Re: [Obo-relations] [Gmod-gbrowse] miRNAs targeting sequences

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

another option would be to use something like the "regulates"  
relationship from GO.  but, this is not yet in the Relationship  
ontology.  Is there something in the RO that could be used?

On Jan 31, 2010, at 11:58 AM, Nicole Washington wrote:

> a follow up to this.
>
> i am also not sure about using "target" as the right attribute for  
> the miRNA, because a single miRNA might target multiple regions in  
> the genome, and i don't think multiple targets are permitted in gff3.
>
>
> On Jan 31, 2010, at 11:24 AM, Nicole Washington wrote:
>
>> hello,
>>
>> how might i properly capture the relationship between a miRNA (who's
>> sequence we know the location of), and its target site (who's genomic
>> location we also know).  i need to capture this in GFF3.  do i just
>> use the Target attribute?  that doesn't seem quite right to me.
>> another option would be to have a new relationship type, like
>> "targets", but that isn't in SO.
>>
>> here's an example, below.
>>
>> I	WormBase	CDS	47472	49416	.	+	.	ID=Y48G1C.12
>> I	CEUP	three_prime_UTR	49417	49819	.	+	.	ID=CEUP_3UTR:Y48G1C.
>> 12;Parent=Y48G1C.12,WBGene00044345;parental_relationship=adjacent_to/
>> Y48G1C.12;external_evidence=modENCODE_2352,modENCODE_2354
>> I	CEUP	miRNA_target_site	49420	49830	.	+	.	ID=miRNA_target:
>> 12345;Parent=CEUP_3UTR:Y48G1C.12
>> I	CEUP	miRNA	50000	50020	.	+	.	ID=miRNA12345;Target=miRNA_target: 
>> 12345
>> 1 20
>>
>> nicole
>>
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>