[seek-kr-sms] OBOE clarifications and questions
Joshua Madin
madin at nceas.ucsb.edu
Tue Jun 13 22:10:30 PDT 2006
Hi Matt,
Thanks for the comments and ideas. I'll insert my responses below.
On Jun 13, 2006, at 4:40 PM, Matt Jones wrote:
> Josh,
>
> Nice job on OBOE. I've been looking it over and learning a lot, but
> there a number of specific areas that I don't understand. Maybe you
> could clarify?
>
> 0) Is OBOE, and are other ontologies, available on the SEEK wiki?
> They
> should be, and probably as links into the CVS tree. The site review
> team requested this. I linked a couple in to the wiki here:
> http://seek.ecoinformatics.org/Wiki.jsp?page=KROntologies
> Can you do the rest? Maybe Rich's ontologies should be made available
> under the 'As-is' Formal Ontologies section for reference purposes?
>
Good idea. I would also like to spend some time improving the KR
area on the SEEK wiki.
> 1) how do counts differ from moles? Isn't the NIST 'amount' the
> same as
> the absolute scale in OBOE?
>
There's probably no really good answer to this. Although,
philosophically, the two might be equated (somehow), I think that we
are talking about two totally different concepts. Count refers to
the "existence" of a thing (any kind of thing) which maps perfectly
on to itself (1:1). Whereas, mole refers to a specific ratio of the
number of particles in a given amount of matter. This is definitely
worthy of more discussion. I think that, in the end, it'll be best
to keep them separate. But we need to justify this.
> 2) how to deal with log units?
>
Here Matt is talking about units like the Richter scale and pH, which
do not have linear relationships with base units. Serguei also
mentioned this problem at the last AHM. As discussed earlier, we
should gather up all the known units that are currently undefinable
using OBOE and work from there. We can try to think of the simplest
fix; if we're lucky we may be able to get away with one or two extra
OWL properties.
> 3) How to deal with multiple relations with integrity constraints?
> For
> example, a 'site' table, and a 'tree measurement' table that has a
> foreign key into the site table. Can we create annotations that refer
> to attributes in both tables?
>
I'm not 100% sure what you mean here. I hope that we can do this.
Shawn might have a better sense for this question.
> 4) context doesn't seem to be enough to handle experiments -- it
> captures some information, such as spatial nesting of experimental
> units, but it doesn't fully capture the dependency information in
> tuples. In particular, it seems to me that experimental manipulations
> are different from spatial nesting. See example below. Can you
> clarify?
> I looked at the GCE examples you sent. They show the 'Experimental
> Treatment' as the subject of the Measurement for Treatment (with unit
> 'Name'). Is this list of subjects controlled? And is 'Experimental
> Treatment' a special characteristic that should be treated specially?
> The value of the Measurement is set to 'N'. Where is the value space
> for these treatments defined? And how does one differentiate between
> manipualted and control values (ie, in the value column in one
> experiment the values 0, 5, 10 might indicate control, 5g/m^2, and 10
> g/m^2 treatments) -- are these defined formally somewhere?
>
> Here's an example to expand on #4. The three relations below (R1, R2,
> and R3) all measure biomass in subplots within plots. In R1, the
> subplots are given both a nitrogen and phosphorus addition treatment
> which affects the interpretation of the biomass measured. So biomass
> has some concrete dependency on the nitrogen and phosphorus
> treatments.
> In relation R2, only a phosphorus treatment is added. R1 and R2
> could
> be combined incorrectly by taking the mean by plot,subplot,nitrogen in
> R1 and then concatenating with R2. Or it could be correctly
> combined by
> taking only those observations in which Phosphorous manipulation is 0
> and combining that set of records with those from R2. Likewise, R3
> has
> no manipulations, so should really only be compared against
> observations
> in R2 where the nitrogen treatment is 0 and R1 where both nitrogen and
> phosphorous are 0. These are the semantics that OBOE should capture
> reagarding the dependecy between the measured value (biomass) and the
> manipulated treatments and their levels. Can OBOE do that?
>
I see the problem. In the examples I sent earlier today "treatment"
was either yes or no -- those examples were not focusing on this
issue, rather the context issue. The one way that I can see around
this, which would also help with "composite data" annotations such as
"mean" or "sd", would be to allow a measurements to have more than
one subject. Take a look at the attached annotation for your
Relation R1. I included an annotation called "addition", which might
be found in some kind of "experimental" extension to OBOE's
characteristics. Another good point for discussion.
> Relation R1
> ----------
> Plot Subplot Nitrogen Phosphorous Biomass
> 1 A 5 3 56
> 1 B 0 3 87
> 1 C 5 0 78
> 1 D 0 0 24
> 2 A 5 3 58
> 2 B 0 3 88
> 2 C 5 0 76
> 2 D 0 0 26
>
> Relation R2
> -----------
> Plot Subplot Nitrogen Biomass
> 1 LR 5 56
> 1 LL 0 87
> 1 UR 5 78
> 1 UL 0 24
> 2 LR 5 58
> 2 LL 0 88
> 2 UR 5 76
> 2 UL 0 26
>
> Relation R3
> -----------
> Plot Subplot Biomass
> 1 1 56
> 1 2 87
> 2 1 58
> 2 2 88
> 3 1 76
> 3 2 26
>
>
> Thanks for the clarifications,
>
> Matt
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Matt Jones Ph: 907-789-0496
> jones at nceas.ucsb.edu SIP #: 1-747-626-7082
> National Center for Ecological Analysis and Synthesis (NCEAS)
> UC Santa Barbara http://www.nceas.ucsb.edu/ecoinformatics
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> _______________________________________________
> Seek-kr-sms mailing list
> Seek-kr-sms at ecoinformatics.org
> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/seek-
> kr-sms
------------------------------------------------------------------------
-
National Center for Ecological Analysis and Synthesis
University of California, Santa Barbara
735 State Street
Santa Barbara CA 93101-3351
madin at nceas.ucsb.edu
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Matt_examples.pdf
Type: application/pdf
Size: 28854 bytes
Desc: not available
Url : http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-kr-sms/attachments/20060613/1ad98659/Matt_examples-0001.pdf
-------------- next part --------------
More information about the Seek-kr-sms
mailing list