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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi Dave<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thank you very much for your detailed and informative reply –
much, much appreciated!<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I will go over in detail all of the information you sent me and
then go from there – but I wanted to reply to you beforehand just to say
thanks!<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Certainly I am willing to help the GMOD community where I can
and will share any information I am able to share (not sure yet about sharing the
schema as it is the property of the hospital for which I work…so I would
need permission first) – but certainly any input I can offer, I will.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>If I have further questions, you may hear from me… <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks again for your help – terrific!<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Have a wonderful weekend </span><span style='font-size:11.0pt;
font-family:Wingdings;color:#1F497D'>J</span><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif";color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Margie<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'> Dave Clements, GMOD Help Desk
[mailto:gmodhelp@googlemail.com] <br>
<b>Sent:</b> December-04-08 7:30 PM<br>
<b>To:</b> Margie Manker<br>
<b>Cc:</b> GMOD Help Desk<br>
<b>Subject:</b> Re: [Gmod-help] new database and GBrowse<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p>Hi Margie,<o:p></o:p></p>
<p>I remember speaking with you in Toronto. I hope that you are still enjoying
working in biology!<o:p></o:p></p>
<div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-right:0cm'>
<div>
<div>
<p style='text-indent:-18.0pt'>-<span style='font-size:7.0pt'>
</span>I am creating two new database schemas that will contain mostly genomic
variation data as well as some phenotype data. These data will also include
information on a study, methods, platforms, subjects, samples, etc.<o:p></o:p></p>
<p style='text-indent:-18.0pt'>-<span style='font-size:7.0pt'>
</span>I would like to create a schema that suits the needs of our
organization. I have reviewed Chado in some detail and it does not suit the
needs of our organization. Ideally, our own schema should be used and I would
like to continue with this approach.<o:p></o:p></p>
</div>
</div>
</blockquote>
<div>
<p class=MsoNormal>Can you describe what you found lacking in Chado? This
will help us improve it in the near future: Chado is extendable and
NESCent (<a href="http://nescent.org">nescent.org</a>) has developed a natural
diversity module for Chado. This is still in Beta (and is likely to change
before it is released). It is based on the GDPDM, which is used at
Gramene and MaizeGenetics for this purpose. One of my deliverables for
2009 is to get the natural diversity module out of Beta and into production
Chado.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Several things should help this along. One is a
NESCent working group that needs this to be done, and secondly we are trying to
schedule a GMOD natural diversity hackathon for 2009 that will move this work
forward. <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>If you are interested the natural diversity module and GDPDM
are described at:<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <a
href="http://heliconiusdb.svn.sourceforge.net/viewvc/heliconiusdb/trunk/schema/doc/">http://heliconiusdb.svn.sourceforge.net/viewvc/heliconiusdb/trunk/schema/doc/</a><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <a href="http://www.maizegenetics.net/gdpdm/">http://www.maizegenetics.net/gdpdm/</a><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>I think all this work may come too late for your needs.
However, I encourage you to look at the current beta release as a
possible solution. When I actually get to work on this (probably starting
in February) I may ask you for any insights you have and for a copy of your
schema. If you are really lucky (!) I might even ask if you are
interested in attending the hackathon. :-)<o:p></o:p></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-right:0cm'>
<div>
<div>
<p style='text-indent:-18.0pt'>-<span style='font-size:7.0pt'>
</span>We will most likely employ GBrowse as the genome browser for display of
data in the above databases.<o:p></o:p></p>
<p style='text-indent:-18.0pt'>-<span style='font-size:7.0pt'>
</span>My highest level questions that I have yet to find appropriate answers
to are these:<o:p></o:p></p>
<p style='margin-left:72.0pt;text-indent:-18.0pt'><span style='font-family:
"Courier New"'>o</span><span style='font-size:7.0pt'> </span>Can I
use my own schema to build the database which underlies Gbrowse? If so, will a
separate 'Bio::DB::GFF' database need to be created to act as a bridge between
my database and Gbrowse?<o:p></o:p></p>
<p style='margin-left:72.0pt;text-indent:-18.0pt'><span style='font-family:
"Courier New"'>o</span><span style='font-size:7.0pt'> </span>What
components would I most likely need from GMOD to get my database and GBrowse to
work together?<o:p></o:p></p>
<p style='text-indent:-18.0pt'>-<span style='font-size:7.0pt'>
</span>From what I can determine based on the documentation, I should be able
to use my own database schema to underlie GBrowse. It looks like my database
would require a GBrowse adaptor (Bio::DB::GFF??) and GBrowse. It also looks
like I might need an annotation pipeline, too.<o:p></o:p></p>
<p style='text-indent:-18.0pt'>-<span style='font-size:7.0pt'>
</span>Other questions that arise are:<o:p></o:p></p>
<p style='margin-left:72.0pt;text-indent:-18.0pt'><span style='font-family:
"Courier New"'>o</span><span style='font-size:7.0pt'> </span>What
is "Bio::DB::GFF"? Is it a database? Schema? Adaptor?<o:p></o:p></p>
<p style='margin-left:72.0pt;text-indent:-18.0pt'><span style='font-family:
"Courier New"'>o</span><span style='font-size:7.0pt'> </span>Where
does annotation data come from? What is the annotation pipeline?<o:p></o:p></p>
</div>
</div>
</blockquote>
<div>
<p class=MsoNormal>GBrowse uses adaptors to read different data sources.
