FW: UnitsML query

["Dragoset, Robert A." <robert.dragoset@nist.gov>]

UnitsML TC,
This topic will be discussed in today's meeting.    -Bob


-----Original Message-----
From: Robert Muetzelfeldt [mailto:r.muetzelfeldt@ed.ac.uk] 
Sent: Tuesday, June 08, 2010 7:32 PM
To: Dragoset, Robert A.
Subject: Re: UnitsML query

Dear Bob,

Thank you very much for your informative reply.

Since writing to you, I have now come across specific reference to the 
issue I raised in my email by a group concerned with the development of 
metadata standards for ecological data. They refer to units qualified in 
the way that I mention as "so-called semantic units" (my emphasis in 
bold below), describing how the domain-specific qualification can be 
handled in OBOE, the Extensible Observation Ontology for ecological data:
"/Measurement standards are composed of one or more measurement-standard 
domains through the hasDomain property. Each domain represents a 
possible value of the standard, and is (implicitly) related to the set 
of entities that have the corresponding characteristic value through the 
hasElement property. Measurement standard domains can be used to 
restrict the type of entities being measured. In the case of complex 
derived units (e.g., areal density, Fig. 5b)---composed from two or more 
independent unit types---each independent unit type can additionally be 
related to a corresponding entity type.* In this way, OBOE provides a 
mechanism to describe so-called semantic units, e.g., grams of carbon 
per cubic meter of seawater, or individuals of rabbit per individuals of 
fox.* For instance, in Table II of Fig. 2, the data value 6 represents 
the density of individuals in a coral, which can be expressed using a 
semantic unit (corresponding to the Individual per Meter Square class) 
defined as the composition of two unit components: the unit component 
Individual linked to the Crab Entity class, and the component Meter 
Square (raised to the power of -1) linked to the Coral Entity class 
(shown as dashed ellipses in Fig. 5b). Semantic units are commonly used 
in ecological data sets, and using OBOE it is possible to formally 
define the meaning of these units, making them available for discovery 
and integration processes (see Section 3)./"
J Madin, S Bowers, S Krivov, D Pennington, F Villa. An ontology for 
describing and synthesizing observational data. Ecological Informatics 
2(3):279-296, 2007.
http://daks.ucdavis.edu/~sbowers/bowers-ecoinf-07.pdf
The extract is from Section 2.3 (Measurement standards), 3rd paragraph

There is no specific web site for OBOE, but further information on it 
and the project (SONet - Scientific Observations Network) within which 
it's being developed can be found at 
https://sonet.ecoinformatics.org/workshops/1st-meeting/Background_Documents

I am not sure I like either the term 'semantic units' nor the way they 
handle them in OBOE, but at least this gives some authority to the 
assertion that this is a well-established (if non-standard and 
misguided) notation within ecological science.

I am sure, as you suspect, that none of this conforms to SI, and maybe 
we should drop 'semantic units' altogether in favour of an approach in 
which this information is incorporated in the quantity name, but that 
would be a hard sell in my community. Moreover, it is probably possible 
to come up with cases where it would not be possible to do this in a 
totally unambiguous way.

I note in passing that SONet/OBOE seems to be another example of an 
initiative that is not using UnitsML or MathML-for-Units, but whether 
that is by choice or ignorance I cannot say.

Thanks again for putting me in the picture, and I look forward to 
hearing the results of your TC meeting.

Best wishes,
Robert



Dragoset, Robert A. wrote:
> Dear Robert,
>
> We're having a UnitsML TC meeting tomorrow and I was planning on bringing up the issue that you address below to discuss with the TC members. I'll send additional comments to you after that meeting.
>
> We're somewhat "between a rock and a hard place" regarding the SI. Whereas NIST strongly supports the adoption of the SI, it is obvious that the U.S. uses units not recommended for use within the SI. UnitsML is designed to be a usable schema that is not restricted by the SI. For this reason we've adopted "counted items" being represented as "units". I'll probably relax the wording in the Guidelines regarding use of units not specifically allowed within the SI. Being in the U.S., I'm not always aware to what extent other countries have adopted the SI. It's interesting to me that in practice your community uses a representation that I suspect would not be strictly allowed for use within the SI.
>
> The Guidelines is very much a draft document. One of the items we'll be discussing in the meeting tomorrow is the location of various pieces of schema documentation: in the Guidelines vs. in the schema. 
>
> Sincerely,
> Bob Dragoset
>
>
> Robert A. Dragoset, physicist
> Physics Laboratory
> National Institute of Standards and Technology
>
> NIST
> 100 Bureau Drive, Stop 8400
> Gaithersburg, MD 20899
> Phone: 301-975-3718
> Email: dragoset@nist.gov
> Website: http://physics.nist.gov
>
>
> -----Original Message-----
> From: Robert Muetzelfeldt [mailto:r.muetzelfeldt@ed.ac.uk] 
> Sent: Friday, June 04, 2010 3:39 PM
> To: Dragoset, Robert A.
> Subject: UnitsML query
>
> Dear Robert,
>
> I'm involved in a project which aims to build a web-based repository of 
> ecological and environment models, all marked up using an XML-based 
> language. We use MathML for the equations, and are now turning our 
> attention to the representation of the units for the model variables.
>
> Within our community, there are a number of attempts to develop standard 
> ontologies for the units of data and/or model variables, but almost all 
> of these use long atomic names for units (e.g. 'metres_per_second') for 
> units. This is of course a dead end.
>
> I am aware of units handling in Systems Biology modelling (e.g. CellML, 
> SBML). These groups have come up with their own bespoke representations 
> for units. I understand that this is precisely the type of situation 
> which has motivated the formation of the UnitsML group.
>
> I have looked at MathML for Units. While I am naturally drawn to this, 
> because of my experience of working with MathML and because of what sem 
> to be nice features (such as the use of semantics and annotation-xml 
> elements), the initiative seems to be moribund, with no source of basic 
> unit definitions etc.
>
> I am pleased to see that the UnitsML group seems to be still active, 
> although some of the material (e.g. the - undated - "Guidelines for the 
> Use of Units Markup Language, Draft Version 0.4.2") seems very 
> incomplete, with various emailed comments included in the text.
>
> I am, however, concerned with a paragraph in the Guidelines which 
> address an issue of considerable importance to my community. You state 
> (page 5):
> "/For example, the expression emission rate = 1.36 e/s, where 'e' 
> represents electron, treats 'electron' as a unit. The correct expression 
> should be electron emission rate = 1.36 s-1, or electron emission rate = 
> 1.36 /s. Even though the UnitsML schema allows for the inclusion of 
> unique items as units, this practice is strongly discouraged and is not 
> acceptable usage in the SI/."
> It is very common in our community to qualifier terms within a units 
> expression in some way, e.g. 'plant_weight = 5.2 kg(carbon) m-2'. Maybe 
> the correct approach is to re-express this as 'plant_weight_as_carbon = 
> 5.2 kg m-2'. But then we have variables in our models which involve all 
> sorts of ratios, e.g. kg(carbon)/kg(nitrogen), and it would be both 
> difficult, if not impossible, to capture all such cases unambiguously in 
> the variable name.
>
> I would like some guidance on this issue, which promoses to be of 
> considerable importance across the whole field of biological, ecological 
> and environmental research, but I'm not sure how whom to turn to or in 
> what forum to discuss this. Can you give me some advice on how to proceed?
>
> Many thanks,
> Robert Muetzelfeldt
>
> Honorary Fellow,
> School of Informatics,
> University of Edinburgh
> and
> Research Director,
> Simulistics Ltd
> htttp://www.simulistics.com
>
>
>
>
>
>
>
>   


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