Should sequence_variant have parents?
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Should sequence_variant have parents?
by Jim Hu
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In the GFF3 conversion, we're getting sequence_variants with parents that are geneids. The GFF3 validator we're using (the one in svn) is complaining. In SO, it looks like there is not parent for sequence_variant. What's the desired behavior/practice? Thanks! Jim ===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 ------------------------------------------------------------------------------ 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 Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: [SO-devel] Should sequence_variant have parents?
by Barry Moore-2
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Hi Jim,
In GFF3 you should be using sequence_alteration and it's children as they are sequence features. I think sequence_variant and it's children are a bit confusing, but if I understand correctly those describe variation related terms that are not necessarily locatable sequence_features (or at least or less likely to be used in annotation allele, CNV, genotype), whereas the variants described under sequence_alteration (insertion, deletion, substitution) always refer to a specific location and are intended to be used in annotation. For example, in GFF3 rather than using allele it would be better to use SNV, insertion, or deletion etc. to describe the individual variants at the sequence level and for CNV you would use insertion, deletion or duplication to describe the sequence boundaries associated with a CNV. We've been doing a bit of house keeping in the sequence_alteration area of SO recently, so would love feed back if you're using those terms and have any problems or concerns. Barry On Oct 27, 2009, at 1:57 PM, Jim Hu wrote:
------------------------------------------------------------------------------ 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 Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: [SO-devel] Should sequence_variant have parents?
by Jim Hu
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Thanks, Barry. We'll look at that.
Jim On Oct 27, 2009, at 3:40 PM, Barry Moore wrote:
===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 ------------------------------------------------------------------------------ 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 Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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