:24 AM, Matthias Samwald <
matthias.samw...@meduniwien.ac.at> wrote:

> Dear all,
>
> I'm about to teach a course to medical informatics students that have
> never used OWL before. Are there any good, up-to-date tutorials or even
> course materials on OWL 2, biomedical ontology building and Protege that
> you could recommend? I was surprised to find that most publicly available
> resources have gathered quite a bit of dust (focused on OWL 1, old versions
> of Protege), or are not very accessible. I'd be especially interested in
> materials that avoid using the Pizza ontology ;)
>
> Thanks,
> Matthias
>
> --
> Assistant Professor
> Center for Medical Statistics, Informatics, and Intelligent Systems
> Medical University of Vienna
> http://samwald.info/
>
>
>


-- 
Oliver Ruebenacker
Solutions Architect at Altisource Labs <http://www.altisourcelabs.com/>
Be always grateful, but never satisfied.

Re: License unknown

[Oliver Ruebenacker]

 Hello,

On Fri, Jun 20, 2014 at 3:44 PM, Joachim Baran 
wrote:

>
> On 20 June 2014 12:41, Oliver Ruebenacker  wrote:
>
>>   Also, makes me wonder why the EBI has not already been contacted and
>> the license determined? Is that because we didn't have the resources to do
>> so or because different end users might end up being granted different
>> licenses?
>>
>   That is my point exactly!
>

>   Even though the licensing information is not available, there is an
> indication where to obtain it from (here, in this example, EBI).
>

  Actually, my point is to first answer the question I asked.

  If not only you don't know the license, but you also don't know why you
don't know, it is indeed hard to say anything about the license.

  If all you want to say is who grants the license, you might want to
consider something like:

  ex:myData   ex:canBeLicensedForEndUseBy   ex:EBI

 Best,
 Oliver

-- 
Oliver Ruebenacker
Founder at Relomics Consulting <http://www.relomics.com>
Be always grateful, but never satisfied.

Re: License unknown

[Oliver Ruebenacker]

gt;>> >> >> > dusty_data a dct:Dataset .
>>> >> >> > dusty_data dct:license cc:zero .
>>> >> >> >
>>> >> >> > And puts all those triples into one store/ontology then queries
>>> will
>>> >> >> > start to return wrong data.
>>> >> >> >
>>> >> >> > SELECT ?datasetWithALicense
>>> >> >> > WHERE {
>>> >> >> > ?datasetWithALicense dct:license ?license .
>>> >> >> > }
>>> >> >> >
>>> >> >> > Will give 2 bindings for ?dataset and ?license one of them being
>>> >> >> > wrong
>>> >> >> > now.
>>> >> >> >
>>> >> >> > If you ask the same question depending on the better modelling
>>> then
>>> >> >> > you get the correct answer in both cases.
>>> >> >> >
>>> >> >> > SELECT ?datasetWIthoutLicense
>>> >> >> > WHERE {
>>> >> >> > ?datasetWIthoutLicense a dct;Dataset .
>>> >> >> > MINUS ( ?datasetWIthoutLicense dct:license ?license )
>>> >> >> > }
>>> >> >> >
>>> >> >> > SELECT ?datasetWIthALicense
>>> >> >> > WHERE {
>>> >> >> > ?datasetWIthALicense a dct;Dataset .
>>> >> >> > ?datasetWIthALicense dct:license ?license .
>>> >> >> > }
>>> >> >> >
>>> >> >> > Both give the expected results.
>>> >> >> >
>>> >> >> >
>>> >> >> > In general in RDF just state what you know and describe what you
>>> >> >> > don't
>>> >> >> > know.
>>> >> >> >
>>> >> >> > Regards,
>>> >> >> > Jerven
>>> >> >> >
>>> >> >> > On Mon, Jun 2, 2014 at 5:25 PM, Gray, Alasdair J G
>>> >> >> > 
>>> >> >> > wrote:
>>> >> >> >
>>> >> >> > Hi,
>>> >> >> >
>>> >> >> > I am working to help shape the Healthcare and Life Sciences
>>> community
>>> >> >> > profile for describing datasets, current version available from
>>> [1]
>>> >> >> >
>>> >> >> > One of our goals is that there is a minimal set of properties
>>> that
>>> >> >> > are
>>> >> >> > available for all datasets, and we would like these properties to
>>> >> >> > include
>>> >> >> > the license. However we have the problem that for several legacy
>>> >> >> > datasets
>>> >> >> > the license is simply unknown. Does anyone know of a resource
>>> that
>>> >> >> > can
>>> >> >> > be
>>> >> >> > used to represent that the license is unknown as the value of a
>>> >> >> > dcterms:license predicate?
>>> >> >> >
>>> >> >> > Thanks
>>> >> >> >
>>> >> >> > Alasdair
>>> >> >> >
>>> >> >> > [1] https://github.com/joejimbo/HCLSDatasetDescriptions
>>> >> >> >
>>> >> >> > Alasdair J G Gray
>>> >> >> > Lecturer in Computer Science, Heriot-Watt University, UK.
>>> >> >> > Email: a.j.g.g...@hw.ac.uk
>>> >> >> > Web: MailScanner has detected a possible fraud attempt from
>>> >> >> > "www.macs.hw.ac.uk" claiming to be
>>> http://www.alasdairjggray.co.uk
>>> >> >> > ORCID: http://orcid.org/-0002-5711-4872
>>> >> >> > Telephone: +44 131 451 3429
>>> >> >> > Twitter: @gray_alasdair
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> > 
>>> >> >> >
>>> >> >> > Sunday Times Scottish University of the Year 2011-2013
>>> >> >> > Top in the UK for student experience
>>> >> >> > Fourth university in the UK and top in Scotland (National Student
>>> >> >> > Survey
>>> >> >> > 2012)
>>> >> >> >
>>> >> >> > We invite research leaders and ambitious early career
>>> researchers to
>>> >> >> > join us
>>> >> >> > in leading and driving research in key inter-disciplinary themes.
>>> >> >> > Please
>>> >> >> > see
>>> >> >> > www.hw.ac.uk/researchleaders for further information and how to
>>> >> >> > apply.
>>> >> >> >
>>> >> >> > Heriot-Watt University is a Scottish charity registered under
>>> charity
>>> >> >> > number
>>> >> >> > SC000278.
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> > --
>>> >> >> > Jerven Bolleman
>>> >> >> > m...@jerven.eu
>>> >> >> >
>>> >> >> >
>>> >> >> > Alasdair J G Gray
>>> >> >> > Lecturer in Computer Science, Heriot-Watt University, UK.
>>> >> >> > Email: a.j.g.g...@hw.ac.uk
>>> >> >> > Web: MailScanner has detected a possible fraud attempt from
>>> >> >> > "www.macs.hw.ac.uk" claiming to be
>>> http://www.alasdairjggray.co.uk
>>> >> >> > ORCID: http://orcid.org/-0002-5711-4872
>>> >> >> > Telephone: +44 131 451 3429
>>> >> >> > Twitter: @gray_alasdair
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> > 
>>> >> >> >
>>> >> >> > Sunday Times Scottish University of the Year 2011-2013
>>> >> >> > Top in the UK for student experience
>>> >> >> > Fourth university in the UK and top in Scotland (National Student
>>> >> >> > Survey
>>> >> >> > 2012)
>>> >> >> >
>>> >> >> > We invite research leaders and ambitious early career
>>> researchers to
>>> >> >> > join us
>>> >> >> > in leading and driving research in key inter-disciplinary themes.
>>> >> >> > Please
>>> >> >> > see
>>> >> >> > www.hw.ac.uk/researchleaders for further information and how to
>>> >> >> > apply.
>>> >> >> >
>>> >> >> > Heriot-Watt University is a Scottish charity registered under
>>> charity
>>> >> >> > number
>>> >> >> > SC000278.
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> --
>>> >> >> Jerven Bolleman
>>> >> >> m...@jerven.eu
>>> >> >>
>>> >>
>>> >> --
>>> >> M. Scott Marshall, PhD
>>> >> MAASTRO clinic, http://www.maastro.nl/en/1/
>>> >> http://eurecaproject.eu/
>>> >> http://semantic-dicom.org/
>>> >> https://plus.google.com/u/0/114642613065018821852/posts
>>> >> http://www.linkedin.com/pub/m-scott-marshall/5/464/a22
>>>
>>
>>
>


-- 
Oliver Ruebenacker
Founder at Relomics Consulting <http://www.relomics.com>
Be always grateful, but never satisfied.

Re: License unknown

[Oliver Ruebenacker]

gt;>> >> >> > And puts all those triples into one store/ontology then queries
>>> will
>>> >> >> > start to return wrong data.
>>> >> >> >
>>> >> >> > SELECT ?datasetWithALicense
>>> >> >> > WHERE {
>>> >> >> > ?datasetWithALicense dct:license ?license .
>>> >> >> > }
>>> >> >> >
>>> >> >> > Will give 2 bindings for ?dataset and ?license one of them being
>>> >> >> > wrong
>>> >> >> > now.
>>> >> >> >
>>> >> >> > If you ask the same question depending on the better modelling
>>> then
>>> >> >> > you get the correct answer in both cases.
>>> >> >> >
>>> >> >> > SELECT ?datasetWIthoutLicense
>>> >> >> > WHERE {
>>> >> >> > ?datasetWIthoutLicense a dct;Dataset .
>>> >> >> > MINUS ( ?datasetWIthoutLicense dct:license ?license )
>>> >> >> > }
>>> >> >> >
>>> >> >> > SELECT ?datasetWIthALicense
>>> >> >> > WHERE {
>>> >> >> > ?datasetWIthALicense a dct;Dataset .
>>> >> >> > ?datasetWIthALicense dct:license ?license .
>>> >> >> > }
>>> >> >> >
>>> >> >> > Both give the expected results.
>>> >> >> >
>>> >> >> >
>>> >> >> > In general in RDF just state what you know and describe what you
>>> >> >> > don't
>>> >> >> > know.
>>> >> >> >
>>> >> >> > Regards,
>>> >> >> > Jerven
>>> >> >> >
>>> >> >> > On Mon, Jun 2, 2014 at 5:25 PM, Gray, Alasdair J G
>>> >> >> > 
>>> >> >> > wrote:
>>> >> >> >
>>> >> >> > Hi,
>>> >> >> >
>>> >> >> > I am working to help shape the Healthcare and Life Sciences
>>> community
>>> >> >> > profile for describing datasets, current version available from
>>> [1]
>>> >> >> >
>>> >> >> > One of our goals is that there is a minimal set of properties
>>> that
>>> >> >> > are
>>> >> >> > available for all datasets, and we would like these properties to
>>> >> >> > include
>>> >> >> > the license. However we have the problem that for several legacy
>>> >> >> > datasets
>>> >> >> > the license is simply unknown. Does anyone know of a resource
>>> that
>>> >> >> > can
>>> >> >> > be
>>> >> >> > used to represent that the license is unknown as the value of a
>>> >> >> > dcterms:license predicate?
>>> >> >> >
>>> >> >> > Thanks
>>> >> >> >
>>> >> >> > Alasdair
>>> >> >> >
>>> >> >> > [1] https://github.com/joejimbo/HCLSDatasetDescriptions
>>> >> >> >
>>> >> >> > Alasdair J G Gray
>>> >> >> > Lecturer in Computer Science, Heriot-Watt University, UK.
>>> >> >> > Email: a.j.g.g...@hw.ac.uk
>>> >> >> > Web: MailScanner has detected a possible fraud attempt from
>>> >> >> > "www.macs.hw.ac.uk" claiming to be
>>> http://www.alasdairjggray.co.uk
>>> >> >> > ORCID: http://orcid.org/-0002-5711-4872
>>> >> >> > Telephone: +44 131 451 3429
>>> >> >> > Twitter: @gray_alasdair
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> > 
>>> >> >> >
>>> >> >> > Sunday Times Scottish University of the Year 2011-2013
>>> >> >> > Top in the UK for student experience
>>> >> >> > Fourth university in the UK and top in Scotland (National Student
>>> >> >> > Survey
>>> >> >> > 2012)
>>> >> >> >
>>> >> >> > We invite research leaders and ambitious early career
>>> researchers to
>>> >> >> > join us
>>> >> >> > in leading and driving research in key inter-disciplinary themes.
>>> >> >> > Please
>>> >> >> > see
>>> >> >> > www.hw.ac.uk/researchleaders for further information and how to
>>> >> >> > apply.
>>> >> >> >
>>> >> >> > Heriot-Watt University is a Scottish charity registered under
>>> charity
>>> >> >> > number
>>> >> >> > SC000278.
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> > --
>>> >> >> > Jerven Bolleman
>>> >> >> > m...@jerven.eu
>>> >> >> >
>>> >> >> >
>>> >> >> > Alasdair J G Gray
>>> >> >> > Lecturer in Computer Science, Heriot-Watt University, UK.
>>> >> >> > Email: a.j.g.g...@hw.ac.uk
>>> >> >> > Web: MailScanner has detected a possible fraud attempt from
>>> >> >> > "www.macs.hw.ac.uk" claiming to be
>>> http://www.alasdairjggray.co.uk
>>> >> >> > ORCID: http://orcid.org/-0002-5711-4872
>>> >> >> > Telephone: +44 131 451 3429
>>> >> >> > Twitter: @gray_alasdair
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> > 
>>> >> >> >
>>> >> >> > Sunday Times Scottish University of the Year 2011-2013
>>> >> >> > Top in the UK for student experience
>>> >> >> > Fourth university in the UK and top in Scotland (National Student
>>> >> >> > Survey
>>> >> >> > 2012)
>>> >> >> >
>>> >> >> > We invite research leaders and ambitious early career
>>> researchers to
>>> >> >> > join us
>>> >> >> > in leading and driving research in key inter-disciplinary themes.
>>> >> >> > Please
>>> >> >> > see
>>> >> >> > www.hw.ac.uk/researchleaders for further information and how to
>>> >> >> > apply.
>>> >> >> >
>>> >> >> > Heriot-Watt University is a Scottish charity registered under
>>> charity
>>> >> >> > number
>>> >> >> > SC000278.
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> --
>>> >> >> Jerven Bolleman
>>> >> >> m...@jerven.eu
>>> >> >>
>>> >>
>>> >> --
>>> >> M. Scott Marshall, PhD
>>> >> MAASTRO clinic, http://www.maastro.nl/en/1/
>>> >> http://eurecaproject.eu/
>>> >> http://semantic-dicom.org/
>>> >> https://plus.google.com/u/0/114642613065018821852/posts
>>> >> http://www.linkedin.com/pub/m-scott-marshall/5/464/a22
>>>
>>
>>
>


-- 
Oliver Ruebenacker
Founder at Relomics Consulting <http://www.relomics.com>
Be always grateful, but never satisfied.

Re: License unknown

[Oliver Ruebenacker]

r student experience
> > Fourth university in the UK and top in Scotland (National Student Survey
> > 2012)
> >
> > We invite research leaders and ambitious early career researchers to
> join us
> > in leading and driving research in key inter-disciplinary themes. Please
> see
> > www.hw.ac.uk/researchleaders for further information and how to apply.
> >
> > Heriot-Watt University is a Scottish charity registered under charity
> number
> > SC000278.
> >
> >
> >
> >
> > --
> > Jerven Bolleman
> > m...@jerven.eu
> >
> >
> > Alasdair J G Gray
> > Lecturer in Computer Science, Heriot-Watt University, UK.
> > Email: a.j.g.g...@hw.ac.uk
> > Web: MailScanner has detected a possible fraud attempt from
> > "www.macs.hw.ac.uk" claiming to be http://www.alasdairjggray.co.uk
> > ORCID: http://orcid.org/-0002-5711-4872
> > Telephone: +44 131 451 3429
> > Twitter: @gray_alasdair
> >
> >
> >
> >
> >
> >
> > 
> >
> > Sunday Times Scottish University of the Year 2011-2013
> > Top in the UK for student experience
> > Fourth university in the UK and top in Scotland (National Student Survey
> > 2012)
> >
> > We invite research leaders and ambitious early career researchers to
> join us
> > in leading and driving research in key inter-disciplinary themes. Please
> see
> > www.hw.ac.uk/researchleaders for further information and how to apply.
> >
> > Heriot-Watt University is a Scottish charity registered under charity
> number
> > SC000278.
>
>
>
> --
> Jerven Bolleman
> m...@jerven.eu
>
>


-- 
Oliver Ruebenacker
Founder at Relomics Consulting <http://www.relomics.com>
Be always grateful, but never satisfied.

Re: odML, open metadata markup language

[Oliver Ruebenacker]

 Hello,

  I don't follow their case for making a distinction between data and
metadata.

  Their example "sample rate with which the acquired data has been
recorded" sounds to me like primary data, not metadata.

  As Alan Ruttenberg said before, to many people "metadata" seems to mean
"data I care less about".

 Best,
 Oliver



On Thu, Dec 5, 2013 at 5:44 AM, Carole Goble
wrote:

>
> heard of this?
> http://www.g-node.org/projects/odml
> open metadata markup language
>
> I'm at a workshop where this seems to be the favoured model for organising
> and indexing experiments
>
> Carole
>
> --
> Professor Carole Goble FREng FBCS CITP
> School of Computer Science
> University of Manchester
> Manchester, UK
>
> tel: +44 161 275 6195
> email: carole.go...@manchester.ac.uk
>
>
>


-- 
Oliver Ruebenacker
Director of Computational Biology at PanGenX (http://www.pangenx.com)
Be always grateful, but never satisfied.

Boston Computational Biologists Networking

[Oliver Ruebenacker]

 Hello,

  We have started a Google Group to network all computational biologists
connected to the Greater Boston Area for activities such as:

 (1) Monthly meetings
 (2) Online calendar
 (3) Announcements
 (4) Collaborations

  And you are invited to join: https://groups.google.com/group/bos-comp-bio

 Best,
 Oliver

-- 
Oliver Ruebenacker
Director of Computational Biology at PanGenX (http://www.pangenx.com)
Be always grateful, but never satisfied.

Re: Ontology Visualization with Domains and Ranges

[Oliver Ruebenacker]

 Hello,

  Apparently, Protege's Ontograf can do that, but only if you run it on
Oracle's JVM. Ontograf won't work on OpenJDK's JVM. Pity.

 Best,
 Oliver



On Thu, Oct 10, 2013 at 1:03 PM, Timothy W. Cook  wrote:

> HI Oliver,
>
> It has been awhile since I have used it but I am quite certain you can do
> that.  I suggest that you ask on the Protege list.
>
> HTH,
> Tim
>
>
>
> On Thu, Oct 10, 2013 at 1:48 PM, Oliver Ruebenacker wrote:
>
>>
>>  Hello Timothy,
>>
>>   I am using Protege, but I don't know how to do the kind of
>> visualization I'm looking for in Protege. I know how to make graphs that
>> show class hierarchies, but I don't know how to make graphs that show
>> property domains, ranges and restrictions.
>>
>>  Best,
>>  Oliver
>>
>>
>>
>> On Thu, Oct 10, 2013 at 12:46 PM, Timothy W. Cook  wrote:
>>
>>> Have you tried Protege?
>>> http://protege.stanford.edu/
>>>
>>>
>>>
>>> On Thu, Oct 10, 2013 at 1:33 PM, Oliver Ruebenacker wrote:
>>>
>>>>
>>>>  Hello,
>>>>
>>>>   I'm looking for a tool to visualize ontologies while showing domains
>>>> and ranges of properties, and property restrictions.
>>>>
>>>>   For example, if a property p has domain A and range B, a graph where
>>>> A and B are nodes and p is an edge from A to B would be useful.
>>>>
>>>>   Do you know any such tools? Thanks!
>>>>
>>>>  Best,
>>>>  Oliver
>>>>
>>>> --
>>>> Oliver Ruebenacker
>>>> IT Project Lead at PanGenX (http://www.pangenx.com)
>>>> Be always grateful, but never satisfied.
>>>>
>>>
>>>
>>>
>>> --
>>> MLHIM VIP Signup: http://goo.gl/22B0U
>>> 
>>> Timothy Cook, MSc   +55 21 94711995
>>> MLHIM http://www.mlhim.org
>>> Like Us on FB: https://www.facebook.com/mlhim2
>>> Circle us on G+: http://goo.gl/44EV5
>>> Google Scholar: http://goo.gl/MMZ1o
>>> LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
>>>
>>
>>
>>
>> --
>> Oliver Ruebenacker
>> IT Project Lead at PanGenX (http://www.pangenx.com)
>> Be always grateful, but never satisfied.
>>
>
>
>
> --
> MLHIM VIP Signup: http://goo.gl/22B0U
> 
> Timothy Cook, MSc   +55 21 94711995
> MLHIM http://www.mlhim.org
> Like Us on FB: https://www.facebook.com/mlhim2
> Circle us on G+: http://goo.gl/44EV5
> Google Scholar: http://goo.gl/MMZ1o
> LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
>



-- 
Oliver Ruebenacker
IT Project Lead at PanGenX (http://www.pangenx.com)
Be always grateful, but never satisfied.

Re: Ontology Visualization with Domains and Ranges

[Oliver Ruebenacker]

 Hello Timothy,

  I am using Protege, but I don't know how to do the kind of visualization
I'm looking for in Protege. I know how to make graphs that show class
hierarchies, but I don't know how to make graphs that show property
domains, ranges and restrictions.

