Version 7 (modified by markjschreiber, 16 years ago)


The Problem

One of the goals of BioSQL was to provide an interchange platform for the Bio* objects. This has not yet succeeded due to differences in the way the Bio* projects interpret an individual sequence record and how they persist it to the database.

Possible Tasks


Random ideas from Jan Aerts

Mind that this is *very* incomplete. Just to help my really bad memory. As the issue is interoperability of the Bio* toolkits, we don't have to synchronize the toolkits at the object level, but rather at the interface level.

First thing to check: what types of objects do we want to synchronize? Of course sequence objects; but what else? The results of a BLAST parsing?

For sequences

Check if each toolkit reads and writes a GenBank/Fasta/... serialization in the same way. Input can either be an original GenBank/Fasta/... file or a dbfetch from any database.

  • What should be conserved:
    • Tags
    • for a sequence: lower/uppercase
  • What not necessarily should be conserved:
    • for a sequence over multiple lines: length of each line

Task achieved

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