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Hi Howard.
I think the thing that is disturbing me is that the locus can be 40MB long and we know that the allele is in there somewhere. Its the uncertainty that bothers me. But I hear what you are saying, they are alleles with fuzzy boundaries.
I think there are similarities to haplotype block, and that is a biological region.
If we move it to biological_feature, what would its parent...
2009-11-21 00:18:09 UTC in Sequence Ontology
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Hi Howard,
IS the QTL not a tool used to understand the alleles, rather than a biological thing in itself?
In a biological setting, what does the QTL do? Its not the same kind of thing as say an exon is it?
--K.
2009-11-20 21:30:01 UTC in Sequence Ontology
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Hi Howard,
I understand the definition and the need for it, but the name screams at me.
Is there any way you can name this terms to be a region of some kind. To call a chunk of sequence a phenotype just seems wrong to me.
--Karen.
2009-11-20 21:18:50 UTC in Sequence Ontology
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Hi Howard.
I think you have brought up some really good points, and there definitely needs to be some work done on SO in this area. We had tried to resolve similar issues, where one group studies a biological phenomenon, and another group uses it as a tool. There was a whole debate about plasmids and reagents for example. I think that transgene fits this category of problem. There are multiple...
2009-11-19 19:49:25 UTC in Sequence Ontology
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Hi Howard,
transgene is a cross product with gene and transgenic (sequence integrated with foreign sequence).
This is a general term, and does not specify whether the transfer is natural or experimental. It could be used to describe a bacterial gene or one of Mario Cappechi's experimental constructs for example.
SO is attempting to delineate experimental from biological terms and this...
2009-11-19 18:29:36 UTC in Sequence Ontology
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YAC_end is_a read
YAC_end part_of YAC
Hope this works,
if not, let me know
--K.
2009-11-19 18:19:49 UTC in Sequence Ontology
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eilbeck committed patchset 348 of module ontology to the Sequence Ontology CVS repository, changing 4 files.
2009-11-19 18:18:54 UTC in Sequence Ontology
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eilbeck committed patchset 347 of module ontology to the Sequence Ontology CVS repository, changing 4 files.
2009-11-10 19:56:31 UTC in Sequence Ontology
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eilbeck committed patchset 346 of module ontology to the Sequence Ontology CVS repository, changing 4 files.
2009-11-10 19:48:55 UTC in Sequence Ontology
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Hi michel,
again, I have added this to chromosome part. If you think it needs to be located somewhere else, let me know.
--Karen.
2009-11-10 01:06:15 UTC in Sequence Ontology
