Activity for Sequence Ontology
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Pankaj Jaiswal posted a comment on ticket #437
And the over/under expression is in comparison to some reference and dependent on...
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I think this is a molecular phenotype of the transcript isoform/gene and not a sequence...
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Karen Eilbeck posted a comment on ticket #436
Hi Nicole We moved the tracker to github and kept this one open a little longer than...
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Hi We have moved this tracker to the github site as the sourceforge is being retired....
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Lynzey Kujan created ticket #437
Overexpression/Underexpression
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Nicole Washington created ticket #436
add lncRNA_gene classes
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Chris Mungall posted a comment on ticket #435
Hi Pascale - just like GO, SO has moved its tracker, now here: https://github.co...
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Pascale Gaudet created ticket #435
Indels at protein level
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Edits for NCBI
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Daniel Lang created ticket #434
CDS_supported_by_peptide_spectrum_match
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June NCBI requested edits - after this we will ...
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new term request: fragile sites
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NTRs - transcript
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We still need to have that phone call.
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Sequence Ontology released /SO_cross_product/so_xp_2_5_3/so-xp_2_5_3.obo
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Maximilian Peters posted a comment on ticket #429
Many thanks! All the best, Max On Thu, May 14, 2015 at 6:45 PM, Karen Eilbeck eilbeck@users.sf.net...
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May tracker updates - H3K27_acetylation, stRNA ...
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intronic_splice_silencer
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remove synonym from SO:0000718
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done
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new term request: recombination_enhancer
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done. SO:0002059
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intronic_splice_silencer
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done SO:00002056
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done SO:0002058
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exonic_splice_silencer
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intron_gain SO:0001573
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yep. done
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SO:0002052 dominant_negative_variant. I added it as a child of functional variant,...
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Create SO term for 'dominant negative'
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stRNA_gene (SO:0001270): merge with miRNA_gene (SO:0001265)?
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Hi COlin This may be a better URL to support the argument http://en.wikipedia.org/wiki/Let-7_microRNA_precursor...
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Constitutive/inducible promoters
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constitutive promotor so:0002050 inducible_promotor SO:0002051
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SO:0002049 Thanks
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New Term: H3K27_acetylation_site
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Sagar created ticket #432
New Term: H3K27_acetylation_site
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Colin Batchelor created ticket #431
stRNA_gene (SO:0001270): merge with miRNA_gene (SO:0001265)?
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David Osumi-Sutherland posted a comment on ticket #430
Primary transcript versions are there, but these refer to transcripts prior to splicing....
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Grr, sourceforge lost my original comment... concise version below: Pre versions...
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NTRs - transcript
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http://purl.obolibrary.org/obo/so.owl now resolves to the most up to date version...
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Constitutive/inducible promoters
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Hi Ben Wow, this is a problem. We will get this fixed. In the meantime the svn repo...
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Ben Hutton created ticket #428
OWL file is not kept up to date
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Hey Keren, Sure, but that seems silly when it's not related to a term and is actually...
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Deanna Church posted a comment on ticket #426
Hi- So, I don't know if this has been described for other types of gene products,...
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Hmmm. If this could be applied to other gene products( kinds of ncRNA) then we should...
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Could you add your feature request on this term tracker? Thanks, Karen
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I can't make feature request tickets
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Create SO term for 'dominant negative'
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JAVIER DIEZ-PEREZ created ticket #425
intron_gain SO:0001573
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intronic_splice_silencer
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exonic_splice_silencer
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Pierre LINDENBAUM created ticket #422
suggestion to extend "genotype" SO:0001027
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Stacia Engel created ticket #421
new term request: recombination_enhancer
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fixed synonym
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remove synonym from SO:0000718
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Daniel Standage posted a comment on ticket #410
Although it doesn't quite roll off the tongue, I think transcript_assembly_nucleotide_match...
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OK. Sorry for making it worse --K On Feb 9, 2015, at 4:01 PM, Stacia Engel wrote:...
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SO:0002048 On Feb 9, 2015, at 4:01 PM, Stacia Engel wrote: dORF Karen Eilbeck Associate...
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disabled reading frame
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The name here is a bit weird as a genome is also an assembly. Could we call it it...
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Hi Karen, that is indeed an error to merge these two terms. blocked_reading_frame...
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ooops. Fixed that. Thanks for noticing.
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Two terms with the name "W_region"
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NTR:transcription pause site
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done SO:0002047 Thanks for the new term.
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There has been a term for a long time, (looks like it was made by Rama) blocked reading...
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NTR: disabled reading frame
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ntr: FRE and TCS elements
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done, done and done SO:0002044 SO:0002045 SO:0002046
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miRNA, transcription pause sites, various TFBS,...
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Rama balakrishnan created ticket #419
ntr: FRE and TCS elements
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trying again shRNA for Scott Cain
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shRNA for Scott Cain
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NTR: disabled reading frame
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MNV update for NCBI
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Jim Hu created ticket #417
NTR:transcription pause site
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Kim Rutherford created ticket #416
Two terms with the name "W_region"
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tracker updates July 2014
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jd690764 posted a comment on ticket #414
HI Karen, Can you send me the SO_id for this term? Thanks, Janos On Fri, Jul 11,...
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rDNA and subtelomere
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promoter regions
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ntr:X element core sequence
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done Thanks for clearing up my confusion
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sSORF & uORF
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uORF SO:0002027 sORF SO:0002028 tnaORF SO:0002029 Thank you for your amazingly good...
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PMID 8165123 intein_encoding_region SO:0002026 kind of gene_component_region
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ntr:intein coding sequence
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NTR: cis-acting homologous chromosome pairing factor
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SO:0002025 done
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Hi Val Does your colleague want to annotate the position of the break, the hotspot...
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Janos Demeter posted a comment on ticket #412
The term you have, 'intein' is a peptide feature. I'd like to have a term for the...
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Hi Janos We already have intein as a feature - a kind of cleaved peptide Does this...
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ntr: X_region
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Hi Karen, Thanks for checking! Actually, can you just make this ('X element core...
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THis term already exists X_element: The X element is a conserved region, of the telomere,...