Re: [Gmod-gbrowse] Selecting the correct SOFA term

[Nicole W. <NLW...@lb...>]

There's also "overlapping_feature_set", which is pretty generic:

http://www.sequenceontology.org/miso/current_cvs/term/SO:0001261

nicole

On Oct 29, 2009, at 9:59 PM, Nicole Washington wrote:

> No need to be limited to SOFA for gff3.  You can use any term from the
> whole of SO:
>
> http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/so.obo
>
> for individual reads, i'd choose "read".  to mark a region on the
> genome where some transcribed sequences occur, then perhaps
> "transcribed_cluster" is appropriate http://www.sequenceontology.org/miso/current_cvs/term/SO:0001457
>
> nicole
>
> On Oct 29, 2009, at 8:36 PM, Wes Barris wrote:
>
>> Hi,
>>
>> I am creating a .gff3 file containing 5kb bins of reads.  Here is
>> an example:
>>
>> ##gff-version 3
>> BTA1    read      SOFA     1       5000    267     .       .
>> Name=BTA1
>> BTA1    read      SOFA     5001    10000   114     .       .
>> Name=BTA1
>> BTA1    read      SOFA     10001   15000   115     .       .
>> Name=BTA1
>> BTA1    read      SOFA     15001   20000   123     .       .
>> Name=BTA1
>>
>> However, I am not sure what to use for the type in the 3rd column.
>> I've browsed through
>>
>> http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12
>>
>> but nothing seems appropriate.  Any suggestions?
>> --  
>> Wes Barris <wes...@cs...>
>>
>> ------------------------------------------------------------------------------
>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart
>> your
>> developing skills, take BlackBerry mobile applications to market and
>> stay
>> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
>> http://p.sf.net/sfu/devconference
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart  
> your
> developing skills, take BlackBerry mobile applications to market and  
> stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>