[seek-kr-sms] OBOE clarifications and questions

[Matt Jones]

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?

1) how do counts differ from moles?  Isn't the NIST 'amount' the same as 
the absolute scale in OBOE?

2) how to deal with log units?

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?

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?

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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~