 Best,
 Oliver



On Thu, Oct 10, 2013 at 12:46 PM, Timothy W. Cook  wrote:

> Have you tried Protege?
> http://protege.stanford.edu/
>
>
>
> On Thu, Oct 10, 2013 at 1:33 PM, Oliver Ruebenacker wrote:
>
>>
>>  Hello,
>>
>>   I'm looking for a tool to visualize ontologies while showing domains
>> and ranges of properties, and property restrictions.
>>
>>   For example, if a property p has domain A and range B, a graph where A
>> and B are nodes and p is an edge from A to B would be useful.
>>
>>   Do you know any such tools? Thanks!
>>
>>  Best,
>>  Oliver
>>
>> --
>> Oliver Ruebenacker
>> IT Project Lead at PanGenX (http://www.pangenx.com)
>> Be always grateful, but never satisfied.
>>
>
>
>
> --
> MLHIM VIP Signup: http://goo.gl/22B0U
> 
> Timothy Cook, MSc   +55 21 94711995
> MLHIM http://www.mlhim.org
> Like Us on FB: https://www.facebook.com/mlhim2
> Circle us on G+: http://goo.gl/44EV5
> Google Scholar: http://goo.gl/MMZ1o
> LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
>



-- 
Oliver Ruebenacker
IT Project Lead at PanGenX (http://www.pangenx.com)
Be always grateful, but never satisfied.

Ontology Visualization with Domains and Ranges

[Oliver Ruebenacker]

 Hello,

  I'm looking for a tool to visualize ontologies while showing domains and
ranges of properties, and property restrictions.

  For example, if a property p has domain A and range B, a graph where A
and B are nodes and p is an edge from A to B would be useful.

  Do you know any such tools? Thanks!

 Best,
 Oliver

-- 
Oliver Ruebenacker
IT Project Lead at PanGenX (http://www.pangenx.com)
Be always grateful, but never satisfied.

Re: Ontology for Somatic Mutations?

[Oliver Ruebenacker]

 Hello,

  Thanks for all the links, has been very helpful!

 Take care
 Oliver


On Fri, Jul 26, 2013 at 7:17 AM, Phillip Lord
wrote:

>
> In what sense? See if we can generate the description of the karyotype
> from a genome sequence? Or at least compare the two?
>
> I agree that this would be interesting. At the moment, the problem that
> we have is the ISCN string is computationally relatively intractable. In
> most cases, though, the ISCN is all we have: there is no sequence, and
> no biological material.
>
> Phil
>
>
> Karen Eilbeck  writes:
>
> > Hi Phil
> > Nice model of ISCN. We currently allow ISCN strings to be annotated in
> GVF to
> > describe a genome structure. It may be interesting to validate against
> whole
> > genome sequence.
> > --K
> >
> > On Jul 23, 2013, at 5:24 AM, Phillip Lord wrote:
> >
> >
> > To the extent that it helps to answer our use case, co-ordination might
> > be useful; our work on the karyotype is reasonably tightly scoped, and I
> > wish to maintain this.
> >
> > Phil
> >
> >
> > Melissa Haendel mailto:haen...@ohsu.edu>> writes:
> > Hi all, It would be great if we could coordinate these efforts - The
> > genotype work we are doing that Chris Baker mentioned earlier on this
> > thread (see
> >
> http://www.unbsj.ca/sase/csas/data/ws/icbo2013/papers/ec/icbo2013_submission_60.pdf
> > )
> > is already being integrated into the sequence ontology.
> >
> > Cheers,
> > Melissa
> >
> > On Jul 22, 2013, at 10:22 AM, Suzanna Lewis  <mailto:s...@berkeleybop.org><mailto:s...@berkeleybop.org>> wrote:
> >
> > Check out the  Sequence Ontology. It is well-established in the genomics
> community.
> > http://sequenceontology.org/
> >
> > On Jul 22, 2013, at 4:53 PM, Phillip Lord
> > mailto:phillip.l...@newcastle.ac.uk
> ><mailto:phillip.l...@newcastle.ac.uk>>
> > wrote:
> >
> >
> > We are working on a karyotype ontology which describes chromosome
> abnormalities.
> >
> > The first paper is available here which also includes links to the
> ontology.
> >
> > http://arxiv.org/abs/1305.3758
> >
> >
> >
> >
> > Oliver Ruebenacker mailto:cur...@gmail.com> cur...@gmail.com>> writes:
> >
> >Hello,
> >
> > Does any one know of an ontology for somatic mutations (including SNPs,
> > chromosomal abnormalities, etc.)?
> >
> >Take care
> >Oliver
> >
> > --
> > Phillip Lord,   Phone: +44 (0) 191 222 7827
> > Lecturer in Bioinformatics, Email:
> > phillip.l...@newcastle.ac.uk<mailto:phillip.l...@newcastle.ac.uk
> ><mailto:phillip.l...@newcastle.ac.uk>
> > School of Computing Science,
> http://homepages.cs.ncl.ac.uk/phillip.lord
> > Room 914 Claremont Tower,   skype: russet_apples
> > Newcastle University,   twitter: phillord
> > NE1 7RU
> >
> >
> >
> > Dr. Melissa Haendel
> >
> > Assistant Professor
> > Ontology Development Group, OHSU Library
> > http://www.ohsu.edu/library/
> > Department of Medical Informatics and Epidemiology
> > Oregon Health & Science University
> > haen...@ohsu.edu<mailto:haen...@ohsu.edu><mailto:haen...@ohsu.edu>
> > skype: melissa.haendel
> > 503-407-5970
> >
> >
> >
> >
> > --
> > Phillip Lord,   Phone: +44 (0) 191 222 7827
> > Lecturer in Bioinformatics, Email:
> phillip.l...@newcastle.ac.uk<mailto:phillip.l...@newcastle.ac.uk>
> > School of Computing Science,
> http://homepages.cs.ncl.ac.uk/phillip.lord
> > Room 914 Claremont Tower,   skype: russet_apples
> > Newcastle University,   twitter: phillord
> > NE1 7RU
> >
> > Karen Eilbeck
> > Associate Professor
> > Department of Biomedical Informatics, University of Utah
> >
>
> --
> Phillip Lord,   Phone: +44 (0) 191 222 7827
> Lecturer in Bioinformatics, Email:
> phillip.l...@newcastle.ac.uk
> School of Computing Science,
> http://homepages.cs.ncl.ac.uk/phillip.lord
> Room 914 Claremont Tower,   skype: russet_apples
> Newcastle University,   twitter: phillord
> NE1 7RU
>



-- 
Oliver Ruebenacker
IT Project Lead at PanGenX (http://www.pangenx.com)
Be always grateful, but never satisfied.

Ontology for Somatic Mutations?

[Oliver Ruebenacker]

 Hello,

  Does any one know of an ontology for somatic mutations (including SNPs,
chromosomal abnormalities, etc.)?

 Take care
 Oliver

-- 
Head of Systems Biology Task Force at PanGenX (http://www.pangenx.com)
Any sufficiently advanced technology is indistinguishable from magic.

To Smalltalk or not to Smalltalk

[Oliver Ruebenacker]

 Hello,

  OK, since the argument does not seem to refer to any specifics, I figure
it can be used to advocate other technologies as well, such as:

  "I have worked on Smalltalk and systems using Smalltalk for over 40 years
now (and on Smalltalk's "non-OO" predecessors before that). The most
important thing I have learned is that while it is possible to do
object-oriented programming *without* Smalltalk, whatever alternative
technology you choose, you soon feel compelled to add features that make it
look like Smalltalk. I particularly see this whenever someone comes to me
advocating the use of Java. Smalltalk is what it is for a reason, *not*
because we arbitrarily threw something together.

  So it is not that Smalltalk "looks bad" or whatever people might be
saying. It is that other technologies and approaches "fall short" of what
object-oriented programming really needs. Let's not please reinvent things
or shove a round peg in a square hole just because someone prefers curly
braces over angle brackets. Issues like that are not interesting (at all),
and we have more important things to do."

 Take care
 Oliver

On Sun, Jun 23, 2013 at 2:52 PM, Helena Deus  wrote:

> This is the best argument i've ever read in favor of RDF. Fwarding from
> the lod mailing list as it may be interesting to the folks scanning this
> one and not the other
>
>
> Helena F. Deus, PhD
> Senior Scientist, Medical Knowledge Engineering
> Foundation Medicine Inc.
> hd...@foundationmedicine.com
>
>
>
> Begin forwarded message:
>
> *Resent-From: *public-...@w3.org
> *From: *
> *Subject: **To RDF or not to RDF*
> *Date: *June 21, 2013 9:41:56 PM EDT
> *To: *
>
> existing thread, and also for probably saying things other folks have
> already brought up]
>
> I have worked on RDF and systems using RDF for over 15 years now (and on
> RDF's "non-Web" predecessors before that). The most important thing I have
> learned is that while it is possible to do Linked Data and Semantic Web
> stuff *without* RDF, whatever alternative technology you choose, you soon
> feel compelled to add features that make it look like RDF. I particularly
> see this whenever someone comes to me advocating the use of JSON. RDF is
> what it is for a reason, *not* because we arbitrarily threw something
> together.
>
> So it is not that RDF "looks bad" or whatever people might be saying. It
> is that other technologies and approaches "fall short" of what Linked Data
> and Semantic Web really need. Let's not please reinvent things or shove a
> round peg in a square hole just because someone prefers curly braces over
> angle brackets. Issues like that are not interesting (at all), and we have
> more important things to do.
>
> Regards,
>
> - Ora
>
> --
> Dr. Ora Lassila  ora.lass...@nokia.com  http://www.lassila.org
> Principal Technologist, Nokia
>
>
>
>
>

Re: owl:sameAs - Harmful to provenance?

[Oliver Ruebenacker]

 Hello Philip,

  Apparently, you are confusing two different cases. I talked about the
same reference meaning two different things. You are talking about
different references talking about the same thing.

  Confusion is the enemy of understanding.

 Take care
 Oliver

On Mon, Apr 8, 2013 at 12:53 PM, Phillip Lord
wrote:

>
> And it is this bit -- "before we can do anything useful" that is utterly
> wrong.
>
> Recently I have spent a lot of time look at Dublin Core creator fields.
> You could not believe how many different ways they are used. String
> literals ("Phillip Lord"), last-first ("Lord, Phillip"), with abbrevs
> ("P. Lord"), multi-author ("Phillip Lord; Lindsay Marshall"), with
> titles ("Dr Phillip Lord") and so on.
>
> So, is everyone using Dublin Core wrong? It is useless till everyone
> uses it the same way? Emphatically no, it is not useless.
>
> Would it better if everybody did use it the same way? The answer is
> probably not. Names are incredibly complex, and representing them is, in
> turn, difficult and hard. Any specificiation which did full justice to
> all the different name forms in existance would be incredibly
> long-winded. Many people using the specification would get it wrong; or
> you could have a mechanism for ensuring people always used it correctly.
> Then I am sure that both people who ended up using this form of spec
> would have great fun integrating their tiny datasets.
>
> In the example, we have a number of sets of assertions which
> individually fulfil their creators use-cases. Then, when they are bought
> together, the assertions become inconsistent, telling you up front that
> there is work to be done. And you ask in what way is this useful?
>
> Perfection is the enemy of Good.
>
>
>
> Oliver Ruebenacker  writes:
> >   So what most people here are saying is that before we can do anything
> > useful, we need to make sure that if two assertions use the same
> reference,
> > they mean the same thing.
> >
> >   To which you respond that you will accept assertions without assuming
> > that same references mean same things. You will just keep them separate.
> > There is no rule against that.
> >
> >   But in what way is this useful?
> >
> >  Take care
> >  Oliver
> >
> > On Mon, Apr 8, 2013 at 10:07 AM, David Booth  wrote:
> >
> >> Hi Pat,
> >>
> >>
> >> On 04/04/2013 02:03 AM, Pat Hayes wrote:
> >>
> >>>
> >>> On Apr 3, 2013, at 9:00 PM, Peter Ansell wrote:
> >>>
> >>>  On 4 April 2013 11:58, David Booth  wrote: On
> >>>> 04/02/2013 05:02 PM, Alan Ruttenberg wrote: On Tuesday, April 2,
> >>>> 2013, David Booth wrote: On 03/27/2013 10:56 PM, Pat Hayes wrote:
> >>>> On Mar 27, 2013, at 7:32 PM, Jim McCusker wrote:
> >>>>
> >>>> If only owl:sameAs were used correctly...
> >>>>
> >>>> Well, I agree that is a problem, but don't draw the conclusion
> >>>> that there is something wrong with sameAs, just because people keep
> >>>> using it wrong.
> >>>>
> >>>> Agreed.  And furthermore, don't draw the conclusion that someone
> >>>> has used owl:sameAs wrong just because you get garbage when you
> >>>> merge two graphs that individually worked just fine.  Those two
> >>>> graphs may have been written assuming different sets of
> >>>> interpretations.
> >>>>
> >>>> In that case I would certainly conclude that they have used it
> >>>> wrong. Have you not been reading what Pat and I have been writing?
> >>>>
> >>>> I've read lots of what you and Pat have written.  And I've learned
> >>>> a lot from it -- particularly in learning about ambiguity from Pat.
> >>>> And I'm in full agreement that owl:sameAs is *often* misused.
> >>>>
> >>>> But I don't believe that getting garbage when merging two graphs
> >>>> that individually worked fine *necessarily* indicates that
> >>>> owl:sameAs was misused -- even when it appears on the surface to be
> >>>> causing the problem.
> >>>>
> >>>
> >>> I agree, but not with your example and your analysis of it.
> >>>
> >>>  Here's a simple example to illustrate.
> >>>>
> >>>> Using the following prefixes throughout, for brevity:
> >>>>
> >>&g

Re: owl:sameAs - Harmful to provenance?

[Oliver Ruebenacker]

 Hello David, all,

  What I hear you saying is primarily that:

  1. It is possible to have sets of assertions such that each set is
consistent, but the union is contradictory.
  2. If I don't know the meaning of these assertions, I can't prove that
they are unjustified.

  That's pretty obvious. It has nothing to do with RDF. It is true for any
sufficiently powerful way of making assertions (e.g. natural language,
math, type declarations in programming languages, ...).

  It is therefore at best misleading to point to these issues and talk
about them as if they were an artefact of the RDF specs.

  So what most people here are saying is that before we can do anything
useful, we need to make sure that if two assertions use the same reference,
they mean the same thing.

  To which you respond that you will accept assertions without assuming
that same references mean same things. You will just keep them separate.
There is no rule against that.

  But in what way is this useful?

 Take care
 Oliver

On Mon, Apr 8, 2013 at 10:07 AM, David Booth  wrote:

> Hi Pat,
>
>
> On 04/04/2013 02:03 AM, Pat Hayes wrote:
>
>>
>> On Apr 3, 2013, at 9:00 PM, Peter Ansell wrote:
>>
>>  On 4 April 2013 11:58, David Booth  wrote: On
>>> 04/02/2013 05:02 PM, Alan Ruttenberg wrote: On Tuesday, April 2,
>>> 2013, David Booth wrote: On 03/27/2013 10:56 PM, Pat Hayes wrote:
>>> On Mar 27, 2013, at 7:32 PM, Jim McCusker wrote:
>>>
>>> If only owl:sameAs were used correctly...
>>>
>>> Well, I agree that is a problem, but don't draw the conclusion
>>> that there is something wrong with sameAs, just because people keep
>>> using it wrong.
>>>
>>> Agreed.  And furthermore, don't draw the conclusion that someone
>>> has used owl:sameAs wrong just because you get garbage when you
>>> merge two graphs that individually worked just fine.  Those two
>>> graphs may have been written assuming different sets of
>>> interpretations.
>>>
>>> In that case I would certainly conclude that they have used it
>>> wrong. Have you not been reading what Pat and I have been writing?
>>>
>>> I've read lots of what you and Pat have written.  And I've learned
>>> a lot from it -- particularly in learning about ambiguity from Pat.
>>> And I'm in full agreement that owl:sameAs is *often* misused.
>>>
>>> But I don't believe that getting garbage when merging two graphs
>>> that individually worked fine *necessarily* indicates that
>>> owl:sameAs was misused -- even when it appears on the surface to be
>>> causing the problem.
>>>
>>
>> I agree, but not with your example and your analysis of it.
>>
>>  Here's a simple example to illustrate.
>>>
>>> Using the following prefixes throughout, for brevity:
>>>
>>> @prefix : . @prefix owl:
>>> > .
>>>
>>> Suppose that Owen is the URI owner of :x, :y and :z, and Owen
>>> defines them as follows:
>>>
>>> # Owen's URI definition for :x, :y and :z :x a :Something . :y a
>>> :Something . :z a :Something .
>>>
>>> That's all.  That's Owen's entire definition of those URIs.
>>> Obviously this definition is "ambiguous" in some sense.  But as we
>>> know, ambiguity is ultimately inescapable anyway, so I have merely
>>> chosen an example that makes the ambiguity obvious. As the RDF
>>> Semantics spec puts it: "It is usually impossible to assert enough
>>> in any language to completely constrain the interpretations to a
>>> single possible world".
>>>
>>
>> Yes, but by making the ambiguity this "obvious", you have rendered
>> the example pointless. There is *no* content here *at all*, so Owen
>> has not really published anything. This is not typical of published
>> content, even in RDF. Typically, in fact, there is, as well as some
>> nontrivial actual RDF content, some kind of explanation, perhaps in
>> natural language, of what the *intended* content of the formal RDF is
>> supposed to be. While an RDF engine cannot of course make use of such
>> intuitive explanations, other authors of RDF can, and should, make
>> use of it to try to ensure that they do not make assertions which
>> would be counter to the referential intentions of the original
>> authors. For example, the Dublin Core URIs were published with almost
>> no formal RDF axioms, but quite elaborate natural language glosses
>> which enable them to be used in formal RDF with considerable success.
>> The fact that formal (and even informal) data is inherently ambiguous
>> does not mean that it is inherently, or even typically, vacuous.
>>
>
> This seems to suggest that natural language can somehow eliminate
> ambiguity, where formal languages cannot.  I don't buy that.  Presumably
> whatever definition one expressed in natural language could be expressed in
> a formal language -- in principle at least.  And certainly the goal of the
> semantic web is to have such information expressed in a formal language
> that is amenable to machine processing.
>
> More precisely, 

Re: owl:sameAs - Is it used in a right way?

[Oliver Ruebenacker]

 Hello David,

On Thu, Mar 28, 2013 at 8:51 AM, David Booth  wrote:
> On 03/27/2013 11:02 AM, Oliver Ruebenacker wrote:
>>
>>   Hello David,
>>
>>So if I understand your view correctly, then it could be expressed
>> in a language close to yours as:
>>
>>"Some people believe that if a URI occurs twice within a graph or
>> statement, it refers to the same thing. But this is a myth! RDF never
>> guarantees that two occurrences of the same URI mean the same thing."
>
>
> No, that's not correct.  If you are talking about what the URI means
> **within that graph**, then:
>
>   - For any interpretation, every occurrence of that URI in that graph
> refers to the same thing; BUT . . .
>
>   - Different interpretations can be applied to that graph, such that the
> URI means one thing in one interpretation, but means something different in
> another interpretation.

  Everything you say relies on one assumption: that interpretations
apply to graphs. You still have not explained what makes you believe
this is always true. In fact, I thought you just conceded in your
previous message that it is not always true.

  Let's say I have a graph G1 containing two statements s1 and s2.
Both s1 and s2 contain the same uri u1. Do you think the RDF specs
allow me to use interpretation I1 for s1 and interpretation I2 for s2?
Could it then be true that u1 in s1 refers to a different thing than
u1 in s2? Even though both occurrences are in G1?

  I'm not interested in whether this is a useful approach, or whether
you would do it this way. I just want to know whether you think the
specs allow this.

> It all comes down to the fact that, in essence, the RDF Semantics spec
> defines a function -- call it RS -- of *two* arguments: one interpretation
> and one graph

  I'm still waiting to hear why one argument needs to be a graph.

> (or a piece of a graph, but that's an unimportant detail).

  No, I don't think that is an unimportant detail. I think that is a
crucial test whether such a view is coherent at all.

 Take care
 Oliver

-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: owl:sameAs - Is it used in a right way?

[Oliver Ruebenacker]

 Hello David,

  So if I understand your view correctly, then it could be expressed
in a language close to yours as:

  "Some people believe that if a URI occurs twice within a graph or
statement, it refers to the same thing. But this is a myth! RDF never
guarantees that two occurrences of the same URI mean the same thing."

