[Biojava-dev] BioJava3 Use Cases

[Mark Fortner]

Hi Richard,
I started to writeup a use-case, and realized that what I was thinking about
was more than just a single use-case, and might be beyond the scope of what
biojava should handle.  So I thought I would ask before writing it up.

It seems that we have a need for a generic parsing and dataloading
framework.  Something that encompasses not only Mark Schreiber's use-case,
but could also handle data from a variety of different instrument files --
everything from MAGE files, ABI trace files, CSV, Excel, or text flat files.

I've been thinking about creating a semantic data loader.  This would be
part framework and part GUI application.  It would allow the user to map
elements of data files to an ontology, and also map parts of an ontology to
different databases.  The user would be able to create a parser definition,
which would parse and load data, verify the data against rules stored in the
ontology and then load the data into the database using the data's ontology
tags as a guide.

A first step in the implementation, might be to retrofit the BioSQL and
parsing code.

Is this within the scope of BioJava?  Is it something that the community
would find interesting and useful in the everyday work they do?  It it
something to which people would like to contribute?

Regards,

-- 
Mark Fortner

blog: http://feeds.feedburner.com/jroller/ideafactory