RE: [Mged-mage] MAGE-stk help needed

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thanks Steffen, lots of good practical advice.

Kaustabh,

One additional point to consider is what you are going to use the data for.

> > My mission is to set up a relational micro array database 
> that I can 
> > use
> to
> > store microarray related data in the lab and also it should 
> be able to 
> > import freely available data from the internet. Actually 
> there is not 
> > much of lab data and we intend to have a huge repository of 
> microarray 

If you simply want people to be able to view the data but not do analysis,
you can take a look at EBI's ArrayExpress database, which matches very
closely the structure of the DTD and the classes in the parsing code.  I
believe the schema is available.  But often, how the data is going to be
used once it is imported imposes constraints on the DB design for the uses
of the data which will make the structure of the DB a fair bit different
than the MAGE-OM model.  There is no getting around deciding what your
application/db is going to do before you have your first data stored.

Much of what I do is map from some source into our schema and back out again
THEN I look at MAGE-ML to see how the data can be/is represented there by
that source.  

Although there's a great deal of work on making how the data is represented
standardized, you are right that there are still some difference.  But you
will probably want to focus on one or two sources of gene expression data to
start (the sources that your uses are interested in!).  There are some
difference between how different vendors and repositories will output MAGE
but pick one to start.  That will give you the core of your code and will
make importing the next source easier.

And find a biologist to be your buddy, if at all possible.

good luck,
Michael

Michael Miller
Senior Application Developer
Rosetta Biosoftware
mic...@ro...
www.rosettabio.com

> -----Original Message-----
> From: mge...@li... 
> [mailto:mge...@li...] On Behalf Of 
> Steffen Durinck
> Sent: Tuesday, May 04, 2004 12:17 AM
> To: kaustubh shinde; mge...@li...
> Subject: Re: [Mged-mage] MAGE-stk help needed
> 
> 
> Hi Kaustubh,
> 
> With MAGE-stk it is possible to parse MAGE-ML, built the 
> objects in memory and then extract the data you need to put 
> in your database. I use the MAGE-stk Java API and a good 
> place to start and look at some code is to check out the 
> ImportExportTest class  of the 
> package:org.biomage.tools.xmlutils.  This class contains a 
> main method so can be run.  It parses MAGE-ML, makes the 
> objects in memory and then writes it back out as MAGE-ML.  
> The class I use to parse MAGE-ML and built the objects is the 
> MAGEReader class you'll find this class also in the package 
> org.biomage.tools.xmlutils.  By using this reader you'll end 
> up with something that represents a top level mage object.  
> Once you have this object you can start to extract 
> information from it by using the other packages (e.g. 
> mageobj.getDesignElementPackage() to extract the 
> DesignElement package).
> 
> Good luck!
> Steffen Durinck
> 
> 
> ----- Original Message ----- 
> From: "kaustubh shinde" <shi...@ho...>
> To: <mge...@li...>
> Sent: Monday, May 03, 2004 8:30 PM
> Subject: [Mged-mage] MAGE-stk help needed
> 
> 
> > Hi,
> > I am a computer scientist new to bioinformatics.
> > My mission is to set up a relational micro array database 
> that I can 
> > use
> to
> > store microarray related data in the lab and also it should 
> be able to 
> > import freely available data from the internet. Actually 
> there is not 
> > much of lab data and we intend to have a huge repository of 
> microarray 
> > data
> from
> > internet. After trying for past 1-1.5 months I have come to the 
> > conclusion that its anything but easy and I could seriously 
> use some 
> > help here.
> >
> > Though MAGE-ML is supposedly the standard for microarray 
> data, its far
> from
> > standard in that its not easy to import mageml doc into a 
> relational 
> > database scema. The problem is that there is no standard relational
> database
> > scema. I have come across many freely available databases 
> and I have 
> > set
> up
> > BASE at my system. Its a nice tool and database for microarray data 
> > but again there is no utility to import external mageml 
> docs into BASE 
> > as is
> the
> > case with other databases.
> >
> > >From whatever research I did regarding this I figured out that 
> > >MAGE-stk
> may
> > be the answer. I think its possible to read mageml and put the data 
> > into a particular relational scema using mage-stk.  So I 
> explored the 
> > mage-stk
> page
> > and i found no examples.
> >
> > So my problem is
> > 1) I am really not sure if it is actually possible to parse 
> mageml and 
> > get the objects and put the appropriate data into 
> relational database 
> > tables using mage-stk
> > 2) If it is, how do i go abt it? The documentaion shows the classes 
> > and hierarchy but it doesn't give any clue to get started. Some 
> > example code
> to
> > do a similar simple thing would be really helpful
> >
> > I will really really appreciate any help regarding this as 
> I am stuck 
> > here for quite and not really sure if I am going in the right 
> > direction. Any ideas are very welcome.
> >
> > Thank you,
> > Kaustubh
> >
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