 Take care
 Oliver

On Wed, Mar 27, 2013 at 9:37 AM, David Booth  wrote:
> Hi Oliver,
>
> On 03/25/2013 04:02 PM, Oliver Ruebenacker wrote:
>>
>>   Hello David,
>>
>>We agree that there are different interpretations. But you haven't
>> shown that the boundaries between interpretations are graphs
>> boundaries (others, including me, think that each interpretation is
>> global).
>
>
> I don't know what you mean by "boundaries between interpretations".
> An interpretation may be applied to any graph or statement to determine its
> truth value (or to a URI to determine the resource to which it is bound in
> that interpretation).
>
> The notion of a graph boundary is purely a matter of convenience and
> utility.  A graph can consist of *any* set of RDF triples.  If you wanted,
> you could apply an interpretation to a graph consisting of three randomly
> selected triples from each RDF document on the web, but it probably wouldn't
> be very useful to do so, because you probably would not care about the truth
> value of that graph.  We generally only apply an interpretation to a graph
> whose truth value we care about.
>
> An interpretation corresponds to the *use* of a graph.  Suppose I have a
> graph that "ambiguously" uses the same URI to denote both a toucan and its
> web page, without asserting that toucans cannot be web pages:
>
>@prefix : <http://example/>
>:tweety a :Toucan .
>:tweety a :WebPage .
>
> When a conforming RDF application takes that RDF graph as input, assumes it
> is true, and produces some output such as "Tweety is a toucan", in effect
> the application has chosen a particular interpretation to apply to that
> graph.  In effect, the choice of interpretation causes the app to produce
> that particular output.  For example, the app might categorize animals into
> species, choosing an interpretation that maps :tweety to a kind of bird.
> But a different conforming RDF application that only cares about web page
> authorship might take that *same* RDF graph as input and choose a different
> interpretation that maps :tweety to a web page, instead outputting "Tweety
> is a web page".  In effect, the app has chosen an interpretation that is
> appropriate for its purpose.
>
> If the graph had also asserted :Toucan owl:disjointWith :WebPage, then the
> graph cannot be true under OWL semantics, and the graph (as is) would be
> unusable to both apps.
>
>>
>>That makes me wonder whether you consider it in conformance with the
>> specs to choose different boundaries?
>>
>>For example, would you consider it conforming to apply a different
>> interpretation to each statement? Or how about a different
>> interpretation for each node of a statement? Do you see anything in
>> the specs against doing so?
>
>
> Sure it is in conformance with the spec.  An interpretation can be applied
> to any graph or any RDF statement.  And certainly you could determine the
> truth value of N different statements according to N different
> interpretations.  But would it be useful to do so?  Probably not.
> Furthermore, if two statements are true under two different interpretations,
> that would not tell you whether a graph consisting of those two statements
> would be true under a single interpretation.
>
> OTOH, it *is* useful to apply different intepretations to different graphs,
> and one reason is that you may be using those graphs for different
> applications, each app in effect applying its own interpretation.  But the
> fact that those graphs may be true under different interpretations does
> *not* tell you whether the merge of those graphs will be true under a single
> interpretation.
>
> The RDF Semantics spec only tells you how to compute the truth value of one
>  pair at a time, but you can certainly apply it to as
> many  pairs as you want -- in full conformance with
> the intent of the spec.  This is the same as if I define a function f of two
> arguments, such that f(x,y) = x+y, that function definition only tells you
> how to compute f(x,y) for one pair of numbers at a time, but you can
> certainly apply it to as many pairs as you want, without in any way
> violating the intent of f's definition.
>
> David



-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: owl:sameAs - Is it used in a right way?

[Oliver Ruebenacker]

 Hello David,

  We agree that there are different interpretations. But you haven't
shown that the boundaries between interpretations are graphs
boundaries (others, including me, think that each interpretation is
global).

  That makes me wonder whether you consider it in conformance with the
specs to choose different boundaries?

  For example, would you consider it conforming to apply a different
interpretation to each statement? Or how about a different
interpretation for each node of a statement? Do you see anything in
the specs against doing so?

 Take care
 Oliver

On Mon, Mar 25, 2013 at 3:18 PM, David Booth  wrote:
> Hi Pat,
>
>
> On 03/25/2013 01:28 AM, Pat Hayes wrote:
>>
>> On Mar 24, 2013, at 10:41 PM, David Booth wrote:
>
> [ . . . ]
>
>>> Given n interpretations and n graphs, it is perfectly valid to use
>>>
>>> the RDF Semantics to determine the truth-values of each of those n
>>> graphs relative to those n interpretations, without in any way
>>> violating the spec.
>>
>>
>> Well, yes, the spec does not actually say anything about what anyone
>> *does*. So there is no law against doing this, so to speak.
>
>
> Thank you!
>
>
>> But
>> calling it "valid" is a stretch. The RDF semantic specification is
>> intended to define a model theory, to be used to specify a semantics
>> in the way conventionally used throughout formal logic, and as
>> described in many textbooks. What you are suggesting here is not
>> using the specification in this way, as a model theory, so it is a
>> mis-use of the specification. For example, using your ideas, none of
>> the inference rules provided in the 2004 specification would be
>> valid.
>>
>> Clearly, however, you are immune to explanations,
>
>
> Well, there's the pot calling the kettle black!  :)
>
>
>> so I think I will
>> give up at this point. If you wish to misuse the specifications in
>> pursuit (a vain pursuit, I will add) of some half-baked fantasy of
>> your own, I guess there is nothing I or anyone else can do to stop
>> you.
>
>
> Fantasy?  [Musing: "There exists a fantasy world in which each URI denotes
> the same resource in *every* RDF graph, and although multiple
> interpretations are permitted, which would map the same URI to different
> resources, discussing more than one interpretation at a time is strictly
> forbidden . . . ."]
>
> It would be absurd to claim that determining the truth-values of both I1(G1)
> and I2(G2), where I1 and I2 are different interpretations and G1 and G2 are
> different graphs, somehow constitutes a "misuse" of the RDF Semantics spec.
>
> Look, *you* may not like using the RDF Semantics spec this way.  But I think
> you are selling your work short by discouraging others from doing so.  The
> spec is an excellent piece of work and there is significant value in taking
> a birds-eye view of it and recognizing that it can be used in more real-life
> ways than you initially expected.
>
> The fact that the RDF Semantics spec was written in the style of model
> theory is all fine and dandy.  I think it works pretty well.  But it is
> **completely irrelevant** to the spec's purpose.  The spec could just as
> well have been written in any other sufficiently precise style --
> denotational semantics, operational semantics, whatever -- and still serve
> the exact same purpose: to define a standard way of determining the
> truth-value of any RDF graph, given any interpretation.
>
> To claim that the model theoretic style in which the RDF Semantics spec was
> written has any bearing whatsoever on the spec's purpose or its "appropriate
> use" would be a serious misrepresentation of its role as a W3C standard.
>
> David Booth
>



-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: owl:sameAs - Is it used in a right way?

[Oliver Ruebenacker]

 Hello,

On Wed, Mar 20, 2013 at 12:20 AM, Pat Hayes  wrote:
> But RDF isnt intended to be used in theology. It is intended for recording 
> data, and most data is pretty mundane stuff about which there is not a lot of 
> factual disagreement.

  I think that's the wrong argument. A logical system like RDF should
enable a community to state whatever they decide worthy of stating.
Whether they agree with others or not should not be a concern of RDF.
Provenance should be a different level than the base logic: we should
only start thinking about provenance once we are done deciding what
consistency means. You find religious groups perfectly agree on some
truths. Scientific truths get overturned in unexpected places all the
time.

 Take care
 Oliver

-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: owl:sameAs - Is it used in a right way?

[Oliver Ruebenacker]

 Hello David,

On Mon, Mar 18, 2013 at 6:31 PM, David Booth  wrote:
> I'm sorry, but I still do not understand your point.  I have been talking
> very narrowly about existing RDF Semantics.  It sounds like you are talking
> much more broadly about context, but I don't know what you mean.  Clearly
> 1.376 has no meaning without context.  To interpret it it correctly, you
> need to know that it is supposed to represent a number, it is represented in
> base 10, etc.  It is completely meaningless without knowing how to interpret
> it.  What is the analogy that you are trying to illustrate?

  If I told people "David Booth is 4.9 foot tall.", would you object?

 Take care
 Oliver

-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: owl:sameAs - Is it used in a right way?

[Oliver Ruebenacker]

 Hello,

On Mon, Mar 18, 2013 at 5:04 PM, David Booth  wrote:
> I see no requirement in the RDF Semantics that interpretation "I" be the
> *same* interpretation for every graph "E" to which this procedure is
> applied.  Am I right, or have I completely misunderstood something
> fundamental?

  An interpretation of a logical system is about connecting the
logical system to external meaning, which is different from deciding
whether the logical system is consistent within itself. The connection
between interpretation and consistency is usually that an inconsistent
system usually has no meaningful interpretation. But the fact that a
logical system can have multiple contradicting interpretations is not
an indicator that it is inconsistent within itself.

  Otherwise, if you see contradicting interpretations as indicator of
inconsistency, then a logical system could never be consistent.
Because even for a single statement, you could claim that one
interpretation says it is true and another says it is false.

  It makes little sense to say, I am combining two sets of statements,
while interpreting the two sets differently. You can only make sense
with one interpretation at a time.

 Take care
 Oliver

-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: owl:sameAs - Is it used in a right way?

[Oliver Ruebenacker]

 Hello David,

On Sun, Mar 17, 2013 at 9:52 PM, David Booth  wrote:
> On 03/17/2013 10:55 AM, Oliver Ruebenacker wrote:
>>
>>   Hello,
>>
>> On Sat, Mar 16, 2013 at 12:30 PM, David Booth  wrote:
>>>
>>> You are in good company in thinking that a URI always denotes the same
>>> resource, because that is a widespread misconception.  (I call it Myth #1
>>> in
>>> http://dbooth.org/2010/ambiguity/paper.html .)  But it simply is not true
>>> in
>>> the RDF semantics.
>>> [...]
>>> That is precisely why it is helpful to keep different perspectives in
>>> different graphs, as Jeremy suggested.
>>
>>
>>That's a little bit like saying, since floating-point numbers are
>> not perfectly precise, the 1.376 in my data may not be the same as the
>> 1.376 in your data, and therefore the two values should be kept in
>> separate spaces.
>
>
> I don't follow what you mean.  A floating point number like 1.376 may be
> used as an approximation of some real number, but it is exactly the same
> floating point number in all RDF graphs.

  I'm not talking about how RDF handles floating point numbers. I'm
just using floating point numbers as an example to show how flawed
your logic is. If your logic would hold, that URIs have no meaning
without context, because they are only approximate, then by the same
logic, it would follow that floating-point numbers have no meaning
without context.

 Take care
 Oliver

-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: owl:sameAs - Is it used in a right way?

[Oliver Ruebenacker]

 Hello,

On Fri, Mar 15, 2013 at 1:05 PM, Umutcan ŞİMŞEK  wrote:
> My question is, does LODD use owl:sameAs properly? For instance, are those
> two resources, dbpedia:Metamizole and drugbank:DB04817 (code for
> Metamizole), really identical? Or am I getting the word "property" in the
> paper wrong?

  Do we mean metamizole in acid form, or metamizole in anion form, or
metamizole sodium? Or some combination of some of the above?

 Take care
 Oliver

-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: owl:sameAs - Is it used in a right way?

[Oliver Ruebenacker]

 Hello,

On Sat, Mar 16, 2013 at 12:30 PM, David Booth  wrote:
> You are in good company in thinking that a URI always denotes the same
> resource, because that is a widespread misconception.  (I call it Myth #1 in
> http://dbooth.org/2010/ambiguity/paper.html .)  But it simply is not true in
> the RDF semantics.
> [...]
> That is precisely why it is helpful to keep different perspectives in
> different graphs, as Jeremy suggested.

  That's a little bit like saying, since floating-point numbers are
not perfectly precise, the 1.376 in my data may not be the same as the
1.376 in your data, and therefore the two values should be kept in
separate spaces.

 Take care
 Oliver

-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: Wow....

[Oliver Ruebenacker]

 Hello,

  James Gosling proved that you can patent the light switch:

http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=44&f=G&l=50&co1=AND&d=PTXT&s1=%22gosling,+james%22.INNM.&OS=IN/%22gosling,+james%22&RS=IN/%22gosling,+james%22

  What is a proper name for filing such patents? Maybe jobsing?

 Take care
 Oliver

On Tue, Feb 5, 2013 at 8:44 AM, Luciano, Joanne S.  wrote:
> Yes, wow.  And what are the implications?
>
> It is an application, which isn't the same as a patent. It's not clear to me 
> that it would be granted because, if I recall correctly, it has to not be 
> obvious how to do it to someone who practices in the field.  My patents are 
> from 2000 and 2001, so it's been a while that I've been through the patent 
> execution process.  That being said, it may be a bit of a heads-up, be on the 
> lookout.
>
> Joanne
>
> On Feb 5, 2013, at 6:21 AM, Robert Stevens 
>  wrote:
>
>> Who'd have thought it? I've not seen one of those before.
>>
>>
>> On 05/02/2013 09:44, Mark Wilkinson wrote:
>>> I have no words...
>>>
>>> http://www.freepatentsonline.com/y2013/0030827.html
>>>
>>> Semantic Interoperability System for Medicinal Information
>>> United States Patent Application 20130030827
>>>
>>>
>>> M
>>>
>>>
>>>
>>>
>>
>> --
>> Robert Stevens
>> Reader in Bio-Health Informatics
>> School of Computer Science
>> University of Manchester
>> Oxford Road
>> Manchester
>> United Kingdom
>> M13 9PL
>>
>> robert.stev...@manchester.ac.uk
>> http://www.cs.man.ac.uk/~stevensr
>> http://robertdavidstevens.wordpress.com
>>
>>
>> KBO
>>
>>
>
>



-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: Tools to integrate (hundreds) of spreadsheets as RDF

[Oliver Ruebenacker]

 Hello,

On Sun, Jan 20, 2013 at 7:38 PM, Rafael Richards  wrote:
> Any other suggestions for any other 'pipeline' tools to keep CSV and RDF in
> sync which are (1) currently maintained and (2) have sufficient
> documentation and examples of importing and converting CSV to RDF?

  If you need to build a pipeline, you probably want to choose a
general purpose production-quality programming language (e.g. Java,
Scala) which has a good RDF library (e.g. Sesame, Jena, Banana RDF).

 Take care
 Oliver

-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: Ontologies for blood glucose, HbA1C measurements?

[Oliver Ruebenacker]

 Hello,

On Thu, Dec 20, 2012 at 1:26 PM, Bhat, Talapady N.
 wrote:
> Hi,
>
> Try this URL and type 'fasting'  ( URL is autocomplete enabled) to get a 
> listing of relevant ontologies for your keyword of interest. 
> http://xpdb.nist.gov/bioroot/bioroot.pl
>
> It shows up for 'fasting'  SNOMED and Mesh as the two possibilities to use. 
> It also shows the way these terms are used by these ontologies. If you click 
> the term it shows how those terms are used
> For instance for 'plasma fasting  glucose measurement' usages are
>
> http://xpdb.nist.gov/bioroot/bioroot.pl?allTrees=1&termid=876068&wrd=Plasma 
> fasting glucose measurement&foundin=::18::
>
> For 'fasting hypoglycaemia'
>
> http://xpdb.nist.gov/bioroot/bioroot.pl?allTrees=1&termid=895990&wrd=Fasting 
> hypoglycaemia&foundin=::18::

  Do you have URIs for SNOMED terms?

 Take care
 Oliver

-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: Ontologies for blood glucose, HbA1C measurements?

[Oliver Ruebenacker]

 Hello,

On Thu, Dec 20, 2012 at 1:00 PM, Sahay, Ratnesh  wrote:
> From SNOMED: http://www.snomedbrowser.com/Codes/Details/36048009

  We are looking less for a procedure, but an outcome.

 Take care
 Oliver

-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: Ontologies for blood glucose, HbA1C measurements?

[Oliver Ruebenacker]

 Hello,

On Thu, Dec 20, 2012 at 12:48 PM, Freimuth, Robert, Ph.D.
 wrote:
> LOINC is specifically designed for this.  See loinc.org.

  Does it have terms for HbA1C or fasting plasma glucose? Thanks!

 Take care
 Oliver

-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Ontologies for blood glucose, HbA1C measurements?

[Oliver Ruebenacker]

 Hello,

  Which ontologies can you recommend to identify different types of
medical measurements, such as fasting plasma glucose or HbA1C?

  Thanks!

 Take care
 Oliver

-- 
IT Project Lead at PanGenX (http://www.pangenx.com)
The purpose is always improvement

Re: Michel Dumontier @ Systems Biology Telco - today at 11AM EST

[Oliver Ruebenacker]

 Hello Sarala,

  We created SBPAX, an extension to BioPAX to integrate quantitative
data and build a bridge to modeling. SBPAX is in line to become part
of BioPAX, and is supported by two popular databases and by upcoming
versions of the Virtual Cell.

  If there is anything you need that SBPAX does not have, then we
would be happy to hear about it and maybe we can extend SBPAX to serve
your needs.

  Please check out http://www.sbpax.org

 Take care
 Oliver

On Tue, Jun 26, 2012 at 5:17 AM,   wrote:
> Hi Michel,
>
> Not at the moment but we are hopping to address this as well.
>
> Cheers,
> Sarala
>
>> Sarala,
>>   Do you convert/extract the (MathML) kinetic expressions?
>>
>> m.
>>
>> On Mon, Jun 25, 2012 at 10:12 PM,  wrote:
>>
>>> Hi Lena,
>>>
>>> We are interested in querying the underlying model representation as
>>> well.
>>> We want to be able to run SPARQL queries on different types of
>>> model/data
>>> repositories eg. cellml. It is not always possible to convert some of
>>> the
>>> model/data we work with to BioPAX. Our rdf schema consists of a general
>>> model representation followed by more specific representations for each
>>> standard.
>>>
>>> Cheers,
>>> Sarala
>>>
>>> > Hello Sarala,
>>> >
>>> > This is great - naive question: is there a reason why you didn't go
>>> with
>>> > the biopax representation?
>>> > Best,
>>> > Lena
>>> >
>>> > On Mon, Jun 25, 2012 at 10:46 AM,  wrote:
>>> >
>>> >> Hi Lena,
>>> >>
>>> >> I'm working on semantic interoperability of data and models. As part
>>> of
>>> >> this work, I have converted all curated sbml models in biomodels into
>>> >> RDF.
>>> >> It would be good to see what you have done, may be see were we can
>>> >> collaborate. I'm in the process of documenting my work but you can
>>> find
>>> >> the rdf models and the schema at
>>> >> https://sites.google.com/site/ricordowp4/file-cabinet/sbmltordf.
>>> These
>>> >> models are stored in a RDF store and can be queried via ws eg.
>>> >> http://wwwdev.ebi.ac.uk/ricordo-rdfstore-ws/service/search/getResources
>>> .
>>> >> A
>>> >> bit more documentation on this can be found at
>>> >> https://github.com/sarala/ricordo-rdfstore-ws. I will be uploading
>>> the
>>> >> converter code to github soon. Please let me know if your work is
>>> >> available to access online.
>>> >>
>>> >> Cheers,
>>> >> Sarala
>>> >>
>>> >> > Mike,
>>> >> >   This might be of interest to harmony/combine folks - which
>>> mailing
>>> >> lists
>>> >> > might Lena post to do indicate she will be presenting on this
>>> topic?
>>> >> >
>>> >> > m.
>>> >> >
>>> >> > On Fri, Jun 22, 2012 at 12:09 PM, Me  wrote:
>>> >> >
>>> >> >> Hi Michael,
>>> >> >>
>>> >> >> My plan for the next telco is to have a much MUCH  more hands-on
>>> >> focus
>>> >> >> than what we've had so far. Me and Laleh (my PhD student) are
>>> >> creating
>>> >> >> RDF
>>> >> >> representations of SBML models so that we can visualize with
>>> google
>>> >> >> fusion
>>> >> >> tables. We hope to have something to show by next telco.
>>> >> >>
>>> >> >> Best,
>>> >> >> Lena
>>> >> >>
>>> >> >>
>>> >> > --
>>> >> > Michel Dumontier
>>> >> > Associate Professor of Bioinformatics, Carleton University
>>> >> > Chair, W3C Semantic Web for Health Care and the Life Sciences
>>> Interest
>>> >> > Group
>>> >> > http://dumontierlab.com
>>> >> >
>>> >>
>>> >>
>>> >
>>> >
>>> > --
>>> > Helena F. Deus
>>> > Post-Doctoral Researcher at DERI/NUIG
>>> > http://lenadeus.info/
>>> >
>>>
>>>
>>>
>>
>>
>> --
>> Michel Dumontier
>> Associate Professor of Bioinformatics, Carleton University
>> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
>> Group
>> http://dumontierlab.com
>>
>
>
>
>



-- 
Oliver Ruebenacker, Bioinformatics and Network Analysis Consultant
President and Founder of Knowomics
(http://www.knowomics.com/wiki/Oliver_Ruebenacker)
Consultant at Predictive Medicine
(http://predmed.com/people/oliverruebenacker.html)
SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)

Re: Computers may predict drugs’ side effects

[Oliver Ruebenacker]

 Hello David,

On Tue, Jun 12, 2012 at 12:58 PM, David Wild  wrote:
> Here it is -- bad name lookup on our part for sulfuric acid - using CID
> instead 1118
>
> http://cheminfov.informatics.indiana.edu:8080/slap/slap.jsp?cid=1118&gene=Insulin
>
> Note the direct relationship is removed in the subgraph / calculation to
> show indirect prediction.

  Wouldn't you expect a bigger graph for a molecule that interacts
with many targets?

