[Gusdev-rad-issues] Re: [Gusdev-gusdev] important correction Re: RAD schema

[Elisabetta M. <man...@pc...>]

Hi Sucheta,
the old configuration files (those in the CBIL RAD repository which 
will be public soon) are a mix of files for older versions of the 
plugins, now deprecated, or for plugins that are specific of our instance 
of RAD. I recommend not to use these. You can get the most recent plugins 
from the Sanger CVS, from the GUS/RAD repository and I recommend you use 
these together with the accompanying sample config files in the same 
repository.
As for Affy data, MAS5 is not the only view we have. We also have 
RMAexpress, MOID, and (this is the most recent in the RAD schema) 
ProbeProfiler. More views of CompositeElementResultImp can be created as 
needed. Same story for ElementResultImp. Also, these are a tables that 
accomodate results straight out of a given quantification software. In 
RAD there are other sets of tables to accomodate other processing steps 
(including ad hoc normalizations) that are done by a user subsequently 
(the Process tables) and also tables to accomodate down stream analysis 
results (the Analysis tables). I should mention that we are 
planning to soon just use the Analysis tables also for processing results 
and to deprecate the Process tables, as the former are more mature in 
their design.
Elisabetta
P.S. I'm cc-ing the gus-rad-issue mailing list. I don't recall if you 
subscribed to this, I would recommend you do and also it would help if you 
could cc this list when you have RAD questions, so we can keep an archive.

---

On Tue, 9 Nov 2004, Sucheta Tripathy wrote:

