[Animl-develop] Discontinuous timelines in AnIML Schema

[<Mar...@gs...>]

VERY LONG AND DETAILED MESSAGE.  This color is MB.  This color is MM.

I would like to introduce a new developer to the group, Mark Mullins (MM) 
of SSI, who is working on an AnIML implementation.  Mark has discovered 
some difficulties with fitting his simple UV chromatography data into 
AnIML, as have I (MB) for report LCMS data.

Here is my understanding of the AnIML to SSI SaMPL concordance (MM has 
SaMPL xml in grey below)

ExperimentStep and DataSource are equivalent - the application of a 
technique or data related to a single detector source
PageSet and DataSet are containers only
Page and RawData are equivalent to a chromatogram or spectrum (2 or more 
dimensional data)
Axis and Vector are equivalent (AnIML has a Vector container called 
VectorSet; SaMPL allows an Axis to have multiple child Axis tags as below 
which is a reasonable way to represent independent and dependent 
variables.  Though less explicit than AnIML, it is more flexible.)
EncodedDataSet and EncodedDataSet are identical

Case 1: 
Scenario:  Data acquisition for 10 minutes with 1 second intervals.  You 
have 30 seconds of missing data points, 3 minutes into the run. 
 
In SaMPL, we represented this with 2 sets of X-Axis vectors as follows: 
This is equivalent to multiple Time Vectors and multiple Intensity Vectors 
in AnIML.  
 
<Dataset datasetID="1" resultType="chromatogram">
  <RawData>
     <Axis axisID="1" name="Time" datapoints="180" datatype="float32" 
units="sec">
        <AutoIncrementDataSet startValue="0" 
increment="1.00"></AutoIncrementDataSet>
        <Axis axisID="2" name="Intensity" datapoints="180" 
datatype="float32" units="millivolts">
           <EncodedDataSet>89213074132847847213473...</EncodedDataSet>
        </Axis>
     </Axis>
     <Axis axisID="3" name="Time" datapoints="390" datatype="float32" 
units="sec">
        <AutoIncrementDataSet startValue="210.0" 
increment="1.00"></AutoIncrementDataSet>
           <Axis axisID="4" name="Intensity" datapoints="390" 
datatype="float32" units="millivolts">
              <EncodedDataSet>89213074132847847213473...</EncodedDataSet>
           </Axis>
     </Axis>
  </RawData>
</Dataset> 
 
The problem I am having with AnIML is at the <VectorSet> node.  This is 
where you specify the 'length' attribute to describe how many datapoints 
your vectors will contain.  In this example, the vectors each need to 
contain a different number of datapoints. 
I've verified this and agree that there is a Length atribute in VectorSet. 
 However, there is a misunderstanding about what it means.  I know this 
because I have Dominic Poetz's documentation printout (but cannot email it 
as I do not have it electronically - Gary Kramer may have it). 
VectorSet.Length actually represents the Vector count, not the count for 
the number of points in each contained vector.  Thus it is ok to have 
multiple Vectors with different lengths, just as in SaMPL.  Nevertheless, 
my inclination is to accomodate segmentation of data like this by allowing 
multiple VectorSets.  I think all Vectors in a VectorSet should have the 
same length
 
 
Case 2: 
Scenario:  3D Data acquisition for 10 minutes with 1 second intervals and 
255 wavelengths. 
 
In SaMPL, we represented this with 1 set of vectors as follows: 
 
<Dataset datasetID="1" resultType="chromatogram">
  <RawData>
     <Axis axisID="1" name="Time" datapoints="600" datatype="float32" 
units="sec">
        <AutoIncrementDataSet startValue="0" 
increment="1.00"></AutoIncrementDataSet>
        <Axis axisID="2" name="Wavelength" datapoints="255" datatype="int" 
units="nm">
           <EncodedDataSet>89213074132847847213473...</EncodedDataSet>
           <Axis axisID="3" name="Absorbance" datapoints="255" 
datatype="float32" units="absorb units">
              <EncodedDataSet>89213074132847847213473...</EncodedDataSet>
              <EncodedDataSet>89213074132847847213473...</EncodedDataSet>
              <!-- There would be 598 more EncodedDataSets here -->
           </Axis>
        </Axis>
     </Axis>
  </RawData>
</Dataset> 
 
The problem I am having is the same as in Case 1 above, since each of the 
contained Vectors will have a different length. 
I believe the intention in AnIML would be to create a chromatogram Page 
with a subordinate PageSet of UV spectra, each spectrum referencing its 
superordinate chromatogram Page point. 

Case 3: 
Scenario:  LCMS Data with standard chromatogram but summed and 
background-subtracted spectral reports (sum and subtract start and stop 
points needed as timeline)
  
Again we have discontinuous timelines as in Case 1, but here each spectrum 
is a separate Page and should be displayed on separate graphs as opposed 
to Case 1 where the segments should be displayed on the same graph.  We 
can have a subordinate PageSet of MS spectra but what do we put in the 
superordinate (top-level) Page?  What I want is a series of (0-many) 
summation (start and stop) and (0-many) subtraction selections describing 
each spectrum. The closest thing in AnIML is Individual Value Set.  I 
would need one set for summation starts, another for summation stops, and 
a third and fourth for subtraction start and stop.  However, as there can 
be 0 - many summations or subtractions per spectrum, I believe we begin to 
run into problems indentical to Case 1 - a segmented timeline representing 
the collection of start-stop segments used in creating each spectrum.