     Take care
 Oliver

-- 
Oliver Ruebenacker
Bioinformatics Consultant (http://www.knowomics.com/wiki/Oliver_Ruebenacker)
Knowomics, The Bioinformatics Network (http://www.knowomics.com)
SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)

Re: Computers may predict drugs’ side effects

[Oliver Ruebenacker]

 Hello,

On Tue, Jun 12, 2012 at 12:32 PM, David Wild  wrote:
>> Hopefully, in the future, we will be able to simulate, for a given
>> chemical structure:
>>
>>  - which proteins (or other bio-molecules) it interacts with
>>  - how that interaction changes the function of the bio-molecule
>>  - how changed function of molecules change biological networks and
>> systemic function
>>
>>  However, what the article says sounds more limited:
>>
>>  "... a database of 73 proteins ..."
>>
>> > As such, Open Linked Data might offer help!
>>
>>  Eventually.
>
>
> The first (drug-target prediction) is something we're working on at IU -
> using a large, heterogenous semantic network of public compound, target,
> gene, expression, pathway, disease data to make drug-target predictions (see
> http://chem2bio2rdf.org/slap
> , http://slapfordrugtargetprediction.wikispaces.com/ , paper in press at
> PLoS Comp. Bio.). Results are promising so far but biggest question is how
> you weight different kinds of paths, nodes and edges - there is no one
> correct answer, but is dependent on the scientist and application using it.
> Right now we're not claiming that it predicts compound-target binding but
> rather an "association" which deserves further investigation. Also have to
> address preconception by many that "large / integrated dataset" = low
> quality, high errors. I argue that if you read 5 papers a day you are
> overall better informed than if you read just one of them, even if that one
> paper is a very high quality newspaper.

  Interesting tool!

  I'm not sure I'm using it correctly, though: I entered sulfuric acid
and insulin, and it found no direct interaction, although I am pretty
sure sulfuric acid directly reacts with insulin.

 Take care
 Oliver

-- 
Oliver Ruebenacker
Bioinformatics Consultant (http://www.knowomics.com/wiki/Oliver_Ruebenacker)
Knowomics, The Bioinformatics Network (http://www.knowomics.com)
SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)

Re: Computers may predict drugs’ side effects

[Oliver Ruebenacker]

 Hello

On Tue, Jun 12, 2012 at 11:49 AM, Lin MD, Simon
 wrote:
> Hi Joanne,
>
> Thank you for sharing this topic with the group! For discussion, I am 
> attaching the manuscript and a related review article.

  Yes, thanks for sharing, very interesting!

> Generally, the prediction models work well in this problem domain (-- If not, 
> the discipline of medicinal chemistry would not exist).
>
> The bottleneck is the availability of large scale data: chemical structure, 
> drug target, protein-protein interaction, indications, know side effects, etc.

  Hopefully, in the future, we will be able to simulate, for a given
chemical structure:

  - which proteins (or other bio-molecules) it interacts with
  - how that interaction changes the function of the bio-molecule
  - how changed function of molecules change biological networks and
systemic function

  However, what the article says sounds more limited:

  "... a database of 73 proteins ..."

> As such, Open Linked Data might offer help!

  Eventually.

 Take care
 Oliver

-- 
Oliver Ruebenacker
Bioinformatics Consultant (http://www.knowomics.com/wiki/Oliver_Ruebenacker)
Knowomics, The Bioinformatics Network (http://www.knowomics.com)
SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)

Re: Systems Biology Task Force Kick-Off - tomorrow (Feb 22) at 11AM EDT

[Oliver Ruebenacker]

 Hello Bob, Anita, All,

  I'm not claiming that numbers determine the content of a paper
entirely. But I do claim they play a central role. I guess it is not
entirely impossible to publish a paper with no numbers, but it appears
to be extremely rare. I would estimate the fraction of biology papers
with no numbers to be less than one percent.

  Images are numbers - radiation intensity measured as a function of
space. Most biologists I know would use images to estimate the amounts
or concentrations of the substances that cause the radiation.

  I suppose it is possible to derive conclusions without numbers. But
in my experience it is extremely rare. Who would report A grows faster
than B without reporting, by how much? How can you even talk about
chemical compositions without providing any numbers about what these
compositions are?

  If you have data plots, that means you have lots of numbers. Most
biologists I know would try to fit the data to a mathematical model.
Who would report that graph A has a bigger slope than graph B without
reporting, what those slopes are?

  Certainly, papers contain other things besides data. It is possible
that two different authors, given the same data, arrive at different
conclusions. But why should I care about things not derived from data?
If it is about established knowledge, I don't need to get it from that
paper - I can get it from somewhere else. And if some statement is
neither derived from the data nor established knowledge, why would I
believe it?

 Take care
 Oliver

On Fri, Feb 24, 2012 at 2:24 PM, Bob Futrelle  wrote:
> Statements are based on a wide variety of things.  Statements are produced
> by author/experimenters who may describe and evaluate gels and other images
> without ever reducing them to numbers. Statements often compare  (not
> numerically) growth, morphology, chemical composition, to those aspects
> found in other portions of an experiment or reported in other papers.  A
> paper will often include data plots, but the authors may report particular
> characteristics of the data behavior or correlation in the plots by looking
> at the plots, not reducing them to numbers.
>
> You cannot discard the authors' evaluations and hope to reach the
> conclusions that those humans have by some analysis of the numbers.
>
> Your system for doing that would have to include the world knowledge of the
> authors.  In other words, these problems are AI-Complete, as are so many
> important, complex, and interesting problems in the real (biological) world.
>
> Anita's comments that followed mine are in the same spirit.
>
>   - Bob
>
>
> On Fri, Feb 24, 2012 at 2:14 PM, Oliver Ruebenacker 
> wrote:
>>
>>     Hello Bob,
>>
>>  There are many statements which contain no numbers. But isn't the
>> evidence that they are true usually based on numbers?
>>
>>  My suggestion is to structure quantitative data based on the
>> statements for which this data is used as evidence.
>>
>>     Take care
>>     Oliver
>>
>> On Fri, Feb 24, 2012 at 1:59 PM, Bob Futrelle 
>> wrote:
>> > A great deal of the content of papers is not about numbers, but
>> > statements
>> > intertwined with propositional attitudes. Good evidence for this is in
>> > the
>> > use of hedging.  See,
>> >
>> > Hyland, K., Hedging in scientific research articles. Pragmatics &
>> > beyond,1998, Amsterdam ; Philadelphia: John Benjamins Pub. Co. ix, 307
>> > p.
>> >
>> >
>> >  - Bob Futrelle
>> >    BioNLP.org
>> >
>> > On Fri, Feb 24, 2012 at 1:46 PM, Oliver Ruebenacker 
>> > wrote:
>> >>
>> >>     Hello Anita, All,
>> >>
>> >>  I'm mostly interested in numbers. Presumably, these statements have
>> >> been derived from numbers that can be found in these papers. The
>> >> challenge is to classify numbers and group them into systems and
>> >> states. Could your epistemic model help do that?
>> >>
>> >>     Take care
>> >>     Oliver
>> >>
>> >> On Fri, Feb 24, 2012 at 12:15 PM, Waard, Anita de A (ELS-NYC)
>> >>  wrote:
>> >> > All,
>> >> >
>> >> > I was struck by the phrase 'turning biological knowledge into
>> >> > mathematical models' and wondering if anyone is interested to model
>> >> > 'epistemic information' in biology articles, added to the knowledge
>> >> > of the
>> >> > type that Oliver mentioned?
>> >> >
>> >> > In particular I am interested in modelling 

Re: Systems Biology Task Force Kick-Off - tomorrow (Feb 22) at 11AM EDT

[Oliver Ruebenacker]

 Hello Bob,

  There are many statements which contain no numbers. But isn't the
evidence that they are true usually based on numbers?

  My suggestion is to structure quantitative data based on the
statements for which this data is used as evidence.

 Take care
 Oliver

On Fri, Feb 24, 2012 at 1:59 PM, Bob Futrelle  wrote:
> A great deal of the content of papers is not about numbers, but statements
> intertwined with propositional attitudes. Good evidence for this is in the
> use of hedging.  See,
>
> Hyland, K., Hedging in scientific research articles. Pragmatics &
> beyond,1998, Amsterdam ; Philadelphia: John Benjamins Pub. Co. ix, 307 p.
>
>
>  - Bob Futrelle
>    BioNLP.org
>
> On Fri, Feb 24, 2012 at 1:46 PM, Oliver Ruebenacker 
> wrote:
>>
>>     Hello Anita, All,
>>
>>  I'm mostly interested in numbers. Presumably, these statements have
>> been derived from numbers that can be found in these papers. The
>> challenge is to classify numbers and group them into systems and
>> states. Could your epistemic model help do that?
>>
>>     Take care
>>     Oliver
>>
>> On Fri, Feb 24, 2012 at 12:15 PM, Waard, Anita de A (ELS-NYC)
>>  wrote:
>> > All,
>> >
>> > I was struck by the phrase 'turning biological knowledge into
>> > mathematical models' and wondering if anyone is interested to model
>> > 'epistemic information' in biology articles, added to the knowledge of the
>> > type that Oliver mentioned?
>> >
>> > In particular I am interested in modelling clauses such as 1 a., 2 a., 3
>> > a., and 3.b in the sentences below - I have a model to classify these and
>> > would like to add this 'knowledge attribution' layer to existing
>> > representations of triples in papers.
>> >
>> > 1 a. These studies have shown that
>> > 1.b. the 5' untranslated region (5'UTR) can be complex
>> >
>> > vs.
>> >
>> > 2. a. It has been reported that
>> > 2. b. 5' untranslated exons, and sometimes introns, can regulate the
>> > expression of genes in two different ways.
>> >
>> > vs.
>> >
>> > 3. a. Thus, our analysis revealed areas of active chromatin remodeling
>> > in the vicinity of exon 1
>> > 3. b. suggesting that
>> > 3. c. this area may be important for CCR3 transcription.
>> >
>> > Is this part of the remit of this group and/or is anyone interested in
>> > collaborating on this topic?
>> >
>> > Thanks,
>> > Best,
>> >
>> > - Anita.
>> >
>> > Anita de Waard
>> > Disruptive Technologies Director, Elsevier Labs
>> > http://elsatglabs.com/labs/anita/
>> > a.dewa...@elsevier.com
>> >
>> >
>> >
>> > -Original Message-
>> > From: Oliver Ruebenacker [mailto:cur...@gmail.com]
>> > Sent: Fri 2/24/2012 11:55
>> > To: Helena Deus; public-semweb-lifesci
>> > Subject: Re: Systems Biology Task Force Kick-Off - tomorrow (Feb 22) at
>> > 11AM EDT
>> >
>> >
>> >     Hello Helena, All,
>> >
>> >  I'm interested in joining the Systems Biology Taskforce. Sorry I
>> > could not make the initial call. My interest is turning biological
>> > knowledge into mathematical models, automatically. A brief description
>> > is below.
>> >
>> >  Thanks!
>> >
>> >     Take care
>> >     Oliver
>> >
>> >  Living organisms are so enormously complex that we need computer
>> > simulations to understand the consequences of their vast biochemical
>> > reaction networks. As we uncover an increasing part of these networks,
>> > our established knowledge is increasingly stored in free web databases
>> > and available for query and download in machine-readable formats,
>> > especially in the RDF/OWL-based community standard Biological Pathways
>> > Exchange (BioPAX) [1]. The available data is massive and growing, e.g.
>> > Pathway Commons [2] stores 1,700 pathways, 414 organisms, 440,000
>> > interactions and 86,000 substances. This data is fully linked with
>> > open controlled terminologies such as gene ontology (e.g. anatomical
>> > features) [3] and other free online databases such as ChEBI
>> > (chemicals) [4], KEGG (genes a.o.) [5], UniProt (proteins) [6] and
>> > PubMed (publications) [7].
>> >
>> >  Automatic use of this knowledge for computer simulations of
>&g

Re: Systems Biology Task Force Kick-Off - tomorrow (Feb 22) at 11AM EDT

[Oliver Ruebenacker]

 Hello Anita, All,

  I'm mostly interested in numbers. Presumably, these statements have
been derived from numbers that can be found in these papers. The
challenge is to classify numbers and group them into systems and
states. Could your epistemic model help do that?

 Take care
 Oliver

On Fri, Feb 24, 2012 at 12:15 PM, Waard, Anita de A (ELS-NYC)
 wrote:
> All,
>
> I was struck by the phrase 'turning biological knowledge into mathematical 
> models' and wondering if anyone is interested to model 'epistemic 
> information' in biology articles, added to the knowledge of the type that 
> Oliver mentioned?
>
> In particular I am interested in modelling clauses such as 1 a., 2 a., 3 a., 
> and 3.b in the sentences below - I have a model to classify these and would 
> like to add this 'knowledge attribution' layer to existing representations of 
> triples in papers.
>
> 1 a. These studies have shown that
> 1.b. the 5' untranslated region (5'UTR) can be complex
>
> vs.
>
> 2. a. It has been reported that
> 2. b. 5' untranslated exons, and sometimes introns, can regulate the 
> expression of genes in two different ways.
>
> vs.
>
> 3. a. Thus, our analysis revealed areas of active chromatin remodeling in the 
> vicinity of exon 1
> 3. b. suggesting that
> 3. c. this area may be important for CCR3 transcription.
>
> Is this part of the remit of this group and/or is anyone interested in 
> collaborating on this topic?
>
> Thanks,
> Best,
>
> - Anita.
>
> Anita de Waard
> Disruptive Technologies Director, Elsevier Labs
> http://elsatglabs.com/labs/anita/
> a.dewa...@elsevier.com
>
>
>
> -Original Message-
> From: Oliver Ruebenacker [mailto:cur...@gmail.com]
> Sent: Fri 2/24/2012 11:55
> To: Helena Deus; public-semweb-lifesci
> Subject: Re: Systems Biology Task Force Kick-Off - tomorrow (Feb 22) at 11AM 
> EDT
>
>
>     Hello Helena, All,
>
>  I'm interested in joining the Systems Biology Taskforce. Sorry I
> could not make the initial call. My interest is turning biological
> knowledge into mathematical models, automatically. A brief description
> is below.
>
>  Thanks!
>
>     Take care
>     Oliver
>
>  Living organisms are so enormously complex that we need computer
> simulations to understand the consequences of their vast biochemical
> reaction networks. As we uncover an increasing part of these networks,
> our established knowledge is increasingly stored in free web databases
> and available for query and download in machine-readable formats,
> especially in the RDF/OWL-based community standard Biological Pathways
> Exchange (BioPAX) [1]. The available data is massive and growing, e.g.
> Pathway Commons [2] stores 1,700 pathways, 414 organisms, 440,000
> interactions and 86,000 substances. This data is fully linked with
> open controlled terminologies such as gene ontology (e.g. anatomical
> features) [3] and other free online databases such as ChEBI
> (chemicals) [4], KEGG (genes a.o.) [5], UniProt (proteins) [6] and
> PubMed (publications) [7].
>
>  Automatic use of this knowledge for computer simulations of
> biological organisms has been an ongoing challenge [8,9,10]. Now,
> Systems Biology Pathway Exchange (SBPAX) [11], a BioPAX extension,
> allows the inclusion of quantitative data and systems biology terms,
> especially the Systems Biology Ontology (SBO) [12]. SBPAX support has
> been implemented by the Virtual Cell [13], Signaling Gateway Molecule
> Pages [14] and System for the Analysis of Biochemical Pathways -
> Reaction Kinetics (SABIO-RK) [15]. For the first time, a mathematical
> model can be automatically built and fully annotated from a pathway of
> interest.
>
>  Citations:
>
>  [1] Biological Pathway Exchange (BioPAX), www.biopax.org
>  [2] Pathway Commons, www.pathwaycommons.org
>  [3] Gene Ontology (GO), www.geneontology.org/
>  [4] Chemical Entities of Biological Interest (ChEBI), www.ebi.ac.uk/chebi/
>  [5] Kyoto Encyclopedia of Genes and Genomes (KEGG), .genome.jp/kegg/
>  [6] UniProt, www.uniprot.org
>  [7] PubMed, www.ncbi.nlm.nih.gov/pubmed/
>  [8] Modeling without Borders: Creating and Annotating VCell Models
> Using the Web, Michael L. Blinov, Oliver Ruebenacker, James C. Schaff
> and Ion I. Moraru,  Lecture Notes in Computer Science, 2010, Volume
> 6053 (2010).
>  [9] Using views of Systems Biology Cloud: application for model
> building, Oliver Ruebenacker, Michael Blinov, Theory in Biosciences,
> Volume 130, Number 1, 45-54 (2010).
>  [10] Integrating BioPAX pathway knowledge with SBML models, Michael
> L Blinov, Oliver Ruebenacker, Ion I Moraru, IET Syst. Biol., 2009,
> Vol. 3

Re: Systems Biology Task Force Kick-Off - tomorrow (Feb 22) at 11AM EDT

[Oliver Ruebenacker]

 Hello Helena, All,

  I'm interested in joining the Systems Biology Taskforce. Sorry I
could not make the initial call. My interest is turning biological
knowledge into mathematical models, automatically. A brief description
is below.

  Thanks!

 Take care
 Oliver

  Living organisms are so enormously complex that we need computer
simulations to understand the consequences of their vast biochemical
reaction networks. As we uncover an increasing part of these networks,
our established knowledge is increasingly stored in free web databases
and available for query and download in machine-readable formats,
especially in the RDF/OWL-based community standard Biological Pathways
Exchange (BioPAX) [1]. The available data is massive and growing, e.g.
Pathway Commons [2] stores 1,700 pathways, 414 organisms, 440,000
interactions and 86,000 substances. This data is fully linked with
open controlled terminologies such as gene ontology (e.g. anatomical
features) [3] and other free online databases such as ChEBI
(chemicals) [4], KEGG (genes a.o.) [5], UniProt (proteins) [6] and
PubMed (publications) [7].

  Automatic use of this knowledge for computer simulations of
biological organisms has been an ongoing challenge [8,9,10]. Now,
Systems Biology Pathway Exchange (SBPAX) [11], a BioPAX extension,
allows the inclusion of quantitative data and systems biology terms,
especially the Systems Biology Ontology (SBO) [12]. SBPAX support has
been implemented by the Virtual Cell [13], Signaling Gateway Molecule
Pages [14] and System for the Analysis of Biochemical Pathways -
Reaction Kinetics (SABIO-RK) [15]. For the first time, a mathematical
model can be automatically built and fully annotated from a pathway of
interest.

  Citations:

  [1] Biological Pathway Exchange (BioPAX), www.biopax.org
  [2] Pathway Commons, www.pathwaycommons.org
  [3] Gene Ontology (GO), www.geneontology.org/
  [4] Chemical Entities of Biological Interest (ChEBI), www.ebi.ac.uk/chebi/
  [5] Kyoto Encyclopedia of Genes and Genomes (KEGG), .genome.jp/kegg/
  [6] UniProt, www.uniprot.org
  [7] PubMed, www.ncbi.nlm.nih.gov/pubmed/
  [8] Modeling without Borders: Creating and Annotating VCell Models
Using the Web, Michael L. Blinov, Oliver Ruebenacker, James C. Schaff
and Ion I. Moraru,  Lecture Notes in Computer Science, 2010, Volume
6053 (2010).
  [9] Using views of Systems Biology Cloud: application for model
building, Oliver Ruebenacker, Michael Blinov, Theory in Biosciences,
Volume 130, Number 1, 45-54 (2010).
  [10] Integrating BioPAX pathway knowledge with SBML models, Michael
L Blinov, Oliver Ruebenacker, Ion I Moraru, IET Syst. Biol., 2009,
Vol. 3, Iss. 5, pp. 317-328 (2009).
  [11] Systems Biology Pathway Exchange (SBPAX), www.sbpax.org
  [12] Systems Biology Ontology, www.ebi.ac.uk/sbo/main/
  [13] Virtual Cell, http://vcell.org
  [14] Signaling Gateway Molecule Pages, www.signaling-gateway.org/molecule/
  [15] System for the Analysis of Biological Pathways – Reaction
Kinetics (SABIO-RK), http://sabio.villa-bosch.de/

On Tue, Feb 21, 2012 at 4:32 PM, Helena Deus  wrote:
> Dear All,
>
> Please join me tomorrow for the kick-off telco of the Systems Biology Task
> Force. Systems Biology is about looking at biological systems from an
> integrated perspective and to use that perspective to understand disease. We
> will be discussing the general goals, strategy and structure of the task
> force.
>
> Please see http://www.w3.org/wiki/HCLSIG/SysBio for an initial motivation,
> and description, of what this task will be focused on (with due flexibility
> according to participants input).
>
>
> * Date of Call: Tuesday February 21, 2012
> * Time of Call: 11:00am Eastern Daylight Time (EDT)
> * Dial-In #: +1.617.761.6200 (Cambridge, MA)
> * [Note: limited access to European dial in numbers below]
> * Dial-In #: +33.4.26.46.79.03 (Nice, France)
> * Dial-In #: +44.203.318.0479 (Bristol, UK)
> * Participant Access Code: 4257 ("HCLS").
> * IRC Channel: irc.w3.org port 6665 channel #HCLS
> For instant IRC access:
> see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or
> see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]), Quick Start: Click
> on
> [http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls mibbit]
>
> * Duration: ~1h
> * Convener: Helena
> * Scribe: TBD
>
> Kind regards,
> Helena



-- 
Oliver Ruebenacker, Computational Cell Biologist
Virtual Cell (http://vcell.org)
SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)
http://www.oliver.curiousworld.org

Evidence of Significance of Semantic Web for Life Sciences

[Oliver Ruebenacker]

 Hello,

  I am looking for evidence I can quote to convince non-experts of the
significance of applying Semantic Web to biomedical research,
especially computational cell biology.

