Re: [gmod-cmap] How are You Importing Data

[Andrew F. <ad...@nc...>]

Hi Ben-
At LIS, we've been mostly using cmap_admin.pl on tab-delimited files, 
with the occasional direct insert or use of the web-based admin pages to 
deal with adding generic xrefs. As someone else mentioned, doing direct 
SQL inserts against CMap can be a bit of a pain when one forgets to 
update the cmap_next_number table before using the perl code to do 
further importing. But sometimes you really want to be able to do a 
batch insert of data via SQL from some related database, rather than go 
the flatfile route. It might be nice to have an option to configure the 
perl so that it assumes the DBMS was managing this (e.g. if the admin 
wanted to change the schema files to use their system's implementation 
of sequences)?

At any rate, we do get most of our map data from collaborators via 
spreadsheets, so it's generally very handy to be able to transform to a 
tab-delimited file and import from that.  The current tab-delimited 
structure strikes a good balance between the simplicity of the core data 
and the flexibility of the representation of xrefs and attributes.

I'm curious about your vision for use of GFF3; are you imagining that 
its use could bring in more of the "controlled vocab/ontology" flavor to 
attributes and types? That could useful. Currently, we use some 
simplistic naming conventions to encode a very shallow hierarchy into 
our feature types, but that approach can only go so far before becoming 
cumbersome.

Hope these comments from the peanut gallery are of some small use.

Regards

-- 

Andrew Farmer
ad...@nc...
(505) 995-4464
Database Administrator/Software Developer
National Center for Genome Resources

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"To live in the presence of great truths and eternal laws,
to be led by permanent ideals-
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