> Hi Elisabetta,
>
> Thanks for yor reply. When you say old configuration file does it mean the
> config files for the older versions of plugins? In that case actually we
> have not updated our RAD plugins lately, so I was wondering if there will
> be a conflict of new cfg files with older plugins.
>
> Regarding the data files we are not sure which views to use, I guesss we
> need to study them more carefully before deciding which one is suitable
> for each plugin.
>
> I am not sure what you use, but we have several issues in using MAS5 for
> normalization, so we may go with other methods, and I don't know if there
> are views to support all these different methods.
>
> Anyway, regarding the choices of views I will get back to you soon, so
> that you can tell us which data files to use.
>
> _sucheta
>
>>
>> Sorry, I guess I didn't make myself clear.
>> The new configuration files are those in the Sanger cvs repository, in the
>> GUS/RAD/config folder. These are already available.
>> The ones that are old are those that are contained in the *CBIL RAD cvs
>> repository*, which is the repository not yet available. (When available,
>> this repository will be useful for other things, but the config files in
>> it are obsolete or not of general application outside of CBIL instances.)
>> Regarding the datafiles, the samples will vary according to the plugin and
>> the view that is used. If you tell me which exact plugin(s) you have in
>> mind and what view(s) you are going to load into (e.g. ArrayResultLoader
>> plugin with AffymetrixMAS5 view), I'll select a subset of data
>> files to send you as samples. We have so many data files that it would
>> be overwhelming to send you all kinds and it might be more efficient to
>> just send you those for views and plugins you will actually be using.
>> Note: for the special case of the BatchResultLoader plugin, the data
>> files are just those out of the relevant software and the work is in
>> building an appropriate xml file, samples of which are in the Sanger
>> repository.
>> Elisabetta
>>
>> ---
>>
>> On Mon, 8 Nov 2004, Sucheta Tripathy wrote:
>>
>>> Hi Elisabetta,
>>>
>>> Since you said the existing cfg files in the repository are old and
>>> should
>>> not be used, I guess here I am confused, where do I look for the new cfg
>>> files.
>>>
>>> Also it will be great if you could provide us small sample data files or
>>> tell us where we find them. The pointers provided in the plugins often
>>> tell
>>> " The file contains the values for attributes in ElementResultImp,
>>> CompositeResultElementImp". Which is kind of unclear about the exact
>>> format.
>>>
>>> Thanks a lot.
>>>
>>> Sucheta
>>>
>>> At 03:49 PM 11/8/2004 -0500, you wrote:
>>>
>>>> Sorry,
>>>> **important correction** regarding sample cfg files. Ignore my the
>>>> second
>>>> to last comment on the CBIL RAD cvs for config files in my previous
>>>> email. The CBIL RAD repository will be made indeed public and will
>>>> contain other useful things, like the latest StudyAnnotator code, etc.
>>>> But the sample cfg files are stored at **the Sanger GUS cvs** in the
>>>> repository GUS/RAD/config and *already available* (there are config
>>>> files
>>>> in the CBIL RAD repository I cited below, but those are old and should
>>>> not be used.) Again, the documentation of each plugin should point to
>>>> the
>>>> location of its sample config file *within the Sanger GUS cvs
>>>> repository*.
>>>> Sorry for the confusion on this point, I got mixed up on our various
>>>> cvs
>>>> repositories...
>>>>
>>>> Elisabetta
>>>>
>>>> ---
>>>>
>>>> On Mon, 8 Nov 2004, Elisabetta Manduchi wrote:
>>>>
>>>>>
>>>>> Hi Sucheta,
>>>>> first a reminder, also for the benefit of others in the cc of this
>>>>> email, that general information on the RAD pipeline and on how to set
>>>>> RAD up is at http://www.cbil.upenn.edu/RAD/php/RAD-installation.php?
>>>>> In terms of the RAD schema, I'm not sure of exactly what you are
>>>>> looking
>>>>> for. RAD is part of GUS, so you if you install the GUS schema
>>>>> (instructions at http://www.gusdb.org/documentation.html) you'll have
>>>>> the RAD schema as well. I believe that the plans are to make available
>>>>> the next release of the schema (3.5?) in the next few weeks.
>>>>> The documentation for the RAD schema is contained in that of the GUS
>>>>> schema at http://www.gusdb.org/cgi-bin/schemaBrowser.
>>>>> All RAD plugins are available from the Sanger CVS and documentation
>>>>> can
>>>>> also be viewed at: http://www.gusdb.org/documentation/plugins.
>>>>> In terms of sample files, configuration sample files for most of the
>>>>> plugins are currently stored in the CBIL RAD cvs repository. This
>>>>> repository will be made public (read-only) very shortly, possibly even
>>>>> tomorrow, and will be added to the repositories currently viewable at
>>>>> http://cvs.cbil.upenn.edu. So, if you check back at this website in a
>>>>> few days you should see our RAD repository. All available sample files
>>>>> (mostly samples of cfg files) are in the directory /DataLoad/config/
>>>>> of
>>>>> this repository and the name of the relevant cfg sample file for each
>>>>> plugin is are specified in the plugin's documentation.
>>>>> We don't currently store sample data files in cvs, but the format is
>>>>> typically explained in the plugin doc and if you need any further
>>>>> clarification feel free to contact us with the specifics of the plugin
>>>>> you are interested in and we can provide additional info and examples.
>>>>> Hope this helps,
>>>>> Elisabetta
>>>>>
>>>>> ---
>>>>>
>>>>> On Mon, 8 Nov 2004, Sucheta Tripathy wrote:
>>>>>
>>>>>> Hi Elisabetta,
>>>>>> How are you? It was nice visiting you all at CBIL.
>>>>>> I have one group here working on a pipeline to upload data to the RAD
>>>>>> module. For that I was wondering if you can point us a place, where
>>>>>> we
>>>>>> get the RAD schema and also sample data files for all the plugins for
>>>>>> RAD.
>>>>>> That will be a great help.
>>>>>> Thanks in advance.
>>>>>> Have a great day.
>>>>>> Sucheta
>>>>>>
>>>>>> At 11:47 AM 9/15/2003 -0400, Elisabetta Manduchi wrote:
>>>>>>
>>>>>>> I've cvs committed a change to GUS/PluginMgr/lib/perl/Plugin.pm,
>>>>>>> suggested
>>>>>>> by Steve, to fix a problem occurring when registering a new plugin
>>>>>>> written
>>>>>>> using the most recent documentation features.
>>>>>>> Elisabetta
>>>>>>>
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>>
>
>
> -- 
> Sucheta Tripathy
> Virginia Bioinformatics Institute Phase-I
> Washington street.
> Virginia Tech.
> Blacksburg,VA 24061-0447
> phone:(540)231-8138
> Fax:  (540) 231-2606
>