  I need a recorded public statement from a source recognizable as
authoritative to a non-expert: e.g. could be from a relevant
government agency, a well-known research institution (including major
grad schools and companies), a well-known (i.e. well-known outside the
field) expert, some one where a brief look at the biography
immediately suggests he or she is an authority, some one quoted in
major media, etc.

  Significance could mean abstract things like advancing science and
health care, but even better would be tangible things like: saves
lives, saves money, cures cancer/malaria/AIDS, creates jobs, etc.

  Thanks a lot!

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
Virtual Cell (http://vcell.org)
SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)
http://www.oliver.curiousworld.org

Re: "molar" for concentration

[Oliver Ruebenacker]

 Hello,

  What is wrong with the URI I provided?

 Take care
 Oliver

On Tue, Aug 16, 2011 at 3:43 PM, Matthias Samwald
 wrote:
> Besides the ontologies already mentioned, the unit ontology /
> UO (http://obofoundry.org/cgi-bin/detail.cgi?id=unit) also has a class for
> "mole" and one for "molar mass unit". But you actually wanted a URI for a
> datatype so this (as well as the other ontologies mentioned before) is
> probably not what you wanted.
>
> Does anybody know of an ontology that defines scientific datatypes in OWL 2?
>
>  - Matthias
>
> From: Helena Deus
> Sent: Tuesday, August 16, 2011 5:23 PM
> To: W3C HCLSIG hcls
> Subject: "molar" for concentration
> Hi all,
> Wondering if anyone ever needed/came across a URI for datatype "M" (molar,
> as in 10 M -> 10 Molar).
> http://en.wikipedia.org/wiki/Molar_concentration
>
> Cheers,
> --
> Helena F. Deus
> Post-Doctoral Researcher at DERI/NUIG
> http://lenadeus.info/
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: "molar" for concentration

[Oliver Ruebenacker]

 Hello,

  UOME has Molar and the URI is http://www.sbpax.org/uome/list.owl#Molar

  UOME aims to supply any unit in common usage and on top of that
provides means to define your own units by deriving them from other
units (e.g. more common ones).

  More info is here: http://www.sbpax.org/uome/index.html

 Take care
 Oliver

On Tue, Aug 16, 2011 at 11:23 AM, Helena Deus  wrote:
> Hi all,
> Wondering if anyone ever needed/came across a URI for datatype "M" (molar,
> as in 10 M -> 10 Molar).
> http://en.wikipedia.org/wiki/Molar_concentration
>
> Cheers,
> --
> Helena F. Deus
> Post-Doctoral Researcher at DERI/NUIG
> http://lenadeus.info/
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: Trying to summarise: Semantic free identifiers

[Oliver Ruebenacker]

 Hello,

On Tue, Jun 21, 2011 at 3:13 PM, James Malone  wrote:
> So.. a long but useful discussion. That will teach me to open my big mouth :)
>
> Is this fair as the PRIMARY reasons for this difference in opinions:
>
> 1. Having semantic information such as a label in a URI makes it easier
> to, at a glance, grasp some sort of meaning of a class/predicate and makes
> SPARQLing and looking at RDF easier.
>
> 2. NOT having semantic information in a URI ensures class definitions need
> to be looked up before they can be used, hence, reducing ambiguity and
> that it potentially improves maintainability.
>
> Can 1 be resolved by tooling? Seems to me 2 is happening already and will
> grow as practice in a lot of the bio-ontology community. If there is a
> lack of tooling surely this group should be looking at doing something
> about that - funding, lobbying..

  I don't think some one who does not look up the class definitions
would bother to keep the tool updated that resolves the meaningless
identifiers.

  I know a group of software developers working on a highly successful
project that uses various kinds of RDF data (mostly BioPAX, MIRIAM and
Dublin Core), but really they don't want to get bothered with the
theoretical intricacies. They just want some simple transparent
light-weight tool to turn the RDF into Java objects, and vice versa,
and if they want to understand what the tool does, rather than
studying RDF, they prefer to look at sample data, or the tool's source
code or use a debugger. They don't like those nasty URIs either and
prefer to deal just with local names.

  They would certainly not appreciate identifiers that are opaque.

  To me, it is just yet another attempt to turn RDF into something
that is marvelous in theory but no one will want to use.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: My task from last week: Semantic free identifiers

[Oliver Ruebenacker]

 Hello,

On Mon, Jun 20, 2011 at 4:15 PM, M. Scott Marshall
 wrote:
> The main reason is that when semantics and natural language are
> inserted into identifiers, some identifers are doomed to become stale
> as thinking evolves or changes about the semantic representation.

  Doesn't the definition itself grow stale?

> Shouldn't we consider RDF to be the bytecode of knowledge?

  Then what is the source code, and the compiler?

 Take care
     Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: My task from last week: Semantic free identifiers

[Oliver Ruebenacker]

 Hello,

On Mon, Jun 20, 2011 at 3:44 PM, Helena Deus  wrote:
>> thing"... By "right thing" I mean that I'm sure Hungarian semantic-webbers
>> would have quite something to say about a decision to make the URI "partOf"
>> rather than "A_0001" + multi-lingual labels.  It's a bit selfish of us
>> English-speakers to create global infrastructures just for ourselves... na?
>>
>
> ++1!!
> And the HCLS domains are filled with examples where label-URI would not
> work: for example, hypothetical proteins
> (http://en.wikipedia.org/wiki/Hypothetical_protein), would not be named are
> not named and yet we know they exist.
> Should we give these hypothetical proteins a numeric URI but all other
> proteins a name? How about when they are "graduated" into real proteins?
> Should everyone just stop using the hypothetical-protein-URI and change into
> the newly named protein-name-URI?
> I think that would be a recipe for disaster :-)

  I understand for proteins. But I'm not sure a relationship that can
not even readily be given a name should be part of the relationship
ontology.

  Suppose that the dominant language was not English, but some other
language that non of us know and "part of" in that language is "tab
tom ba". In that case, I would still find "tab tom ba" easier to
remember than some random number. And I can always write:

prefix part_of: <http://purl.obolibrary.org/obo/tab_tom_ba>

  So the advantage of using numbers is not clear to me.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: Lightweight RDF/OWL library for Java?

[Oliver Ruebenacker]

 Hello,

On Mon, May 2, 2011 at 5:02 PM, Jim McCusker  wrote:
> On Mon, May 2, 2011 at 4:44 PM, Oliver Ruebenacker  wrote:
>>  Mostly we are looking for a small library (code). Small API is a
>> plus (and tends to come with small code anyway).
>
> Looks like this has been discussed at stack overflow:
>
> http://stackoverflow.com/questions/73445/what-are-some-good-java-rdf-libraries
>
> One suggestion there that seems to be in line with what you want is
> JRDF (http://jrdf.sourceforge.net)

  Thanks, will look into.

>>  Strongly preferred is a library that works with JDOM, because our
>> project already uses that.
>>
>>  Jena is very powerful and very large. I think with all supporting
>> libraries it adds up to something like 10MB, if I remember correctly.
>
> Is this a dependency management issue? I generally use maven to track
> dependencies for me, I just have the one entry in for Jena. 10 MB
> isn't that big anymore, in the grand scheme of things. The Stack
> Overflow post has some discussion on how to cut down on the included
> jars.

  Interesting. When I started using Jena maybe five years ago, it
depended on something like 10 libraries. I tried to remove those
libraries and got UnsatisfiedLinkException or something like that for
almost every one.

>> Part of its complexity is comes from its layered structure. Main
>> classes of the API such as Resource, Statement and Model wrap around
>> other classes (Node, Triple and Graph).
>
> For me, that's been a benefit of using Jena, I can work at the level
> of abstraction that I need, and ignore the stuff at the lower level.

  For my taste, an RDf data model only needs one layer. I started in
Jena with the Resource/Statement/Model level, until I wanted to use
queries, which required the Node/Triple/Graph level. Although, for
most purposes I gave up on using queries for anything more complicated
than what can be accomplished with Model.listStatements(...), because
it costed too much time.

  I like abstraction, but it has a cost when it comes to debugging.

>> A Resource links to a Model
>> which can be convenient but also very confusing if you have multiple
>> models, so I could gladly do without that.
>
> Almost all APIs support multiple models and/or graphs (depending on
> the API under discussion). Most of my use cases call for multiple
> models, so I'd end up shying away from an API that did away with that.
> :-)

  Misunderstanding. I meant keeping the multiple models and doing away
with resources linking to a model, precisely because the same resource
can be in multiple models at the same time.

 Take care
 Oliver

>
> Jim
> --
> Jim McCusker
> Programmer Analyst
> Krauthammer Lab, Pathology Informatics
> Yale School of Medicine
> james.mccus...@yale.edu | (203) 785-6330
> http://krauthammerlab.med.yale.edu
>
> PhD Student
> Tetherless World Constellation
> Rensselaer Polytechnic Institute
> mcc...@cs.rpi.edu
> http://tw.rpi.edu
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: Lightweight RDF/OWL library for Java?

[Oliver Ruebenacker]

 Hello Jim, All,

On Mon, May 2, 2011 at 3:09 PM, Jim McCusker  wrote:
> Smaller and simpler in which respect? Code size, API compexity, memory
> overhead, something else?

  Mostly we are looking for a small library (code). Small API is a
plus (and tends to come with small code anyway).

  Strongly preferred is a library that works with JDOM, because our
project already uses that.

  Jena is very powerful and very large. I think with all supporting
libraries it adds up to something like 10MB, if I remember correctly.
Part of its complexity is comes from its layered structure. Main
classes of the API such as Resource, Statement and Model wrap around
other classes (Node, Triple and Graph). A Resource links to a Model
which can be convenient but also very confusing if you have multiple
models, so I could gladly do without that.

  Thanks!

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Lightweight RDF/OWL library for Java?

[Oliver Ruebenacker]

 Hello,

  We are looking for a library to read and write RDF/OWL within a Java
project. Currently, we are using Jena, but would prefer something
smaller and simpler. Any advice? Thanks!

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: Watson

[Oliver Ruebenacker]

 Hello,

  They reported about it on NPR morning edition:

  http://www.npr.org/2011/02/14/133697585/on-jeopardy-its-man-vs-this-machine

 Take care
 Oliver

On Tue, Feb 15, 2011 at 11:09 AM, Michel_Dumontier
 wrote:
> Given that IBM’s AI system called Watson is competing in Jeopardy against
> grand champions, you might find the following overview of interest :
>
>
>
> http://www.youtube.com/watch?v=3G2H3DZ8rNc
>
>
>
> m.
>
>
>
> Michel Dumontier
>
> Associate Professor of Bioinformatics
>
> Carleton University
>
> http://dumontierlab.com
>
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: LODD Telcon

[Oliver Ruebenacker]

  Today is National Opt-Out Day
(http://www.huffingtonpost.com/2010/11/24/opt-out-day-how-_n_788002.html)

On Wed, Nov 24, 2010 at 7:18 AM, Oliver Ruebenacker  wrote:
> opting out?
>
> On Wed, Nov 24, 2010 at 5:27 AM, M. Scott Marshall
>  wrote:
>> Regrets. Traveling to Hinxton today.
>> -Scott
>>
>> On Nov 23, 2010 2:12 PM, "Susie Stephens"  wrote:
>>
>> Here's the reminder for Wednesday's LODD telcon.
>>
>> Susie
>>
>>
>> == Conference Details ==
>> * Date of Call: Wednesday November 24, 2010
>> * Time of Call: 11:00am Eastern Time (ET), 16:00 British Time (BT), 17:00
>> Central European Time (CET)
>> * Dial-In #: +1.617.761.6200 (Cambridge, MA)
>> * Dial-In #: +33.4.26.46.79.03 (Paris, France)
>> * Dial-In #: +44.203.318.0479 (London, UK)
>> * Participant Access Code: 4257 ("HCLS").
>> * IRC Channel: irc.w3.org port 6665 channel #HCLS
>> * Duration: ~1h
>> * Convener: Susie
>>
>> == Agenda ==
>> * J Cheminformatics paper
>> * Best practices for mapping experimental data
>> * Data updates
>> * AOB
>>
>
>
>
> --
> Oliver Ruebenacker, Computational Cell Biologist
> Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
> Turning Knowledge Data into Models
> Center for Cell Analysis and Modeling
> http://www.oliver.curiousworld.org
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: LODD Telcon

[Oliver Ruebenacker]

opting out?

On Wed, Nov 24, 2010 at 5:27 AM, M. Scott Marshall
 wrote:
> Regrets. Traveling to Hinxton today.
> -Scott
>
> On Nov 23, 2010 2:12 PM, "Susie Stephens"  wrote:
>
> Here's the reminder for Wednesday's LODD telcon.
>
> Susie
>
>
> == Conference Details ==
> * Date of Call: Wednesday November 24, 2010
> * Time of Call: 11:00am Eastern Time (ET), 16:00 British Time (BT), 17:00
> Central European Time (CET)
> * Dial-In #: +1.617.761.6200 (Cambridge, MA)
> * Dial-In #: +33.4.26.46.79.03 (Paris, France)
> * Dial-In #: +44.203.318.0479 (London, UK)
> * Participant Access Code: 4257 ("HCLS").
> * IRC Channel: irc.w3.org port 6665 channel #HCLS
> * Duration: ~1h
> * Convener: Susie
>
> == Agenda ==
> * J Cheminformatics paper
> * Best practices for mapping experimental data
> * Data updates
> * AOB
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Thickness of lines in this figure

[Oliver Ruebenacker]

 Hello,

  Can any one explain what in this figure determines the different
thicknesses of lines? Thanks!

  
http://sourceforge.net/apps/mediawiki/bio2rdf/nfs/project/b/bi/bio2rdf/4/4a/Bio2rdfmap_blanc.png

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: When does a document acquire (web) semantics?

[Oliver Ruebenacker]

 Hello Andrea,

On Tue, Feb 2, 2010 at 11:41 AM, andrea splendiani (RRes-Roth)
 wrote:
> What is "meaning" for you ?

  That's precisely what I am trying to find out.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: When does a document acquire (web) semantics?

[Oliver Ruebenacker]

 Hello,

  When asking for a practical example, I was more concerned about the
consumer rather than the producer of data. It is easy to claim some
data has meaning, but the question is to what extend that meaning can
be appreciated by others.

  Why don't we build a little meaning detector. Some device that takes
a document and makes beep if it finds meaning in it. With such a
device, it would be easy to find out, when exactly the document
acquired the meaning. Or at least, design an experiment where the
outcome is predicted by a theory based on the meaning of the document.

  If it turns out that such a device can not be build, or such an
experiment can not be designed, then I would assume that the document
alone has no meaning, and that instead, meaning resides in a system
larger than the document. That system than needs to be identified.

 Take care
 Oliver

On Mon, Feb 1, 2010 at 4:53 PM, John Madden  wrote:
> Hi Oliver,
>
> I don't want to speak for Eric, and I'm not even sure I've accurately 
> represented his point here. Nor am I sure that they *are* different scenarios.
>
> Instead of saying they are or aren't, let me throw out a scenario that 
> concerns me, and in the context of which they *might* be different, and ask 
> for people to comment.
>
> Suppose I publish a medical document in English, and purport to attach to it 
> an "official" RDF/OWL graph.
>
>        A problem (sidebar):
>
>        Is this possiible? If so, what makes it "official"? Not sure. Maybe 
> the graph is connected to the document
>        with grddl transform that I have published, which makes explicit the 
> rules I use to go from English to RDF.
>        Maybe the graph contains some assertions that reference some 
> provenance/trust vocabulary, such that
>        triples are contained in it that assert -- in some way -- that it is a 
> privileged graph. Maybe the RDF/XML
>        document has an XMLSig on it and I've stated to the world that I 
> nobody is allowed, under penalty of my
>        wrath, to represent this document by RDF/OWL graphs except provided 
> that ones I've signed are provably
>        consistent with them (which is an inane thing for me to do, and not 
> only because I don't know anybody who
>        is afraid of my wrath.)
>
>        (For a medical document, it might not be *me* that insists on this 
> claim; it might be my employer/hospital.
>        They don't want people attributing meanings to the document other than 
> those they have had a chance
>        to approve, because they don't want somebody claiming the RDF/OWL they 
> published led to a subsequent
>        adverse event (by, e.g. being used in a decision support system at 
> some later time that attributed a different
>        meaning to some vocabulary item). So for example they might only allow 
> locally defined classes properties
>        to be used in the graph.)
>
> Anyway, I somehow put a stake in the ground and loudly assert that **this** 
> is what it means.
>
> Now later Eric comes along and wants access to my document, and many others 
> in a bunch of different databases, because he is aggregating data about 
> patient encounters for a research project of his. In his SPARQL query, he 
> does a bunch of joins, that in effect are mappings between the local 
> vocabularies in the existing RDF graphs and whatever vocabularies he's 
> attempting to aggregate to. In this process, my "official" RDF triples get 
> left behind.
>
> Is this a possible scenario? Where does it fail? Is it that the SemWeb 
> doesn't support any notion of an "official" graph? Is it that there is no 
> such thing as an "official graph" at all (on the sem web or anywhere else)?
>
> John
>
>
>
>
>
>
> On Feb 1, 2010, at 3:14 PM, Oliver Ruebenacker wrote:
>
>>     Hello,
>>
>> On Mon, Feb 1, 2010 at 1:30 PM, John Madden  wrote:
>>> We had an interesting call in TERM today. One of the topics I would like to 
>>> boil down to the question "When does a document acquire its semantics?" or, 
>>> "when does a document come to mean something?"
>>>
>>> I argued the (admittedly intentionally) radical view that documents have no 
>>> semantics whatsoever until a reader performs an act of interpretation upon 
>>> the document, which in the Semantic Web world would be the same as 
>>> attributing an RDF/OWL graph to the document.
>>>
>>> Even if the author of the document attributes a a particular RDF/OWL graph 
>>> to her won document, I argued that this graph is not privileged in any way. 
>>> That othe

Re: When does a document acquire (web) semantics?

[Oliver Ruebenacker]

 Hello,

On Mon, Feb 1, 2010 at 1:30 PM, John Madden  wrote:
> We had an interesting call in TERM today. One of the topics I would like to 
> boil down to the question "When does a document acquire its semantics?" or, 
> "when does a document come to mean something?"
>
> I argued the (admittedly intentionally) radical view that documents have no 
> semantics whatsoever until a reader performs an act of interpretation upon 
> the document, which in the Semantic Web world would be the same as 
> attributing an RDF/OWL graph to the document.
>
> Even if the author of the document attributes a a particular RDF/OWL graph to 
> her won document, I argued that this graph is not privileged in any way. That 
> others could justifiably argue that the author's own RDF/OWL graph is 
> incomplete, or flawed, or irrelevant, or even incorrect. And the same is true 
> of any subsequent interpreters (i.e. authors of RDF/OWL graphs that purport 
> to represent the "meaning" of the same document).
>
> Eric argued a really interesting point. He argued (and Eric, correct me if 
> I'm interpreting you wrong here), that semantics instead come into existence 
> (or perhaps *can* come into existence) at the point when somebody executes a 
> SPARQL query on a set of RDF/OWL graphs. That is to say, maybe I'm wrong and 
> semantics doesn't even come into existence when somebody attributes an 
> RDF/XML graph to a document; but rather it only comes into existence when 
> somebody queries across (possibly) many graphs of many different people.
>
> What do you think?

  Can you give an example were this difference is relevant?

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
Turning Knowledge Data into Models
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: Jena as RDF Adapter

[Oliver Ruebenacker]

 Hello,

  Very nice! And this woks by implementing Jena's Graph interface?

