[BioRuby] Fwd: Re: BioSQL development

[Julian Nordt]

One more thing in regard to the mapping between BioSQL and GFF3:

I tried to follow the mapping given by the biosql wiki and blue collar  
bioinformatics. The mapping is acceptable in the sense that you can store  
*most* or even all (?) of the features that GFF3 offers. The further I got  
though within the development the unclearer things got me, especially in  
terms of the "attribute" column.

If you compare the table at the biosql wiki (for the attribute column)  
with the one at blue collar bioinformatics, one will notice that the there  
are keywords that occour in one, but not at the other table. That not  
mentioning the todos on the wiki regarding the "standard" columns. I  
havn't looked in that detail though through blue collars code, maybe the  
answer is given there.

However I wrote a small library that managed to store most - but not all  
the given information of the GFF3-files - correctly to BioSQL. There were  
some points where the mapping has been unclear to me and where I stored  
the given information where I thought it would fit best.

Considering that I chose a standard db schema to avoid any ambiguously and  
the fact that I experienced performance issues with MYSQL+Rails (not  
related to BioSQL) at the project made it enough for me to switch to CHADO  
backed by POSTGRES.

The documentation regarding CHADO is in my opinion richer and most  
importantly one can follow gmod_bulk_load_gff3.pl for the mapping  
relatively easy, since it is well documented.

I would very much welcome other opinions on the topic, especially in  
combination with the use of web applications.

-- Julian





On Sun, 22 Aug 2010 16:17:45 +0200, Rob Syme <rob.syme at gmail.com> wrote:

> I've had a look around and a pretty solid mapping seems to be available:
> http://www.biosql.org/wiki/Annotation_Mapping#GFF3
>
> Blue collar bioinformatics gave it a shot here:
> http://bcbio.wordpress.com/2009/02/22/exploring-bioperl-genbank-to-gff-mapping/
>
> -r
>
> On 22 Aug 2010 22:02, "Hilmar Lapp" <hlapp at drycafe.net> wrote:
> Is the issue with GFF3 in the Bioruby to BioSQL mapping, or is somehow in
> the BioSQL schema?
>
> I recall there was a thread on GFF recently which I wasn't able to  
> follow,
> so if the answer is in that thread and isn't easy to sum up here, just  
> point
> me there.
>
>        -hilmar
>
>
>
> On Aug 22, 2010, at 6:30 AM, Julian Nordt wrote:
>
>> Hi Rob,
>>
>> I just wanted to point that there ...


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