RE: [Animl-develop] Proposal for changes to AnIML core schema

[Mark M. <Mar...@sc...>]

Hello Maren,

I really appreciate your time you have taken to look through this.  The =
following are my comments:

1.  In the ParameterCategorySet node under the MeasurementData node, we =
would be placing general information about the sequence run that is =
being performed.  For example, the creator of the sequence, the date of =
creation for the sequence, etc. =20

I noticed that you saved this same information - just down 1 level under =
the ExperimentStep node.  This is also where you placed the Method =
information.  This is fine and will work, however the problem I have =
with this is just the overall size of the resulting AnIML file.  For =
example, our general sequence information, the method configuration, =
instrument configuration, and injector configuration data could very =
easily account for 200K - 300K worth of data.  This data will be the =
same for every line of the sequence.  So if we have a 100 line sequence, =
we could easily end up with an AnIML file that is an extra 20MB in size. =
 After we have generated our AnIML files, we need to store these in a =
database.  So, we would like to keep these as small as possible.

2.  No comments.

3.  I see what you have done with the storage of the vectors.  Instead =
of using sub-pagesets, you have used sub-experimentsteps.  I like this =
because you get the added advantage of additional ParameterCategorySets =
and the ability to specify technique files. =20

My only comment here is for the last channel in the file (Channel_4).  =
Here you have an ExperimentStepSet with 2 ExperimentSteps =
(Channel_4_Chrom and Channel_4_UV).  I believe that the 2nd =
ExperimentStep must be a sub-experimentstep of the Channel_4_Chrom) =
ExperimentStep.  This is because of the References.  They must refer to =
a Vector in a super-ordinate page (not a sibling page).  Otherwise, you =
will not be able to determine with Vector they are related to (as all of =
the siblings are allowed to have Vectors with the same ID.


Again, thank you so much for taking the time to look over this.

Best regards,
Mark Mullins

=20

-----Original Message-----
From: Mar...@wa... [mailto:Mar...@wa...]=20
Sent: Tuesday, December 07, 2004 8:06 AM
To: Mark Mullins
Cc: ani...@li...; =
ani...@li...
Subject: Re: [Animl-develop] Proposal for changes to AnIML core schema


Hello Mark,

> 1.  Added a ParameterCategorySet node under the MeasurementData node.
> This allows custom parameters to be added that describe the=20
> measurement data itself.
This would probably be incompatible with the current technique =
definitions.
What kind of parameters would you put there?

> 2.  Modification of "length" attribute information inside of the
VectorSets.
These modifications are fine with me. It looks like a good way to =
accommodate discontinuous data.

> 3.  Added a References node under the IndividualValueSet,=20
> EncodedValueSet, and AutoIncrementedValueSet nodes.
OK.

> I have also attached a sample XML file that illustrates the above=20
> heirarchy with some fictional data.  Note that in the VectorSets I=20
> have been able to store the following types of multi-channel=20
> chromatographic data:
The sample file you sent is not using AnIML as intended (although I =
admit that getting the intention is hard with no documentation =
available...). I cannot see any use of the technique definition either.
Please find attached a revised version of your sample file.

(See attached file: animl-core 1.04_MF.xml)

I urgently ask the other readers to participate in this discussion!


Mit freundlichen Gr=FC=DFen / Best regards

Dr. Maren Fiege
Product Manager

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