 Take care
 Oliver

On Thu, Oct 1, 2009 at 8:31 AM, Kei Cheung  wrote:
> Andrea Splendiani wrote:
>
>> Hi,
>>
>> do you have a link to some docs ?
>> (other than the paper that should come out tomorrow ?)
>
> The special issue just came out:
>
> http://www.biomedcentral.com/1471-2105/10?issue=S10
>
> The paper is accessible at:
>
> http://www.biomedcentral.com/1471-2105/10/S10/S10
>
> It provides links to the following supplemental materials:
>
> AIDA Toolkit: The software is available at
> http://www.adaptivedisclosure.org/aida and may be freely downloaded under
> the Apache license.
>
> FeDeRate: The data and software are available at
> https://sourceforge.net/projects/swobjects and may be freely downloaded and
> used with no license requirements.
>
> HCLS KB hosted by DERI, Galway, Ireland http://hcls.deri.org/sparql
>
> HCLS KB hosted by the Freie Universitaet Berlin:
> http://www.corporate-semantic-web.de/hcls.html
>
> Cheers,
>
> -Kei
>
>
>
>>
>> ciao,
>> Andrea
>>
>> On 30 Sep 2009, at 23:45, M. Scott Marshall wrote:
>>
>>> Hi Oliver,
>>>
>>> Are you aware of SWObjects http://sourceforge.net/projects/swobjects/
>>> from Eric Prud'hommeaux? We've used it in a few demo's now:
>>>
>>> http://hcls.deri.org/coi/demo/
>>>
>>> http://www.w3.org/2009/08/7tmdemo
>>>
>>> Kei-Hoi Cheung, H. Robert Frost, M. Scott Marshall, Eric  Prud'hommeaux,
>>> Matthias Samwald, Jun Zhao, Adrian Paschke, A Journey to Semantic Web
>>> Query Federation in Life Sciences, BMC Bioinformatics Volume 10
>>> Supplement 10, Oct 2009.
>>>
>>> Cheers,
>>> Scott
>>>
>>> --
>>> M. Scott Marshall
>>> Leiden University Medical Center / University of Amsterdam
>>> http://staff.science.uva.nl/~marshall
>>>
>>> Oliver Ruebenacker wrote:
>>>
>>>>    Hello,
>>>>
>>>>  On http://esw.w3.org/topic/RDFImportersAndAdapters it is said that:
>>>>
>>>>  "Jena Framework: Jena's Graph interface could be used to implement
>>>> adapters. [...] D2RQ is an example of an adapter implemented as a  Jena
>>>> graph."
>>>>
>>>>  Do we know of any implementations other than adapters to relational
>>>> databases (such as D2RQ)?
>>>>
>>>>  While I am convinced above statement is true, it would be nice to
>>>> have a citation to convince others, too. Do you know any?
>>>>
>>>>  Thanks!
>>>>
>>>>    Take care
>>>>    Oliver
>>>>
>>>
>>>
>>>
>>>
>>>
>>
>> ---
>> Andrea Splendiani
>> Senior Bioinformatics Scientist
>> Rothamsted Research, Harpenden, UK
>> andrea.splendi...@bbsrc.ac.uk
>> +44(0)1582 763133 ext 2004
>>
>>
>
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Jena as RDF Adapter

[Oliver Ruebenacker]

 Hello,

  On http://esw.w3.org/topic/RDFImportersAndAdapters it is said that:

  "Jena Framework: Jena's Graph interface could be used to implement
adapters. [...] D2RQ is an example of an adapter implemented as a Jena
graph."

  Do we know of any implementations other than adapters to relational
databases (such as D2RQ)?

  While I am convinced above statement is true, it would be nice to
have a citation to convince others, too. Do you know any?

  Thanks!

 Take care
     Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

ISWC/SWASD and "Springer Style"

[Oliver Ruebenacker]

 Hello,

  On the ISWC/SWASD 2009 website [1], it says research papers "must be
formatted in the style of Springer". Can any one elaborate what this
means for the author in practical terms? Thanks!

 Take care
 Oliver

  [1] http://esw.w3.org/topic/HCLS/ISWC2009/Workshop

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: Can RDFa be used on XML: pharma information

[Oliver Ruebenacker]

 Hello,

  A nice example of the traps of data linking. The data seems to say
that Einstein was born in the Federal Republic of Germany. In fact, he
was born before the FRG was founded.

 Take care
 Oliver

On Tue, Jun 23, 2009 at 9:22 AM, Rick Jelliffe wrote:
> Egon Willighagen wrote:
>>
>> The problem here is to define what attributes your XML will use to
>> define the RDFa hooks... what attributes will define a new subject,
>> the predicate, and how you define the object...
>>
>>
>
> Yes, we lose the  html:base element and html:link, but why would we lose the
> predicates?   @rel and @rev would presumably be available on any element:
> couldn't it be used so that instead of
>
> http://dbpedia.org/resource/Albert_Einstein";>
>  Albert Einstein
>  1879-03-14
>  http://dbpedia.org/resource/Germany";>
>   Federal Republic of
> Germany
>  
> 
>
> I can have
>
> http://dbpedia.org/resource/Albert_Einstein";>
>  Albert Einstein
>  1879-03-14
>   resource="http://dbpedia.org/resource/Germany";>
>   Federal Republic of
> Germany
>  
> 
>
> It seems to me that where-ever RDFa does not rely on HTML semantics, it
> "should" be free (there is no conceptual impediment) to use on XML: it can
> certainly determine whether an XML element has a legit XMLliteral or mixed
> or element content.
>
>> Because the XML is using a local namespace, it will be unrecognizable
>> for any client... however, given you define those attributes (or via
>> new elements), you should be able to embed this RDFa in the HTML more
>> easily too...
>>
>
> What is the necessary difference, for an RDFa engine, between
>
>           property="dc:title">
>     Canteen Cuisine
> 
>
> and
>
>           property="dc:title">
>     Canteen Cuisine
> 
>
> Cheers
> Rick Jelliffe
>
>
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: Question about standardization

[Oliver Ruebenacker]

 Hello Bijan, All,

  The sympathy might not come across as intended if you throw such
weighty issues as rechartering at newcomers.

  The rhetorical question was not intended as a blow, but to elicit
some more information on what makes a thing substantially worthy of
standardization. I was hoping to get something more enlightening than
an all too obvious example.

  My impression is that the SBML community is more than capable of
providing an engineer day per week. I am wondering, are we talking
here about developing or recognizing a standard, or is there any such
distinction at all at W3C? I can imagine that developing a standard is
costly, but I would guess recognition to be way less costly. (For
grouchy people: Forgive my know-nothing arrogance. This is neither
intended as a rhetorical question nor a dialectical blow)

 Take care
 Oliver

On Wed, May 13, 2009 at 6:21 AM, Bijan Parsia  wrote:
> On 13 May 2009, at 10:48, Oliver Ruebenacker wrote:
>
>>     Hello Bijan, Michael, All,
>>
>>  The group does not deliver standards, but can submit something for
>> consideration to W3C.
>
> Hence my care in distinguishing what the group can and cannot do.
>
>>  I remember this being discussed indetail in one
>> of the phone conferences.
>
> Well, if you would read a little more carefully, you wouldn't have to
> remember.
>
>>  If SBML is not deserving of being a standard, the what is?
>
> HTML.
>
>> Something
>> no one uses?
>
> Ah yes, non sequiturial rhetorical questions that were obviously intended as
> a crushing dialectical blow, and succeed at being such --- just not in the
> intended direction.
>
> There are a host of reasons to undertake standardization in a formal
> standards body and a host of reasons not to. The best one, in my opinion, is
> ensuring interoperability of existing systems (i.e., to reduce competition
> at one level to enable better competition at another level). In my opinion,
> standardization shouldn't be regarded as something akin to publishing a
> journal article (i.e., a sanctioned archival representation of a body of
> significant work). (BTW, this is just to give an example of what I would
> consider a bad reason, not to remotely suggest that this is "the reason" for
> pursuing SBML standardization. I don't *know* what the reasons are for
> pursuing SBML standardization, hence my asking for, you know, a reasonable
> discussion of the rationale. That discussion has to happen as there lots of
> people you have to convince aside from me.)
>
> Standardization has costs that can harm efforts. It drains time, energy,
> money, control. For example, the standard expected commitment of an
> organization to a W3C WG is on engineer day a week (more, if you're an
> editor). A WG is a committee that you do not control the membership of.
> Indeed, that is the W3C...you have to convince a lot of people who *properly
> do not care about SBML* (or OWL, or...) that it's worth diverting the
> *extremely limited* resources the W3C has to SBML.
>
> There's a lot of politics since there are limited resources. Your sort of
> know-nothing arrogance will, I suspect, play rather poorly. It is so playing
> with me and I started this conversation fairly sympathetic to SBML.
>
> I've been involved in lots of W3C WGs both inside and outside the semantic
> web area and am trying to offer considered, reasoned, helpful advice based
> on my experience and understanding of the process. If you don't want that
> input, then yay. I'll stop now.
>
> Cheers,
> Bijan.
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: Question about standardization

[Oliver Ruebenacker]

 Hello Bijan, Michael, All,

  The group does not deliver standards, but can submit something for
consideration to W3C. I remember this being discussed indetail in one
of the phone conferences.

  If SBML is not deserving of being a standard, the what is? Something
no one uses?

 Take care
 Oliver

On Wed, May 13, 2009 at 4:31 AM, Bijan Parsia
 wrote:
> On 13 May 2009, at 03:12, Michael Hucka wrote:
>
>> Hi,
>>
>>>> I hope this is not too off-topic -- I'm new to this
>>>> group and still am trying to get a sense for what it's
>>>> about.
>>
>>  bparsia> The way to figure out it's formal scope is to
>>  bparsia> read the charter:
>>  bparsia> http://www.w3.org/2008/05/HCLSIGCharter
>>
>> In fact, I did that before posting.  But there is enough
>> breadth and room for interpretation in the statements
>
> I don't see how. If you look at:
>  http://www.w3.org/2008/05/HCLSIGCharter#deliverables
> you see that the group deliverables do not include standards.
>
>> there
>> that I still was not entirely certain whether my question
>> would be considered appropriate,
>
> I think you are conflating standardization with the other activities. I
> think SBML is the kind of thing for which HCLSIG could, if the members felt
> up to it, implement use cases, produce technical collateral, etc.
>
> Thus, if you are looking for a wider forum for SBML, HCLSIG is appropriate.
>
> If you really want (and need) to produce a *standard*, that is, a
> specification of a language that has the formal endorsement of the W3C, then
> HCLSIG is merely a place to start building consensus for the chartering of
> such a group.
>
> [snip]
>>
>>  bparsia> Well, given that standardization is a costly
>>  bparsia> endeavor, I'd ask about the motivations and
>>  bparsia> expected benefits for moving development into a
>>  bparsia> standards body, per se.n There are lots of
>>  bparsia> different sorts of standards body and lots of
>>  bparsia> different reasons for pursuing standardization.
>>
>> Indeed.  Standardization of SBML has been discussed over
>> many years in the SBML community,
>
> Pointers?
>
>> but generally pushed back
>> due to various reasons, such as the question of whether SBML
>> was ready, and whether we had the resources to pursue
>> official standards recognition.
>
> And is there a reason? I mean, if you have interop already and buy-in from
> key players, then all that's left is publicity (or badge collecting). These
> can be worthwhile, but they come at considerable cost, not just for you, but
> for the W3C.
>
>>  We may still lack the
>> resources (depends on what's involved), but aside from that,
>> my sense is that it is time to look into it seriously now.
>
> [snip]
>
> But, again, why? I mean, what goals do you have for standardization? Are
> there implementations that don't comply? Are there vendors who can't sell
> their SBML tool to govt agencies due to the procurement requirement to use
> "recognized standards" thus they are forced to use older, inadequate
> standards? Or is there a user base that likely *would* use (and benefit)
> from it but just need to know they are working "with a standard"? Or are
> there patent implications you are trying to work around?
>
> Cheers,
> Bijan.
>
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: Question about standardization

[Oliver Ruebenacker]

 Hello Michael,

  I would say you have come to the right place. Great to have you here.

  SBML is a mature and widely adopted format that is more than worthy
to be submitted as a interest group recommendation (if "interest group
recommendation" is the right term).

  You just have to allow some time for people here to get familiar
with SBML, and to navigate the buerocracy.

  Systems Biology is a central theme in the HCLSIG, although it is not
very clear where it fits into the current organization: HCLSIG has six
task forces, of which at least about half have a strong connection to
Systems Biology, although none of them really focusses on it.

  I think Systems Biology is way too important not to have a task
force, even keeping in mind that I have been told we may already have
too many of them.

 Take care
 Oliver

On Tue, May 12, 2009 at 2:22 AM, Michael Hucka  wrote:
> Hello there,
>
> I hope this is not too off-topic -- I'm new to this group
> and still am trying to get a sense for what it's about.
>
> Those of us working on SBML (the Systems Biology Markup
> Language -- see http://sbml.org) would like to pursue
> standards-body recognition of SBML.  Would this (HCLSIG) be
> an appropriate group within which to pursue that goal?  If
> not, what alternative(s) would people recommend?
>
> Thanks for your time,
> MH
>
> --
> Mike Hucka, Ph.D.  mhu...@caltech.edu  http://bnmc.caltech.edu
> Senior Research Fellow, Control and Dynamical Systems
> Co-director, Biological Network Modeling Center (BNMC)
> Beckman Institute @ the California Institute of Technology
>
>
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Is a Protein an Object Aggregate?

[Oliver Ruebenacker]

 Hello,

  Consider: (a) Protein in BioPAX Level 2 (b) Protein in the Protein
Ontology (c) A class protein how it is usually understood by
biologists.

  Is it a sub class of BFO's object aggregate? Or of BFO's object? Or what else?

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Wacek, All,

On Tue, Mar 31, 2009 at 9:00 AM, Wacek Kusnierczyk
 wrote:
> Oliver Ruebenacker wrote:
>>   What about this statement:
>>
>>   "Two grams of hydrogen react with 16 grams of oxygen to 18 grams of water"

> what about it?

  Can we make a correct statement that says what appears to be
intended to be said in above statement ;)

 Take care
     Oliver


-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Wacek, All,

On Tue, Mar 31, 2009 at 8:30 AM, Wacek Kusnierczyk
 wrote:
> i'd agree that having non-integer *molecule numbers* sounds nonsense,
> but having non-integer *relative molecule numbers* certainly doesn't.
> in any case, the equation
>
>    N2O2 -> 2 NO2 + 1/2 O2
>
> is equivalent to
>
>    2 N2O2 -> 4 NO2 + O2
>
> and you can always (i guess) avoid non-integer coefficients by
> multiplying both sides by a constant.

  What about this statement:

  "Two grams of hydrogen react with 16 grams of oxygen to 18 grams of water"

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Is OWL useful at all for Quantitative Science?

[Oliver Ruebenacker]

 Hello, All,

  There recent discussion has made me wonder, whether OWL is at all
useful to do quantitative science, if we insist that it is used
correctly (incorrect OWL seems to be useful).

  Can any one give me a simple example of a useful application of
correct OWL in quantitative science?

  I have tried to come up with a simple example. Feel free to come up
with a simpler one:

  Express in correct OWL: Washington DC is further away from Boston
than New York City

  Use case: I want to fly with my helicopter from Boston to either DC
or NYC, whichever is closer.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Pat, All,

  Let me try to take a step back and summarize what I think I learned so far:

  The Ontologists have gained impressive mastery over what I would
call the World of Discrete Particulars. They know how to deal with
particulars, classes of particulars and cardinality restrictions, in
other words, integers and intervals of integers.

  They know how to say, for example, that a particular petri dish has
2000-3000 cells, each of which has 150-200 mitochondria, each of which
has 30-40 ATP molecules.

  However, the Science community typically deals with what I would
call the World of Reproducible Fluxes. They think in terms of
reproducible scenarios, expectation values, variances, continuous
change, Gaussian distribution and differential equations. (Literally,
these is what I learned in the first meeting of the Physics 101 class
when I went to College.)

  They know how to say, for example, that if you dump a typical human
liver cell into a 0.2 percent solution of some drug, the ATP
concentration in the mitochondria will drop by a relative rate of 1.2
percent per second during the first ten minutes.

  Asking a scientist to define "expectation value" is akin to asking
an Ontologist to define "class".

  When the Ontologists say, they have "solved mereology long time
ago", they seem to mean: In the World of Discrete Particulars. Not in
the World of Reproducible Fluxes.

  As it happens, Scientists discover OWL to produce ontologies that
live in the World of Reproducible Fluxes, such as BioPAX. Even
Scientists agree that it has weaknesses.

  Ontologist: BioPAX is nonsense! BioPAX is ill-defined! It is not an
ontology. It is not OWL.

  Scientist: I know it has weaknesses, but is it really that bad?

  Ontologist: Totally! We need to rebuild it from scratch.

  Scientist: OK, if you say so.

  (Ontologist goes and much later comes back with a new BioPAX, living
entirely in the World of Discrete Particulars)

  Ontologist: Here! A wonderful new BioPAX. Perfect ontology, perfect
OWL. Everything is clear and well-defined.

  Scientist: I am sorry, I can not use that.

  Ontologist: Why not?

  Scientist: It lacks the most basic terms Science is based on, such
as reproducible scenarios, expectation values and rate of change.

  Ontologist: You need to translate those terms into the World of
Discrete Particulars, and then I will include them.

  Scientist: How do I do that?

  Ontologist: I have no clue.

  But one thing both the Ontologist and the Scientist would agree:
Mereology in the World of Discrete Particulars is not Rocket Science.

 Take care
 Oliver

On Mon, Mar 30, 2009 at 12:35 PM, Pat Hayes  wrote:
>
> On Mar 30, 2009, at 9:59 AM, Oliver Ruebenacker wrote:
>
>>    Hello Pat, All,
>>
>> On Sun, Mar 29, 2009 at 11:35 PM, Pat Hayes  wrote:
>>>
>>> On Mar 29, 2009, at 11:15 AM, Oliver Ruebenacker wrote:
>>>>
>>>>  I am assuming that these classes all make a commitment about what
>>>> their instances mean, so users could declares instances and rely on
>>>> that commitment to be useful, right?
>>>
>>> As I have been taken to task (offline) for agreeing with you, allow me to
>>> intercede. On this point, I think everyone is right. Yes, classes are
>>> things
>>> that have, or can have, instances, and that is all that a class is, in
>>> effect. (RDFS makes this quite explicit by _defining_ classes to be
>>> things
>>> in the range of the rdf:type property.) On the other hand, it is
>>> certainly
>>> correct that ontologies can say a lot about classes without ever
>>> mentioning
>>> instances. On the other hand, it is also the case that, were someone to
>>> (not
>>> unreasonably) wish to connect such classes with their instances, the
>>> resulting conclusions should be correct, and if they were not, then this
>>> would be a serious critique of the ontology.
>>
>>  I have no idea what the person who took you to task was thinking,
>> but it seems related to the ongoing controversy over whether
>> substances should be instances or classes.
>
> Which seems like a much more interesting topic, indeed.
>
>>  In BioPAX, we have a class physical entity with subclasses such as
>> protein. EGFR would be an instance of protein, and we could say in
>> BioPAX that EGFR has a sequence. (I would argue it should rather say
>> that EGFR matches a sequence pattern, but that is another story.)
>>
>>  The problem is that there are certain assumptions which BioPAX users
>> are encouraged to follow, such as (1) if two physical entities refer
>> to the same record, they are identical (2) if two physical entities
>> refer to different records in the same sourc

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Bijan, All,

On Mon, Mar 30, 2009 at 12:20 PM, Bijan Parsia  wrote:
> On 30 Mar 2009, at 17:13, Oliver Ruebenacker wrote:
>>  A class may not be instantiated in every single use, but it is
>> intended to be instantiated in some cases. To dispute that, you would
>> have to give me an example of a class that is never instantiated.

> Any NCI Thesaurus class.

  Not an ontology.

> NCI Thesarus is a controlled vocabularies generated by an ontology. This is
> a standard use of ontologies. I guess I should be surprised that you don't
> know that, but it turns out I'm not!

  Irrelevant point. You can use an ontology to create toilet paper,
but that does not mean that toilet paper is an ontology.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Bijan, All,

On Mon, Mar 30, 2009 at 12:07 PM, Bijan Parsia  wrote:
> On 30 Mar 2009, at 16:38, Oliver Ruebenacker wrote:
>>  Then it is not clear to me what you are claiming.
>
> I'm claiming that classes in OWL are not typically intended to be
> "instantiated" by users (in OWL).

  A class may not be instantiated in every single use, but it is
intended to be instantiated in some cases. To dispute that, you would
have to give me an example of a class that is never instantiated.

> It could be that the class hierachy *is* the intended output (most
> controlled vocabularies, e.g., NCI Thesaurus, SNOMED).

  Not all controlled vocabularies are ontologies.

> Even there, a lot of interesting uses will no neatly fit in that mental
> model. I think it's unhelpful.

  What mental model?

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Bijan, All,

On Mon, Mar 30, 2009 at 11:39 AM, Bijan Parsia  wrote:
> On 30 Mar 2009, at 16:23, Oliver Ruebenacker wrote:
>>  That is probably the most used phrase in the Semantic Web community.
>
> And least adhered to?

  Most used as an empty cliche.

> What's your problem with providing application requirements?

  None, but that was not the topic.

>>  I have no idea what that paradigm is.
>
> http://portal.acm.org/citation.cfm?id=1064.1066&coll=GUIDE&dl=GUIDE&CFID=15151515&CFTOKEN=6184618

  Still no idea.

>>  An ontology should be independent of a particular application.
>
> First, there's a big difference between being tied to a particular
> application and being informed by intended applications. I sincerely doubt
> the general utility of an ontology designed without *any* thought to the
> class of applications for which it is intended to be used. Advice that is
> not at all informed by the broad characteristics of the applications for
> which the ontology shall be used is worthless.

  Class of applications = Systems Biology applications

> As far as I can tell it's a format converter and visualizer. No ontologies
> needed at a first approximation.

  Uses an ontology to integrate BioPAX and SBML. If you know an
alternate way, you should publish.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Bijan, All,

On Mon, Mar 30, 2009 at 11:31 AM, Bijan Parsia  wrote:
> On 30 Mar 2009, at 16:12, Oliver Ruebenacker wrote:
>>  Can you name any popular ontology that does not primarily declare
>> classes and properties?
>
> I don't have to, since I'm not claiming that.

  Then it is not clear to me what you are claiming.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Bijan, All,

On Mon, Mar 30, 2009 at 7:40 AM, Bijan Parsia
 wrote:
> On 29 Mar 2009, at 16:48, Oliver Ruebenacker wrote:
> My first advice would be to develop a clear set of requirements,

  That is probably the most used phrase in the Semantic Web community.
We should invent a catchy acronym for it. Maybe DACSOR?

> perhaps in
> terms of the ASK/TELL paradigm,  for the role of the ontology in typical
> Systems Biology applications you are trying to support.

