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RE: "molar" for concentration

From: Rich Cooper <rich@englishlogickernel.com>
Date: Wed, 17 Aug 2011 10:27:07 -0700
To: "'Jim McCusker'" <james.mccusker@yale.edu>, "'Helena Deus'" <helenadeus@gmail.com>
Cc: "'Michael Miller'" <Michael.Miller@systemsbiology.org>, "'W3C HCLSIG hcls'" <public-semweb-lifesci@w3.org>
Message-ID: <66CC4393CE9A455495F2CAEF4F0CF236@Gateway>
Most DBMSs have the ability to define "domains".
One common solution to the problem you describe is
to define a domain called "units", which can be
expressed in a defining XML reference file using
an XML enumerated datatype, with each conceivable
kind of unit given one code.  

For example, the enumerations might include grams,
miles, seconds and moles/liter (aka
LiquidConcentration).  The given XML suite of unit
declarations can then be referenced by many DBMSs,
and the value of the unit so specified in each
database row can then be a real number, or an
integer, or a fixed point number, or a date time,
or whatever you choose to represent each
enumerated unit as.  

So the "unit" domain itself can be an integer, and
the specific value of the unit column for a given
table might be specified as the integer 731, or
whatever enumerated position is specified in the
XML reference structure to represent the unit
"moles/liter".  Other rows could be set to the
integer 13 to represent miles, etc.  Conversion
routines between miles, kilometers, fortnights,
seconds, or whatever domains are mutually
convertible.  

That makes all DBs compatible which reference the
same XML specification as their domain
declaration, and allows each DB to use an integer
representation within each row based on two's
complement (nearly always the integer
representation chosen; I don't know of any 1's
complement DBMS integers in present day
technology, fortunately).  

Since the retrieval of each column is in textual
form, it isn't important whether the unit
enumeration is in BCD or other kind of integer
representation - each DB will return query values
that are strings representing decimal integer
values.  A case statement can then switch to the
appropriate conversion routine, if its even needed
for your application.  

That attached PDF file (my patent) describes other
ways of identifying variations in representations.


HTH,
-Rich

Sincerely,
Rich Cooper
EnglishLogicKernel.com
Rich AT EnglishLogicKernel DOT com
9 4 9 \ 5 2 5 - 5 7 1 2

-----Original Message-----
From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On
Behalf Of Jim McCusker
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=un
it) 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 17:28:23 UTC

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