[Biodevelopers] RE: Biodevelopers digest, Vol 1 #104 - 1 msg

[Mike Benway]

Thanks Adam!  When I mentioned "array" I meant it as a data type for a column, but you might be talking about a microarray. Anyway it doesn't matter because the question I meant to ask is also answered. My logical error was in thinking of a plate as the base entity here, and a plate has 384 or 1536 wells. What is the best and correct thing to do is to model the WELL as the entity. So there, a plate has wells, and wells have well_row, well_column, well_data, plate_id, and so fourth. Then a plate entity can have  assay_id, detection_technology, reader_type, device_protocol_id, reader_id, etc..then assays and readers and so forth are the other entities. It's making sense to me now. I'd still love to see how others have modelled this kind of thing in practice, like Spotfire or whatever. Thanks again. Mike

"Margolin, Adam" <margolia at wharton.upenn.edu> wrote:Mike,
If you are using a relational database I certainly would not make tables
with variable numbers of columns depending on the array configuration.
What you want to do is make a table called Spotting_plates with every
row uniquely identified by the Plate_ID and the well. When you spot an
array you want to map each spot back to an entry in this table. To do
this, define a table called Print_map with each row uniquely defined by
an array configuration, and row, column, block on the spotted array that
maps these values to a well on a spotting plate.

This is the general idea, but of course, there are some other
intermediate steps. I can send you the scheme that we have developed
for our arrays if you like, or for a more involved description you can
surf around on this site: www.gusbd.org.

-Adam


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Sent: Thursday, May 01, 2003 12:01 PM
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Subject: Biodevelopers digest, Vol 1 #104 - 1 msg

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Today's Topics:

1. 98/384/1536 well microplate database schema? (Mike Benway)

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Message: 1
Date: Thu, 1 May 2003 08:03:34 -0700 (PDT)
From: Mike Benway 
To: biodevelopers at bioinformatics.org
Subject: [Biodevelopers] 98/384/1536 well microplate database schema?
Reply-To: biodevelopers at bioinformatics.org

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Hi.I have a process that generates lot's of data from 384 well plates.
That is, three hundred -eighty four real numbers.The entity is the
plate. Some plates can even be 1536 well formats. That's a lot of real
numbers for a database table.384 columns might even be too many for any
available database?It strikes me that this must be a very common
application, and there has got to be a better schema for representing
plate data. (as columns of arrays, or as blobs or what?)Does anyone have
any knowledge of an open-source implementation that stores plate data in
a database that I could look at?I can't believe that databases would be
used just to store links to spreadsheets.Thanks

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Hi.
I have a process that generates lot's of data from 384 well plates.
That is, three hundred -eighty four real numbers.
The entity is the plate. Some plates can even be 1536 well formats.
That's a lot of real numbers for a database table.
384 columns might even be too many for any available
database?
It strikes me that this must be a very common application, and
there has got to be a better schema for representing plate data. (as
columns of arrays, or as blobs or what?)
Does anyone have any knowledge of an open-source implementation
that stores plate data in a database that I could look at?
I can't believe that databases would be used just to store links to
spreadsheets.
Thanks

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