[Gmod-help] new database and GBrowse

[Margie Manker]

Hi Dave

 

We met when you were here in Toronto for the GMOD community meeting in June
of this year.

 

I work with The Centre for Applied Genomics and am revamping the design of
the Database of Genomic Variants and consolidating several autism databases.

 

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.

 

I'll try to summarize what I am doing and what my questions are:

 

-          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.

-          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.

-          We will most likely employ GBrowse as the genome browser for
display of data in the above databases.

-          My highest level questions that I have yet to find appropriate
answers to are these:

o   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   What components would I most likely need from GMOD to get my database
and GBrowse to work together?

-          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.

-          Other questions that arise are:

o   What is "Bio::DB::GFF"? Is it a database? Schema? Adaptor?

o   Where does annotation data come from? What is the annotation pipeline?

 

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.

 

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.

 

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.

 

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.

 

Thanks so much for your time.

 

Kind regards,

 

Margie Manker

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