The data source can be flat files (GFF3 + FASTA if you want the
sequence), or databases, or any other data source you can imagine. I
believe that all adaptors are written in Perl. Each adaptor has an
expected input format. The database adaptors expect a specific schema to
talk to. <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>So Bio::DB::GFF is a Perl module that is a GBrowse adaptor.
It expects to read from a database with a specific schema.
(Bio::DB::GFF also assumes GFF2, a now deprecated format.)<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>However, writing an adaptor is not a small undertaking.
Probably a much easier way to tackle this is to write a program to export
GFF3 and FASTA formatted files from your database and then load it into a into
a Bio::DB::SeqFeature::Store MySQL database. This will likely be faster
than running directly off of your source database. GFF3 is a flat file
format for specifying genomic features (genes, exons, SNPs, ...) and
relationships between them. FASTA is a flat file format for specifying
sequence.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Since you have a custom database, there is not going to be
any program that will create GFF3 or FASTA for you. FASTA should be trivial to
create (if you have the sequence). GFF3 will require more work.
Some code you could look at for inspiration is the GMODTools suite (<a
href="http://gmod.org/wiki/GMODTools">http://gmod.org/wiki/GMODTools</a>).
It does conversion from several formats to GFF3.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Where does annotation data come from? From an
annotation pileline!<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Wait. That answer isn't helpful, darnit. A
pipeline is usually a series (thus a pipeline) of programs that performs some
analysis on sequence. For example, you might have an already annotated
reference genome, and a slew of short sequences reads from ESTs* from the
latest high-throughput sequencer and you want to annotate the reference genome
with the new data. your pipeline might be:<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>1. Assemble the short reads into a series of contigs (put
the short reads together into longer chunks, hopefully each as long as the
complete EST). <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>2. Align the contigs to the reference genome (figure out
where they came from)<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>3. Create a GFF3 file and a FASTA file (not sure on the
FASTA) describing where each EST aligns to and load it into GBrowse.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>All of these steps may involve heavy magic. Fortunately,
most of that magic is already done by the people who have written the programs
to do the steps.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>ESTs = a relatively easy way to find out what part of the
genome is being transcribed (what the active genes are)<o:p></o:p></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-right:0cm'>
<div>
<div>
<p>As I said, I am relatively new to GMOD and I find the online documentation
is plentiful, but not easily navigated by the newbie. After two weeks of
reading the documentation I find I am now going in circles looking for answers
to my questions – and information on how to design an information system
employing components of GMOD. <o:p></o:p></p>
<p>Ideally a diagram that displays a database and how it interacts with the
components of GMOD would be great to see. I haven't yet found anything like
this in the documentation. At the very least, if someone could steer me in the
right direction as far as what components I should focus on and what specific
documentation I can read, it would be appreciated.<o:p></o:p></p>
</div>
</div>
</blockquote>
<div>
<p class=MsoNormal>It is possible to use GBrowse as a standalone tool, without
any other GMOD tools. A lot of people actually do this. It sounds
like this might work fine for you. <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Thanks for the documentation suggestions. We just did
a community survey and one of the top priorities for the help desk was
improving the documentation. Look for progress in 2009.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Finally, although you didn't ask for it, I can think of two
GBrowse instances that might show datatypes that are sort of similar to what
you are doing:<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <a href="http://hapmap.org">http://hapmap.org</a><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <a
href="http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/">http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/jwsequence/</a>
or<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <a
href="http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/cvsequence/">http://jimwatsonsequence.cshl.edu/cgi-perl/gbrowse/cvsequence/</a><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Please let em know if you have any questions or comments.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Dave C<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>541 914 6324<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>AIM or Skype user: tnabtaf <o:p></o:p></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-right:0cm'>
<div>
<div>
<p> <o:p></o:p></p>
<p>Any assistance you can provide on these questions would be tremendously
appreciated. And if I can, in turn, provide some input on how to create some
"newbie" documentation, I will do so – to help others in my
situation.<o:p></o:p></p>
<p> <o:p></o:p></p>
<p>Also…I have 15 years' experience working with relational
databases…but not genomic databases…so you can assume a level of
technical understanding, but with the caveat that genomic databases are new
territory for me.<o:p></o:p></p>
<p> <o:p></o:p></p>
<p>Thanks so much for your time.<o:p></o:p></p>
<p> <o:p></o:p></p>
<p>Kind regards,<o:p></o:p></p>
<p> <o:p></o:p></p>
<p><span style='color:#888888'>Margie Manker<o:p></o:p></span></p>
</div>
</div>
</blockquote>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'>Was this helpful? Let us
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