  I have no idea what that paradigm is.

> Classic applications of (description logic based) ontologies include
> terminology development (e.g., see the caImages site), form management (see
> Galen), and data integration and navigation (see Tambis).
>
> If your applications resemble these (or other standard applications) then
> it's easy to give a wealth of advice, methodologically and technically. If
> your application is radically different, then more work has to be done to
> understand the application requirements.

  An ontology should be independent of a particular application.

  But if you are interested in what type of application I am working
on check http://vcell.org/biopax

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Bijan, All,

On Mon, Mar 30, 2009 at 7:35 AM, Bijan Parsia
 wrote:
>>  Isn't that the typical way, that ontologies define classes and
>> properties and users of these ontologies instantiate these classes?
>
> Nope. It's "a" way, but it's hardly typical and the way you talk about it is
> seriously misleading.

  Can you name any popular ontology that does not primarily declare
classes and properties?

> "Instantiating classes" suggests something akin to what one does in an
> object oriented programming language. I.e., it suggests that individuals are
> "created" from templates (aka classes). While OWL Classes are used this way
> in KA systems, it requires careful thought (and the intervention, typically
> of a "sanctioning" mechanism which indicates which parts of the description
> are salient for the KA).

  If you do not like the word "instantiate", what word you would use instead?

> So, that's just not a helpful way to think about things in the owl context.
> I myself do use the "TBox=schema; ABox=data" analogy sometimes, but I fear
> that its utility is limited and risk of misinterpretation very high.

  It's not an analogy. It's a typical use.

> Second, there's lots of ways to use ontologies with out having to use
> logical constants (i.e., individuals). Alignment of database schemas comes
> to mind. There you might never lift the database data into the ontology, but
> merely use information from the alignment to rewrite queries.

  You mean, you rewrite queries never to be run? Then, what are you
rewriting them for?

> That's not to say that anyone writes class descriptions intending them to be
> necessarily empty (i.e., unsatisfiable). Just that instance retrieval is one
> task among many.

  I wasn't talking about tasks, but of a pattern I found almost all
ontologies I have seen so far to conform to. Instead of philosophizing
about it, why don't you just show me a popular ontology that does not
fit that pattern?

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Pat, All,

On Sun, Mar 29, 2009 at 11:35 PM, Pat Hayes  wrote:
> On Mar 29, 2009, at 11:15 AM, Oliver Ruebenacker wrote:
>>  I am assuming that these classes all make a commitment about what
>> their instances mean, so users could declares instances and rely on
>> that commitment to be useful, right?
>
> As I have been taken to task (offline) for agreeing with you, allow me to
> intercede. On this point, I think everyone is right. Yes, classes are things
> that have, or can have, instances, and that is all that a class is, in
> effect. (RDFS makes this quite explicit by _defining_ classes to be things
> in the range of the rdf:type property.) On the other hand, it is certainly
> correct that ontologies can say a lot about classes without ever mentioning
> instances. On the other hand, it is also the case that, were someone to (not
> unreasonably) wish to connect such classes with their instances, the
> resulting conclusions should be correct, and if they were not, then this
> would be a serious critique of the ontology.

  I have no idea what the person who took you to task was thinking,
but it seems related to the ongoing controversy over whether
substances should be instances or classes.

  In BioPAX, we have a class physical entity with subclasses such as
protein. EGFR would be an instance of protein, and we could say in
BioPAX that EGFR has a sequence. (I would argue it should rather say
that EGFR matches a sequence pattern, but that is another story.)

  The problem is that there are certain assumptions which BioPAX users
are encouraged to follow, such as (1) if two physical entities refer
to the same record, they are identical (2) if two physical entities
refer to different records in the same source, they are not identical
(3) if they are not identical, they have no overlap.

  I don't think these assumptions are even asserted in the ontology or
the documentation, but some BioPAX developers actively encourage users
to rely on them ("Come on, they are true at least 95 percent of the
time"), and BioPAX lacks support for cases where they break down.

  The fix I advocate is straight-forward: let the language be explicit
about whether above assumptions are met or not and add support for
cases where they are not. This would include a property that expresses
that EGFR includes human EGFR, but since EGFR is not a class, it would
not be owl:subClass.

  Others advocate a different approach: make all reference to
substances references to classes, e.g. EGFR would be a subclass of
protein. This, they say, is "more natural".

  The obvious benefit is that it makes it clear that two distinct
substances may have overlap, since two distinct classes may have a
non-empty intersection, e.g. human EGFR and phospho-EFR would have the
intersection human phospho-EGFR (assuming EGFR to be defined to
include phospho-EGFR).

  The obvious drawback is that everything becomes more complicated
since instead of properties of instances we would have property
restrictions over classes (e.g. instead of "EGFR matches EGFRSequence"
we would say "Every element of EGFR matches EGFRSequence"). That alone
is a serious issue, since typical users like it as simple as possible.

  But that is not the most serious issue.

  The most severe problem seems to be that the class approach seems to
be incompatible with (1) observables being about statistical ensembles
and (2) populations being defined by location, not individual
membership - at least, if we want to avoid extreme complexity.

  (note: in what follows, all numbers are made up and probably not realistic)

  For example, how would we describe that "the concentration of ATP in
the mitochondrion is (3.2 +/- 0.7) mol per liter"? What does the
concentration inhere in?

  Maybe the concentration is just a proxy for the particle number?
Say, the particle number of ATP in the mitochondrion is 24.7 +/- 1.6.
What does that number inhere in?

  Can we restrict ourselves to cases of definite particle numbers? In
Systems Biology, we often use differential equations to model how
things change over time, and that assumes they change gradually. But
nevertheless, let us say that the number of ATP in the mitochondrion
is 23. What does that number inhere in? One particular set of 23
molecules? But are we talking only about one particular cell, or are
we making a more general statement that applies to many cells?

  A new ATP molecule is created, increasing the number of ATP
molecules to 24. The original set of 23 molecules still exists, and
its number is still 23. But that's not the number of ATP molecules in
the mitochondrion any more. Also, what happens when an ATP molecule is
destroyed, or wanders off to some place else?

  Finally, what happens when the number of ATP molecules in the
mitochondrion drops to zero? What does the zero inhere in - in the
empty set? What if the

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Pat, All,

On Sun, Mar 29, 2009 at 11:23 PM, Pat Hayes  wrote:
> On Mar 29, 2009, at 10:48 AM, Oliver Ruebenacker wrote:
>>  Perhaps the question should read: What would you advice to some one
>> who wants to build an ontology to describe pathways for Systems
>> Biology purposes?
>
> I really have no advice to give, as I know virtually nothing about systems
> biology. My remarks were based on your raising the topic of statistical
> ensembles, which is enough to make me want to go and do something else, I'm
> afraid.

  There is no reason to be scared of statistical ensembles!

  Forget for the moment about Systems Biology and think of Science in general.

  A scientist applies a method to obtain results. Talking about the
method means talking about things particular to the discipline and the
tools used (e.g "On March 14, I placed the soccer ball on my table and
held my yellow ruler next to it.").

  The results can also be expressed in this language (e.g. "My yellow
ruler read 27.3 inches when held next to the soccer ball on my
table"), which is useful for those interested in the method, but it is
not required for those only interested in the results. In fact, if we
want to collect, combine and compare results obtained by different
methods, details particular to methods are usually counter-productive
(ruler? measuring tape? caliper? laser? red? yellow? table? chair?).
The consumer of the results is typically interested in a statement
such as "the diameter of a soccer ball is 27.4 inches plus-minus 0.3
inches". An expectation value and a variance.

  But what does the "diameter of 27.4 inches plus-minus 0.3 inches" in
above statement inhere in? Certainly not one particular soccer ball.
How about the set of all the soccer balls in the world? But why would
we be interested in all the soccer balls in the world? What if in some
strange place, people produce soccer balls of unusual sizes, would
that change the result for us?

  What we really mean when we say that a soccer ball has a diameter of
such and such, is that we imply that there are standard ways to obtain
soccer balls (e.g. going to the next sports store and buying one, or
taking one from the equipment room of the next gym, or participating
in a soccer match), and that these ways are equivalent in the expected
results. So there will be a range of possible scenarios (e.g. a soccer
ball of 27.2 inches, a soccer ball of 27.342 inches, a soccer ball of
9*pi inches, etc.) and each outcome comes with a probability. These
probabilities are usually not all the same, and since the number of
possible scenarios is typically infinite, it makes no sense to assume
they are. The probability distribution over the set of possible
outcomes is a ensemble.

  Enter Systems Biology. Systems Biology is a consumer of results from
many disciplines. Its objective is to put together results obtained by
a wide range of experimental, theoretical and computational methods in
Biological Physics, Molecular Biology, Physical Chemistry,
Biochemistry, Computer Science and Applied Math. Some of these methods
involve tracking single molecules, of definite sets of molecules. Some
do not. so Systems Biology needs a language to talk about these
results without referring to artefacts of methods used, which is the
language of ensembles.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Matthias, All,

On Sun, Mar 29, 2009 at 11:13 AM, Matthias Samwald  wrote:
> Oliver wrote:
>>  As I understand it, an owl:Class is simply something intended to be
>> instantiated. I declare something a class if and only if I intend
>> there to be instances.
>
> This is how you might choose to use OWL, but it is important to emphasize
> that many ontologies (including the OBO ontologies and parts of the
> Neurocommons Knowledge Base / Banff HCLS demo) encode a lot of useful
> information just by using classes and property restrictions, without
> instances.

  Isn't that the typical way, that ontologies define classes and
properties and users of these ontologies instantiate these classes?

  I am assuming that these classes all make a commitment about what
their instances mean, so users could declares instances and rely on
that commitment to be useful, right?

>> In Systems Biology, as I understand it, EGFR is
>> an instance of class Protein which is subclass of Substance. I don't
>> intend there to be instances of EGFR, so I don't declare it a class.
>
> Well, that is an arbitrary choice you make here. Is you EGFR protein
> resource specific to a certain species?

  There is a whole family of operators: (1) specific to a species
(e.g. human EGFR) versus not (2) specific to a cellular location (e.g.
EGFR in cytosol) versus not (3) specific to a certain set of
post-translational modifications (e.g. phospho-EGFR) versus not

> Maybe they want to refer to a certain subclass of EGRF out there, e.g.,
> those from a certain species?

  I don't see a way to define those as instances of EGFR in a way that
makes sense. For example, if human EGFR is an instance of EGFR, what
are mammalian EGFR, or phospho-EGFR, or human phospho-EGFR?

> Why do you say that it is 'probably' a
> mistake? Why? And why are you not certain?

  Since I don't intend instances, I make no commitment what these
instances mean, so any one creating instances must rely on a
commitment made elsewhere, not by me. I can not imagine a commitment
that makes sense, but maybe that is just my limited imagination and
maybe some clever person somewhere found a way to define meaningful
instances, but then it will be probably impractical to communicate the
meaning to others.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Pat, All,

On Sun, Mar 29, 2009 at 12:10 AM, Pat Hayes  wrote:
> On Mar 28, 2009, at 3:52 PM, Oliver Ruebenacker wrote:
>>  Arithmetic can be described by ontologies.
>
> Not full arithmetic, because of Goedel's incompleteness theorem. You might
> manage with Peano arithmetic, but I doubt it. I suspect you would need at
> least complex analysis.

  Isn't Goedel Incompleteness something that does not apply only to
Math, but to Formal Logic in general? Wouldn't that imply that it is a
concern for ontology building regardless of whether it is about Math
or any other area?

  The way I understand it: It depends on how deep you want to dig. For
example, if you want to talk about the real number one, you could just
declare a symbol for it and define in words that this is the real
number one and rely on every one agreeing what it is and you will not
be confronted with incompleteness. Or you could try to formalize the
definition of real numbers by formalizing field axioms. For example,
you can base real numbers on set theory, and then you have the choice
of naive set theory, which leaves some things undefined, or more
sophisticated approaches, and then you would definitely be concerned
about incompleteness.

>>  What would you do?
>
> I wouldn't. Its far too complicated and too far from existing ontology work.
> Statistical ensembles are just way outside the state of the
> logical-formalizing art, I would guess. If you can cite any work, however,
> I'd be delighted to be proved wrong.

  Perhaps the question should read: What would you advice to some one
who wants to build an ontology to describe pathways for Systems
Biology purposes?

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Pat, All,


On Sat, Mar 28, 2009 at 4:32 PM, Pat Hayes  wrote:
> On Mar 28, 2009, at 11:15 AM, Oliver Ruebenacker wrote:
>>  Why not? I don't see any fundamental problem.
>
> Well, the very idea of a statistical ensemble is way more complicated than
> anything any ontology language semantics is able to deal with. You would
> need at least arithmetic to describe this, surely.(?)

  Arithmetic can be described by ontologies. But for starters, before
we have an ontology that describes all this, let us have one that is
at least compatible with this.

> We humans do this all the time, yes, and not just in technical areas but
> also in daily life. But machines are not very good at this kind of
> cross-domain elision. In fact, they can hardly do it at all. Notice that if
> this kind of reasoning were ubiquitous, sameAs would be close to
> meaningless.

  Obviously, being the same as is different from being isomorphic to.

> I understand. However, speaking now as an ontology engineer, I would not
> advise anyone to attempt to formalize all this in anything remotely like OWL
> or even full first-order logic.

  What would you do?

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Pat, All,

On Sat, Mar 28, 2009 at 10:54 AM, Pat Hayes  wrote:
>>  Actually, I doubt a protein is a set. It seems to me, in Systems
>> Biology, a protein is an operator working on statistical ensembles,
>> from which we can derive expectation values and variances.
>
> Um. OK, you obviously know more about this than I do, but I very much doubt
> if any ontology notation is capable of expressing what you here describe.

  Why not? I don't see any fundamental problem.

  As I understand it, an owl:Class is simply something intended to be
instantiated. I declare something a class if and only if I intend
there to be instances. In Systems Biology, as I understand it, EGFR is
an instance of class Protein which is subclass of Substance. I don't
intend there to be instances of EGFR, so I don't declare it a class.
If some one else wants to declare instances of EGFR, that's their
responsibility and it is probably a mistake.

  People shift effortlessly between domains. In college, we learn in
Quantum Mechanics to make a sharp distinction between an operator and
its expectation value. Once we advance through grad school, we start
use the same symbol for both operator and expectation value and stop
talking about the distinction. The context either makes it clear,
which one is meant (e.g. p = ), or it does not matter (e.g. p =
mv).

  Systems Biologists use knowledge from Molecular Biology, Chemistry
or Biological Physics, where they talk about single molecules or sets
of molecules. But the typical Systems Biology picture, the picture
behind the Virtual Cell, SBML, BioPAX, is not one of single molecules
or sets of molecules, but of quantifiable observables. An observable
can be understood as the result of a series of measurements, which
yields an expectation value and a variance. A simple understanding of
an observable is enough to do Systems Biology, but at the same time,
the concept easily integrates thermodynamic statistical ensembles,
quantum uncertainty and averaging across different samples.

  Even if the observable is the number of molecules, it may not be an
integer, because it is an expectation value. That's why in SBML and
BioPAX, stoichiometric coefficients are floats, not integers, and in
SBML, they even can carry units. Often, we are interested not in the
molecule number, but in the concentration. Or, in something
non-countable, such as heat.

  To understand what EGFR is, we build an imaginary EGFR detector, a
device that we direct to some space, push a button, and it gives us a
measurement of the amount of EGFR in that space, which is an
approximate value. Pushing the button repeatedly gives us expectation
value and variance. Can you use it to track a single molecule? It is
physically impossible to make it certain that there is exactly one
EGFR molecule in a space. The best you can do is having an expectation
value close to one, and a variance close to zero.

> I was referring to OWL 2, not OWL Full. It is the new version of OWL, in
> last call as we write. The DL version of it runs at DL efficiencies and
> allows classes of classes, kinda (using punning, it works for most
> applications). And BTW, instantiating classes is fast and easy in just about
> any formalism. The speed cost comes from the fact that more expressive
> languages allow stranger edge cases which have to be checked by complete
> reasoners. But all these complexity results are worst-case, and normal-case
> behavior is often very different.

  Looking forward to Jena implementing an OWL 2 DL reasoner, or more
importantly, an OWL 2 Mini reasoner.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Isomorphic Domains

[Oliver Ruebenacker]

 Hello, All,

  There seem to exist frequently isomorphisms between different
domains, for example

  1. A protein has a sequence - a protein record has a sequence entry
  2. An EGFR molecule is a protein molecule - a spoonful of EGFR is a
spoonful of protein
  3. Operators in quantum mechanics - number in classical mechanics
  4. Properties in reality - variables in a mathematical model
  5. Entities - words
  6. Entities - data objects
  7. Actions - intentions

  Suppose I want to construct ontologies for two domains that seem to
be partially isomorphic. Is there a systematic way to exploit such
isomorphisms?

  Side note: It seems reflection inherently causes an infinite number
of domains. For example, records of entities can be considered a
reflection of entities. Records about different types of entities are
different types of records. Therefore, a record about a protein is
distinct from a record about a record about a protein, which is
distinct from a record about a record about a record about a protein,
and so forth. Managing an infinite number of reflection domains seems
only possible with a systematic approach to isomorphisms.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

On Thu, Mar 26, 2009 at 5:54 PM, Peter Ansell  wrote:
> It would be infinitely better than seeAlso where you have no idea what
> the intent is, other than it isn't owl:sameAs or anything else in
> between.

  owl:usersWhoLookedAtThisRecordAlsoLookedAt :)


-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Matthias, All,

On Thu, Mar 26, 2009 at 4:30 PM, Matthias Samwald  wrote:
>>  I think more useful for Systems Biology is that they participate in
>> the same reactions with the same kinetics.
>
> But that is a very personal opinion, right? Without doubt, when two classes
> of proteins have the same dispositions and functions (to use BFO - lingo),
> this is a very important thing to know. Nonetheless, if their structures are
> completely different, most biologists would describe them as distinct
> classes of proteins. The notion that any molecule or molecular complex
> should be called "Insulin" just because it has the same effect on regulating
> blood sugar seems quite avantgarde to me.

  If the only reaction you are interested in is the regulation of
blood sugar in the way Insulin does, you would probably not call a
substance Insulin, but perhaps blood sugar regulating hormone, or
Insulin substitute.

  The name Insulin would probably be defined to take into account
other reactions, too, most likely including its transcription, which
would enforce it consisting of amino acids. If another, similar
sequence leads to the same effects, it would probably be called
Insulin.

 Take care
 Oliver


-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Philip, All,

On Thu, Mar 26, 2009 at 8:20 AM, Phillip Lord
 wrote:
> Besides which, the issue being discussed here is one of equality. When
> are two proteins the same protein?

  Some people involved in BioPAX think they are the same if and only
if they have the same sequence.

  I think more useful for Systems Biology is that they participate in
the same reactions with the same kinetics.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Pat, All,

On Thu, Mar 26, 2009 at 3:28 AM, Pat Hayes  wrote:
>>  Just because it refers to a set of things does not mean I need to
>> model it by an owl:Class.
>
> No, but if it really is a set, that would be a very good idea.

  Actually, I doubt a protein is a set. It seems to me, in Systems
Biology, a protein is an operator working on statistical ensembles,
from which we can derive expectation values and variances.

> Well, it was a problem with OWL DL that an class couldnt be an instance of
> another class. I gather this has been fixed (about time) in OWL 2,  There is
> obsolutely no logical or fundamental reason why classes should not be
> allowed to be in other classes, for examples like this one.

  An OWL Full reasoner takes much longer to compute than an OWL DL
reasoner. What good are classes if you don't intend to instantiate?

>> Similarly, a typical approach would be to have a class Protein and an
>> instance EGFR ("a protein") that refers to a large number of molecules
>> scattered all over the globe.

> Um.. this seems confused to me, mixing up ideas from mereology with classes.
> A 'large number of molecules scattered all over the globe' sounds like a
> mereological sum. Which is fine, and pretty well axiomatized already with
> off-the-shelf ontologies. BUt there is no point in also having a class of
> these things, since this just confuses sums with classes. What are the
> elements of the class? The sum or the individual molecules? If the latter,
> we don't need the sum; if the former, we don't need the class.

  Ensemble operators are not sets. The whole is more than the sum of its parts.

> I agree it makes sense. But to be exact, whats been found in fruit fly
> embyos are molecules of the (same) protein, not the same molecules of the
> protein. If this is important for reasoning (and I bet it will be), then
> your ontology needs to distinguish protein molecules from proteins. And if
> it doesn't, then I'd predict it is going to get its knickers in a twist.

  You may be talking of single molecules, but I am not, so your
confusion does not apply to me.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: Less strong equivalences (was Re: blog: semantic dissonance in uniprot)

[Oliver Ruebenacker]

 Hello Bijan,

  If a few simple and obvious question is already unwelcome, then
there is no need to engage.

