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