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<p class=MsoNormal>Hi Dave<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>We met when you were here in Toronto for the GMOD community
meeting in June of this year.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I work with The Centre for Applied Genomics and am revamping
the design of the Database of Genomic Variants and consolidating several autism
databases.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I have been doing a thorough review of the GMOD
documentation online for the past couple of weeks. However, I am still left
searching for the answers to some of my questions…as a “newbie”
to GMOD.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I’ll try to summarize what I am doing and what my questions
are:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>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 class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>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>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>We will most likely employ GBrowse as the genome
browser for display of data in the above databases.<o:p></o:p></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>My highest level questions that I have yet to find
appropriate answers to are these:<o:p></o:p></p>
<p class=MsoListParagraph style='margin-left:72.0pt;text-indent:-18.0pt;
mso-list:l0 level2 lfo1'><![if !supportLists]><span style='font-family:"Courier New"'><span
style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]>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 class=MsoListParagraph style='margin-left:72.0pt;text-indent:-18.0pt;
mso-list:l0 level2 lfo1'><![if !supportLists]><span style='font-family:"Courier New"'><span
style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]>What components would I most likely need from
GMOD to get my database and GBrowse to work together?<o:p></o:p></p>
<p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>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 class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]>Other questions that arise are:<o:p></o:p></p>
<p class=MsoListParagraph style='margin-left:72.0pt;text-indent:-18.0pt;
mso-list:l0 level2 lfo1'><![if !supportLists]><span style='font-family:"Courier New"'><span
style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]>What is “Bio::DB::GFF”? Is it a
database? Schema? Adaptor?<o:p></o:p></p>
<p class=MsoListParagraph style='margin-left:72.0pt;text-indent:-18.0pt;
mso-list:l0 level2 lfo1'><![if !supportLists]><span style='font-family:"Courier New"'><span
style='mso-list:Ignore'>o<span style='font:7.0pt "Times New Roman"'>
</span></span></span><![endif]>Where does annotation data come from? What is
the annotation pipeline?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>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 class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>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>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>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 class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>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 class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks so much for your time.<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Kind regards,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Margie Manker<o:p></o:p></p>
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