 Take care
 Oliver

On Wed, Mar 25, 2009 at 4:46 PM, Bijan Parsia
 wrote:
> On 25 Mar 2009, at 20:35, Oliver Ruebenacker wrote:
>
>>    Hello Bijan, All,
>
> Hello Oliver.
>
>>  These are not even transitive, right?
>
> Which? I have 4 or so sketches.
>
> Similarity can be transitive, for example. Transitivity isn't the only thing
> one might want to do.
>
>> So what can we do with them
>> reasoning-wise?
>
> Depends on the relation proposed. Thus far we've just sketched things in a
> very broad way. Clear requirements haven't been developed.
>
> I'm not sure why you are so knee jerk against exploring possibilities.
>
>>  Isn't likeness too much in the eye of the beholder
>
> No.
>
> Similarity is one sort of possible relation and there are many similarity
> metrics possible. And many ways of user defining it. Thats sort of the point
> of having a logic.
>
>> to be agreed upon
>> universally?
>
> I regard universal agreement as a non-goal.
>
>> Why not move such concepts to more specialized ontologies
>> instead of OWL?
>
> OWL isn't an ontology.
>
> We're talking about what might be useful relations to have expressible with
> standard behavior up to and including inference support. I.e., thinks which
> are extensions or layers on OWL.
>
> Of course, you can axiomitize arbitrary distinct equivalence relationship in
> OWL since you have Transitivity, Reflexivity, and Symmetry. So that is, of
> course, another option. It won't work with counting, but perhaps that's ok
> for some purposes. It should be mentioned as an option of course.
>
> Of course, if people don't think investigations along these lines are
> fruitful, I'm happy to drop it.
>
> Cheers,
> Bijan.
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: Less strong equivalences (was Re: blog: semantic dissonance in uniprot)

[Oliver Ruebenacker]

 Hello Bijan, All,

  These are not even transitive, right? So what can we do with them
reasoning-wise?

  Isn't likeness too much in the eye of the beholder to be agreed upon
universally? Why not move such concepts to more specialized ontologies
instead of OWL?

 Take care
 Oliver

On Wed, Mar 25, 2009 at 4:05 PM, Bijan Parsia
 wrote:
> Oh, another possibility, 4) probabilistic sameAs. That's probably more
> researchy than similarity logics, but more in the next few year timeline
> rather than in the "have no idea" timeline.
>
> Cheers,
> Bijan.
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Wacek, All,

On Wed, Mar 25, 2009 at 4:20 PM, Wacek Kusnierczyk
 wrote:
> hmm, so a mixture of all sorts of substances, incidentally *containing*
> exactly one polypeptide chain, would be a protein?  a box *containing*
> exactly one polypeptide chain would be a protein?

  Sorry: I think it was any compound containing exactly one polypeptide chain.

> clear enough, really?  i think the following, taken from stryer's
> biochemistry, 5e p. 41, is more resonable:
>
> "Proteins are linear polymers built of monomer units called amino acids."

  If I add a phospho group, is it still a protein?

  If yes, it's like the above.

 Take care
 Oliver


-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Mark, All,

On Wed, Mar 25, 2009 at 1:28 PM, Mark Wilkinson  wrote:
> Well... human beings are notoriously good at making sense of the
> nonsensical... that's why we're so bad at creating formal ontologies :-)

  It does not look nonsensical to me to begin with. It seems to me
that using the definitions most typical in Systems Biology, it makes
perfect sense, and that it becomes nonsensical if you use definitions
less typical in Systems Biology. To me, it looks like a clear
statement, so clear, in fact, that it is easy to tell that it's wrong.
If it was not clear, it would be difficult, if not impossible, to
prove it wrong.

 Take care
     Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Mark, All,

On Wed, Mar 25, 2009 at 1:13 PM, Mark Wilkinson  wrote:
> Well, the statement would *imply* that it is... so given that the individual
> "embryo" that was referred to as a uniprot tissue is the same individual
> "embryo" that the plant ontology was talking about, we can therefore
> conclude that (as Ben pointed-out) that this particular fly embryo is
> somehow embedded in some particular plant seed endosperm.

  Just because it refers to a set of things does not mean I need to
model it by an owl:Class. I can also have an owl:Class Population and
an instance of it populationOfTheUS, which would be an instance, not
an owl:Class, although it seems to correspond to a set of people.
Similarly, a typical approach would be to have a class Protein and an
instance EGFR ("a protein") that refers to a large number of molecules
scattered all over the globe.

  The statements from UniProt, as I understand them, make perfect
sense: there is a protein that has been isolated from that plant, and
can also be found in fruit fly embryos. I don't have the knowledge to
check whether it is true, but it seems to make sense to me.

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Philip, All,

On Wed, Mar 25, 2009 at 1:05 PM, Phillip Lord
 wrote:
> My own feeling is that it's biology which wove the web; we're just
> caught in the middle. What role for the web and semantics? Well, I think
> we need a coordinated, controlled and defined way of expressing our
> mutual confusion. I'd love to have a clear definition of gene (or
> protein). In it's absence, a good way of expressing "err..." is probably
> the best we can do.

  I don't know whether the BioPAX Level 2 definition of protein is the
most useful one, but at least it sounds clear to me:

  protein = anything containing exactly one polypeptide chain

  Clear enough?

 Take care
 Oliver


-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Mark, All,

On Wed, Mar 25, 2009 at 12:25 PM, Mark Wilkinson  wrote:
> I agree - the issue also came up at the BioHackathon last week... basically,
> as Tom Oinn phrased it, "if you're thinking of using owl:sameAs... don't!"

  Is that a suggestion to abolish owl:sameAs?

> Another predicate is needed that is less "rigourous" - owl:kindOfLike  :-)

  What do we gain from non-rigorous statements? I am assuming that
when UniProt says "same as", they really mean "same as". It is better
to know a statement is wrong than to not know whether it's right or
wrong.

  Besides, how do we know it's wrong? Two species can have the same
protein for different functions, right?

> I think there is another, potentially more nefarious concern in the
> statement that Ben was objecting to in his post.  The statement was:
>
> http://www.uniprot.org/tissues/229 (subject)
> http://www.w3.org/2002/07/owl#sameAs (predicate)
> http://purl.uniprot.org/po/0009009 (object)
>
> my concern is whether http://purl.uniprot.org/po/0009009 is intended to be a
> class, or intended to be an instance... since owl:sameAs is only supposed to
> be used to claim the "identicalness" of two individuals, not an individual
> to a class...

  Must be an individual, then, doesn't it?

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Wacek, All,

  It is quite common to use terms from two different domains
interchangeably, if there is a natural isomorphism between the two
domains. I am sure every one on this list has at some point used
references to functions and function equations interchangeably and it
has not caused any harm (except maybe in a math exam where knowledge
about this distinction was tested).

  For every well-formed record, there is the set of all those
molecules or compounds the record is about. Two well-formed records
are equivalent, if they are about the same set.

  That makes a natural isomorphism between equivalence classes of all
well-formed records that can be possibly generated and all those sets
of molecules or compounds any of these records are about.

  This isomorphism has a sub-isomorphism between equivalence classes
of actually existing well-formed records and all those sets of
molecules or compounds they describe.

  Further, for any set of molecules or compounds that can be
identified by a finite piece of information, I can create a
well-formed record that contains this piece of information and is
about that set. Therefore, the isomorphism covers all relevant cases.

  The practical problems with records are primarily these:

  (1) A record is ambiguous on whether it
(1a) is about a particular set of molecules or compounds
(1b) is equivalent to a particular other record
  (2) a record about a particular set is desired but none exists for this set
(2a) in particular places
(2b) anywhere known

  These problems are not caused by using references to records and
entities interchangeably, and are not solved by making the distinction
clear. Rather, they can only be solved by creating more or better
records.

 Take care
 Oliver

On Wed, Mar 25, 2009 at 7:16 AM, Wacek Kusnierczyk
 wrote:
> Michel_Dumontier wrote:
>>
>> And I'm trying to explain that there is no pragmatic reason to make
>> explicit the distinction between a biomolecule (and what we know about
>> it) and a database record (and what we know about the biomolecule)
>> unless they are actually different.
>
> hmm, since a biomolecule and a database record are actually different
> (or?), there seems to be, following your statement, a pragmatic reason
> to make explicit the distinction between them.
>
> what we know about them is yet another issue.
>
> vQ
>
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Bijan, Philip, All,

  I understand that what you are referring to are real problems, but I
wonder why the most accurate way to characterize them is as "confusion
between a thing and its record".

  It sounds as if there was a person who would one day exclaim "Oh my
God! I always thought this is a reference to a thing! But no, it is a
reference to a record of the thing! Now I'm doomed!"

  Does this ever happen?

  Is it possible that referring to records instead of things is not
the result of confusion, but rather of cost-benefit considerations -
that records are cheap and identification is costly and open-ended?
What is it that can not be achieved by having better records instead?

  And what does it take to identify something? We may have thought we
know what a couch is, until we realize that we have no consensus over
whether the pillows are part of the couch or not, and that it would be
more accurate to distinguish between bare couches (without pillows)
and fully featured couches (with pillows). How far are we going to go?

 Take care
 Oliver

On Tue, Mar 24, 2009 at 8:10 AM, Phillip Lord
 wrote:
>
>
> Oliver Ruebenacker  writes:
>> 2009/3/23 Michel_Dumontier :
>>> I do not think this would be a wise "simplification".  This is only a
>>> simplification from one perspective: because it avoids having to mint
>>> and maintain pairs of URIs instead of a single URI.  But the downstream
>>> cost is that it creates an ambiguity (or "URI collision")
>>> http://www.w3.org/TR/webarch/#URI-collision
>>> that may cause trouble and be difficult to untangle later as the data is
>>> used in more and more ways.  For example, if any of the same predicates
>>> need to be used on both the record and the molecular entity, they will
>>> become hopelessly confused.  Also, if disjointness assertions are
>>> included then this overloading may cause logical contraditions.
>>
>>   Can any one name a real world example of where confusion between an
>> entity and its record was issue?
>
>
> Yes, sure. All proteins have a Uniprot ID (conflating protein and
> uniprot records). Then we integrate this with drugbank; this represents
> many things including proteins which are not in Uniprot, or represents
> several proteins where Uniprot has one. Consider insulin for instance.
> We now have a problem because not all proteins have a Uniprot ID.
>
> The flip side is that if you always say
>
> Protein Record --> contains knowledge about --> protein
>
> it's much more complicated. You are making your data model more
> difficult to work with all of the time, to cope with edge cases which
> occur only some of the time.
>
> There's no way around this; either way it's a compromise and what is
> good in one context may not be good in another.
>
> Phil
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello All,

2009/3/23 Michel_Dumontier :
> I do not think this would be a wise "simplification".  This is only a
> simplification from one perspective: because it avoids having to mint
> and maintain pairs of URIs instead of a single URI.  But the downstream
> cost is that it creates an ambiguity (or "URI collision")
> http://www.w3.org/TR/webarch/#URI-collision
> that may cause trouble and be difficult to untangle later as the data is
> used in more and more ways.  For example, if any of the same predicates
> need to be used on both the record and the molecular entity, they will
> become hopelessly confused.  Also, if disjointness assertions are
> included then this overloading may cause logical contraditions.

  Can any one name a real world example of where confusion between an
entity and its record was issue?

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Scott, All,

  Pardon my ignorance, but how exactly do we know that these
statements are wrong? Suppose the instance representing the fruit fly
protein is defined as a sequence pattern that matches a number of
proteins. Suppose isolatedFrom, applied to such a sequence pattern, is
defined as an organism from which proteins can be isolated that match
that pattern. Suppose, the same pattern matches proteins isolated from
both fruit flies and sporophytes. These look like perfectly reasonable
assumptions to me, and they would make the two statements true. Am I
missing something?

 Take care
 Oliver

On Fri, Mar 20, 2009 at 1:35 PM, M. Scott Marshall
 wrote:
> FYI:
> http://i9606.blogspot.com/2009/02/semantic-dissonance-in-uniprot.html
>
> I thought that the above blog entry would interest some of you (it
> apparently already has interested a few of you that have added comments :)
> ). The blog is from Benjamin Good (from Mark Wilkinson's Lab) and was
> referenced during a napkin discussion I had with Marco Roos and Ben about
> how one could best refer to a protein in text-mined triples. One of the best
> options seemed to be to use a PURL that referred to a record associated with
> the protein. Sound familiar? Those of you who have been with us for more
> than a year will think so. See http://sharednames.org for an attempt to
> approach the issue.
>
> -Scott
>
>
>
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Peter, All,

On Sun, Mar 22, 2009 at 5:06 PM, Peter Ansell  wrote:
> 2009/3/22 Oliver Ruebenacker :
>>  There is an infinite number of possibilities. What is the criteria
>> for being relevant?
>
> The possibility I was referring to was the option for going through
> and defining the properties of the class of molecules as distinct from
> a random instance with instance specific variables. I would define the
> relevance of that method to be relative to the usefulness of the extra
> complexity involved in making sure that in each case the properties
> assigned to the random instance of the class were specific/precise
> enough to be more useful to scientists than the case where everything
> is placed as a property on the class of molecules. As you can't likely
> define all the configurations for a given instance of a complex
> molecular structure with respect to its environment, this would be
> difficult, but if you found an application that was grounded in a
> given environment it would be a possibility.

  I must have misunderstood you. I thought you were talking about not
making a commitment whether the world should be viewed through the
lens of a typical Systems Biologists (ensembles) or a Nano-Physicist
(single particles). My reply would have been that (a) Systems
Biologists already have such a hard time developing an ontology that
serves there own needs that serving other people's needs seems like a
luxury we can not afford and (b) should we consider other people's
needs, it is not clear which other people should have priority.

>>  Can you give an example?
>
> For example... How do you define a gene? Tough question I know, but do
> you define everything that can be transcribed as being a gene? How do
> you really associate genes across organisms considering mutations? If
> a gene acts as a promoter for its transcription in one gene but
> doesn't in another due to a mutation in the relevant upstream region
> can you really say the same sequence is the same gene? Even though its
> position in the intracellular space could still be the same, and its
> protein 3D conformation is still the same, there would be a duality
> where you would then have to redefine the gene as being a regulator
> for itself if you wanted to include its molecular functions inside the
> cell as part of its property set. It sounds counterintuitive to have
> to refer to the gene in two different ways just because in one
> organism its function didn't bind to its environment.
>
> One non-biological example I was referring to was the wave-particle
> duality for light, where if you wanted to be really in depth and
> define the light "thing", then you would either contradict yourself
> per current theory or you would create a dual distinct model that
> violated someones previous god-like decision that ":wave
> owl:distinctWith :particle"

  Sorry if I was not clear. I meant an example of how decisions you
consider "god-like" can be avoided. What is the alternative?

 Take care
 Oliver

-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello Peter, All,

On Sat, Mar 21, 2009 at 5:48 PM, Peter Ansell  wrote:
> 2009/3/22 Egon Willighagen :
>> Chemists are not interested in single molecules (well, most are not,
>> but with increasing nanotechnology...). I was told recently that upper
>> ontologies have proper mechanisms to point out the difference between
>> (in Java terminology) objects and classes, or instances and concepts.
>
> There is that possibility.

  There is an infinite number of possibilities. What is the criteria
for being relevant?

> Having different identities might be the rational scientific way to do
> things. They might be caused by different perspectives on the one
> item, or they might be caused by an actual duality of theory based on
> an actual inability to describe something in a single theory. Making
> god-like decisions about which class particular records actually
> belong to as ontologists might sound fun but in the world case it
> seems counterintuitive because it doesn't promote progress in both
> areas concurrently.

  Can you give an example?

 Take care


-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: blog: semantic dissonance in uniprot

[Oliver Ruebenacker]

 Hello, All,

  We just started a discussion on identifying compounds at the last
meeting of the BioPAX OBO Workgroup and will continue at the next
meeting, to which any one interested is invited. We meet both locally
and virtually. Either stop by at 346 Stata MIT or log into Skype and
ask a participant (e.g. me) to invite you to text and voice chat. Next
meeting is this week, Tuesday, 4pm to 6pm EST.

  Action item for next meeting: Getting familiar with PRO.

  The topic lies at the center of the pathway community and has been
subject to bitter battles. Usually, a pathway is defined in terms of
connected smaller processes which are defined in terms of
participating compounds and their roles. Connected means that a
participant of process A is the same as (owl:sameAs?) a participant in
process B. As important as knowing what is connected is knowing what
is disjoint (owl:disjointWith?). Inevitably, there is tension between
simplicity and rigour, between those who want to make it easy to stuff
data into databases and those who demand stricter criteria to make
pulling the data out again more useful. The community spans all the
way from the experimenter to the modeller to the drug designer, from
the qualitative to the quantitative, the conceptual to the precise.

 Take care
 Oliver

On Fri, Mar 20, 2009 at 1:35 PM, M. Scott Marshall
 wrote:
> FYI:
> http://i9606.blogspot.com/2009/02/semantic-dissonance-in-uniprot.html
>
> I thought that the above blog entry would interest some of you (it
> apparently already has interested a few of you that have added comments :)
> ). The blog is from Benjamin Good (from Mark Wilkinson's Lab) and was
> referenced during a napkin discussion I had with Marco Roos and Ben about
> how one could best refer to a protein in text-mined triples. One of the best
> options seemed to be to use a PURL that referred to a record associated with
> the protein. Sound familiar? Those of you who have been with us for more
> than a year will think so. See http://sharednames.org for an attempt to
> approach the issue.
>
> -Scott
>
>
>
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

Re: Introduction

[Oliver Ruebenacker]

 Hello Kei, All,

  I don't know NEURON or it's format, but after a brief glance, my
first impression is that NEURON works quite like a typical
SBML-compatible simulator (tracking concentrations in an arrangement
of compartments), so there should be a way to convert to and from
SBML, or otherwise it should be possible to convince some one to
create such a way. Do you know people involved with NEURON you could
ask?

 Take care
 Oliver

On Fri, Jan 2, 2009 at 11:24 PM, Kei Cheung  wrote:
> Hi Oliver,
>
> Thanks for the information. I've gone through the list of Vcell models
> available at http://vcell.org/applications/published%20_models.html. I found
> two models related to Purkinje cell or neuron:
>
> http://www.ncbi.nlm.nih.gov/pubmed/16169982?dopt=Abstract
> http://www.ncbi.nlm.nih.gov/pubmed/18487300?ordinalpos=10&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
>
> These two models may be complementary to some of the purkinje cell related
> models listed in SenseLab's ModelDB
>
> http://senselab.med.yale.edu/modeldb/ModelList.asp?id=271
>
> If so, it might be interesting.
>
> Cheers,
>
> -Kei
>
> Oliver Ruebenacker wrote:
>
>>Hello Kei, All,
>>
>>  Thanks for the interest. I think yes, there are also neuron models.
>>
>>  Here are models published by VCell users, which you can access by
>> logging onto the VCell:
>>
>>  http://vcell.org/applications/published%20_models.html
>>
>>  You can also import any model in SBML, for example from here:
>>
>>  http://biomodels.net/
>>
>>  Our project (http://vcell.org/biopax) is opening the way for BioPAX
>> import to the VCell. We recommend most BioPAX data from Reactome:
>>
>>  http://reactome.org/
>>
>>  Other pathway databases supporting BioPAX can be found here:
>>
>>  http://www.biopaxwiki.org/cgi-bin/moin.cgi/
>>
>>  I think all of these sources have models relating to neurons.
>>
>>Take care
>>Oliver
>>
>>
>> On Sun, Dec 14, 2008 at 5:36 AM, Kei Cheung  wrote:
>>
>>>
>>> Hi Oliver,
>>>
>>> Thanks for the introduction. I just wonder if Virtual Cell includes model
>>> of
>>> neurons (a kind of nerve cell).
>>>
>>> Cheers,
>>>
>>> -Kei
>>>
>>> Oliver Ruebenacker wrote:
>>>
>>>
>>>>
>>>>  Hello All,
>>>>
>>>> I just joined the SWHCLSIG and thought I introduce myself:
>>>>
>>>> I work for the Virtual Cell [1] at the Center for Cell Analysis and
>>>> Modeling [2] at the University of Connecticut Health Center [3].
>>>>
>>>> My current project [4] aims to integrate formats for molecular
>>>> pathways, especially BioPAX [5] and SBML [6], aiming to include other
>>>> formats in the future. For this project, we have developed a Java
>>>> application called Systems Biology Linker (Sybil), which makes
>>>> extensive use of Semantic Web technologies (including querying,
>>>> reasoning and program-based ontology-building) with the help of Jena
>>>> [7] and an ontology we developed called Systems Biology Pathway
>>>> Exchange (SBPAX).
>>>>
>>>> I am also facilitating the bi-weekly meetings of the BioPAX-OBO
>>>> group [8], which aims to integrate BioPAX into the OBO Foundry [9], a
>>>> task that requires an extensive revision of BioPAX.
>>>>
>>>> I am looking forward to working with others on the greater goal of
>>>> integrating biomedical knowledge using Semantic Web technologies.
>>>>
>>>>  Take care
>>>>  Oliver
>>>>
>>>> [1]  Virtual Cell - http://vcell.org
>>>> [2]  Center for Cell Analysis and Modeling - http://www.ccam.uchc.edu
>>>> [3]  University of Connecticut Health Center - http://www.uchc.edu
>>>> [4]  My current project - http://vcell.org/biopax/
>>>> [5]  BioPAX - http://www.biopax.org/, http://www.biopaxwiki.org/
>>>> [6]  SBML - http://sbml.org
>>>> [7]  Jena - http://jena.sourceforge.net/
>>>> [8] Every second, fourth and last Tuesday, 3pm to 6pm, in Stata
>>>> Center, MIT. Contact me if interested.
>>>> [9]  OBO Foundry - http://www.obofoundry.org/
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>>
>
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org