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RE: "molar" for concentration

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Wed, 17 Aug 2011 10:26:16 -0700
Message-ID: <4e0c1421c17610867a2ee4eb56b24cd1@mail.gmail.com>
To: Helena Deus <helenadeus@gmail.com>
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>, Jim McCusker <james.mccusker@yale.edu>
hi lena,

> > Would something like:
> > <assay>  <concentration>  "5"^^[<http://someuri/mole>
> > <http://someuri/division> <http://someuri/liter>]
> > Work?

the trouble with considering Molar as a datatype is that datatypes have
operations. int datatypes have +, -, *, / among others.

what would it mean for:

Molar a = 5;
Molar b = 2;

a ^ b where ^ is some operator associated with Molar as a datatype?

perhaps you have a point, one could define it as the equality operator,
which would fit in the XMLSchema definition except what if the solutions a
and b are of different compounds?

but to me, Molar is a value of concentration, not really in the spirit of
a datatype.  so i see it as a distinct concentration property of a
solution rather than a datatype.

i think jim is on the right track.

cheers,
michael

> -----Original Message-----
> From: Jim McCusker [mailto:james.mccusker@yale.edu]
> Sent: Wednesday, August 17, 2011 9:35 AM
> To: Helena Deus
> Cc: Michael Miller; W3C HCLSIG hcls
> Subject: Re: "molar" for concentration
>
> Ah, I thought you were looking for predicates for datatype properties.
> This makes much more sense now. When I said you could compose a molar
> unit for concentration, I was thinking more that it would be a new URI
> that uses MUO's predicates for describing molar concentration in terms
> of moles/liter, which is easy in MUO. They might even accept a new
> unit for that, they may just have not seen the need before.
>
> Jim
>
> On Wed, Aug 17, 2011 at 12:14 PM, Helena Deus <helenadeus@gmail.com>
> wrote:
> > Hi Michael,
> > I was looking for a way to say in RDF that some concentration is
> measured in
> >  "molar";
> > e.g.
> > <assay>  <concentration>  "5"^^<http://someuri/molar>
> > Yes, Molar = mole/Liter, but from my (limited) understanding of
> datatypes,
> > there are no restrictions as to what can be used in the datatype URI
> > I'm not sure how to express the statement above if I need to combine
> mole
> > and liter to create a datatype...
> > Would something like:
> > <assay>  <concentration>  "5"^^[<http://someuri/mole>
> > <http://someuri/division> <http://someuri/liter>]
> > Work?
> > Cheers,
> > Lena
> >
> > On Wed, Aug 17, 2011 at 4:03 PM, Michael Miller
> > <Michael.Miller@systemsbiology.org> wrote:
> >>
> >> hi lena,
> >>
> >>
> >>
> >> after looking at wikipedia i see what you mean that it isn't a unit
> per
> >> se, it is a concentration of a solution, that is by definition a
> combination
> >> of a value of 1 with an SI unit of 1 mol\L.  so it is certainly a
> property
> >> of the solution but i don't see how it is a datatype.  in
> programming terms
> >> i define a variable to be of a certain datatype:
> >>
> >>
> >>
> >> int count = 5
> >>
> >>
> >>
> >> what does it mean to say,
> >>
> >>
> >>
> >> Molar solution = ??
> >>
> >>
> >>
> >> cheers,
> >>
> >> michael
> >>
> >>
> >>
> >> From: Helena Deus [mailto:helenadeus@gmail.com]
> >> Sent: Tuesday, August 16, 2011 3:17 PM
> >> To: Michael Miller
> >> Cc: Jim McCusker; Matthias Samwald; W3C HCLSIG hcls
> >>
> >> Subject: Re: "molar" for concentration
> >>
> >>
> >>
> >> Hi Michael,
> >>
> >>
> >>
> >> I did mean datatype. I do like the MUO / SI solution, but it's
> strange
> >> that they don't describe "Molar" (much more widely used) along with
> "mole"?
> >> Sure enough I can "build" a Molar, as Jim indicated... but I can
> also
> >> "build" a month or an acceleration from days or meters+time, and yet
> they
> >> provide it... Interesting...
> >>
> >>
> >>
> >> Thanks all,
> >>
> >> Cheers,
> >>
> >> Lena
> >>
> >>
> >>
> >> On Tue, Aug 16, 2011 at 9:15 PM, Michael Miller
> >> <Michael.Miller@systemsbiology.org> wrote:
> >>
> >> hi all,
> >>
> >> i did take a quick look at MUO and it does seem sane.
> >>
> >> "For instance, MUO has the ability to assert units of measure on n-
> ary
> >>
> >> observations, ..."
> >>
> >> and MUO appears based on SI.
> >>
> >> cheers,
> >> michael
> >>
> >> > -----Original Message-----
> >> > From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-
> >>
> >> > lifesci-request@w3.org] On Behalf Of Jim McCusker
> >> > Sent: Tuesday, August 16, 2011 12:58 PM
> >> > To: Matthias Samwald
> >> > Cc: Helena Deus; W3C HCLSIG hcls
> >>
> >> > Subject: Re: "molar" for concentration
> >> >
> >>
> >> > In general, you really want to be able to have additional levels
> of
> >> > qualification. For instance, MUO has the ability to assert units
> of
> >> > measure on n-ary observations, as well as to provide prefUnit
> >> > annotations on properties. An ontology that generates property
> URIs
> >> > for every quality and unit of measure would be huge and very
> >> > cumbersome, and I think the consensus is to annotate your own
> >> > properties with units of measure.
> >> >
> >> > Jim
> >> >
> >> > On Tue, Aug 16, 2011 at 3:43 PM, Matthias Samwald
> >> > <matthias.samwald@meduniwien.ac.at> 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/
> >> > >
> >> >
> >> >
> >> >
> >> > --
> >> > Jim McCusker
> >> > Programmer Analyst
> >> > Krauthammer Lab, Pathology Informatics
> >> > Yale School of Medicine
> >> > james.mccusker@yale.edu | (203) 785-6330
> >> > http://krauthammerlab.med.yale.edu
> >> >
> >> > PhD Student
> >> > Tetherless World Constellation
> >> > Rensselaer Polytechnic Institute
> >> > mccusj@cs.rpi.edu
> >> > http://tw.rpi.edu
> >>
> >>
> >>
> >> --
> >> Helena F. Deus
> >>
> >> Post-Doctoral Researcher at DERI/NUIG
> >>
> >> http://lenadeus.info/
> >>
> >>
> >
> >
> > --
> > Helena F. Deus
> > Post-Doctoral Researcher at DERI/NUIG
> > http://lenadeus.info/
> >
>
>
>
> --
> Jim McCusker
> Programmer Analyst
> Krauthammer Lab, Pathology Informatics
> Yale School of Medicine
> james.mccusker@yale.edu | (203) 785-6330
> http://krauthammerlab.med.yale.edu
>
> PhD Student
> Tetherless World Constellation
> Rensselaer Polytechnic Institute
> mccusj@cs.rpi.edu
> http://tw.rpi.edu
Received on Wednesday, 17 August 2011 17:27:15 UTC

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