[Gusdev-gusdev] RE: GUS features

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Chris=20
Here is my attempt to map GUS to SO (I've also attached it as because
I'm not sure how well my browser preserves the tabs) There are some big
gaps, such as "source", protein features and miscellaneous features.

Cheers
Matt
...

SUBCLASS_VIEW		=09
<BindingSiteFeature: names of binding sites>		=09
CentromereFeature:		=09
 	predicted centromere 	????	SO:0000577	centromere
DNARegulatory:		=09
 	-10_signal 		SO:0000175	-10 signal
 	-35_signal 		SO:0000176	-35 signal
 	CAAT_signal 		SO:0000172	CAAT signal
 	GC_signal 		SO:0000173	GC-rich region
 	TATA_signal 		SO:0000174	TATA box
 	attenuator 		SO:0000140	attenuator
 	enhancer 		SO:0000165	enhancer *
 	promoter 		SO:0000167	promoter *
 	terminator 		SO:0000141	terminator *
DNAStructure:		=09
 	D-loop 		SO:0000297	D-loop
 	primer_bind 	????	SO:0005850	primer binding site
(sub-class of LTR-retrotransposon)
 	rep_origin 		SO:0000296	origin of replication
ExonFeature		=09
 	ExonFeature 		SO:0000147	exon *
GeneFeature		=09
 	CDS 	????	SO:0001254	coding sequence predicted
 	GeneFeature 		SO:0000704	gene element
 	gene 		SO:0000008	gene (sensu
yourfavoriteorganism)
 	snRNA 		SO:0000274	small nuclear RNA
 	tRNA 		SO:0000253	transfer RNA
HexamerFeature		=09
 	hexamer 	????	=09
Immunoglobulin		SO:0000460	vertebrate immunoglobulin/T-cell
receptor gene
 	C-region 	????	SO:0000478	C-gene
 	D_segment 	????	SO:0000458	D-gene
 	J_segment 	????	SO:0000470	J-gene
 	N_region 	????	=09
 	S_region 	????	=09
 	V_region 	????	SO:0000466	V-gene
 	V_segment 	????	=09
 	iDNA 	????	=09
LowComplexityNAFeature		=09
 	low complexity sequence 	????	=09
Miscellaneous		=09
 	misc_binding 	????	=09
 	misc_feature 	????	=09
 	misc_signal 	????	=09
 	protein_bind 	????	=09
 	stem_loop 		SO:0000313	stem loop
 	unsure 	????	=09
PolyAFeature		=09
 	PolyAFeature 	????	SO:0000610	polyA sequence
	????	SO:0000553	polyA site
PromoterFeature		=09
 	PromoterFeature 	???? How does this differ from
DNARegulatory>Promoter ?		differ from
DNARegulatory>Promoter ?
 	various promoter sets 	????	=09
 ProteinFeature	 		=09
 	mat_peptide 	???? N/A	=09
 	sig_peptide 	???? N/A	=09
 	transit_peptide 	???? N/A	=09
RNAFeature		=09
 	PREDICTED REFSEQ 	????	=09
 	PROVISIONAL REFSEQ 	????	=09
 	REFSEQ 	????	=09
 	REVIEWED REFSEQ 	????	=09
 	RNAFeature 	????	SO:0000184	transcript region
 	assembly 	????	=09
 	mRNA 		SO:0000234	messenger RNA
RNAStructure		=09
 	RBS 		SO:0000552	5'-ribosome binding site
 	misc_RNA 	????	=09
RNAType		=09
 	rRNA 	???? is this different to the GeneFeature>rRNA?	=09
 	scRNA 	????	=09
 	snRNA 	???? is this different to the GeneFeature>rRNA?	=09
 	tRNA 	???? is this different to the GeneFeature>rRNA?	=09
<Repeats: names of repeats>		=09
RestrictionFragmentFeature		=09
 	RestrictionFragmentFeature 	???? Is this to describe the DNA
source?	=09
<SAGETagFeature: locations on chromosomes>		=09
STS		=09
 	STS 	????	=09
ScaffoldGapFeature		=09
 	assembly gap 	????	=09
SeqVariation		=09
 	SNP 		SO:0000694	single nucleotide polymorphism
 	allele 	????	=09
 	conflict 	????	=09
 	misc_difference 	????	=09
 	misc_recomb 	????	=09
 	modified_base 		SO:0000199	modified DNA base
feature
 	mutation 	????	SO:1000170	uncharacterised
chromosomal mutation
 	old_sequence 	????	=09
 	variation 		SO:1000128	sequence variation
feature
Source		=09
 	source 	????	=09
TandemRepeatFeature		=09
 	tandem repeat 		SO:0000705	tandem repeat
TelomereFeature		=09
 	predicted telomere 	????	SO:0000624	telomere
Transcript		SO:0000673	transcript
 	3'UTR 		SO:0000205	3'-untranslated region
 	3'clip 		SO:0000557	3'-clip
 	5'UTR 		SO:0000204	5'-untranslated region
 	5'clip 		SO:0000555	5'-clip
 	CDS 	????	SO:0001254	coding sequence predicted
 	exon 		SO:0000147	exon
 	intron 		SO:0000188	intron
 	mRNA 		SO:0000234	messenger RNA
 	polyA_signal 		SO:0000551	polyA signal sequence
 	precursor_RNA 	????	=09
 	prim_transcript 		SO:0000185	primary
transcript

> -----Original Message-----
> From: Chris Stoeckert [mailto:sto...@pc...]=20
> Sent: 26 November 2002 19:37
> To: Matthew Berryman
> Cc: gusdev-gusdev
> Subject: Re: GUS features
>=20
>=20
> Hi Matt,
> I've generated a list of the 26 subclass views of NAFeatureImp and=20
> looked at the distinct names associated with. These are given below.=20
> Will now start looking at the SO and SO lite for these.
> Chris
>=20
> On Friday, November 22, 2002, at 12:59  PM, Matt Berriman wrote:
>=20
> > Hi Chris
> > Do you have a list of GUS sequence features?  The SO group are
> > preparing a "SO Lite" -- it would be good to check that=20
> everything is=20
> > represented.
> >
> > cheers
> > Matt
>=20
> SUBCLASS_VIEW
> <BindingSiteFeature: names of binding sites>
> CentromereFeature:
> 	predicted centromere
> DNARegulatory:
> 	-10_signal
> 	-35_signal
> 	CAAT_signal
> 	GC_signal
> 	TATA_signal
> 	attenuator
> 	enhancer
> 	promoter
> 	terminator
> DNAStructure:
> 	D-loop
> 	primer_bind
> 	rep_origin
> ExonFeature
> 	ExonFeature
> GeneFeature
> 	CDS
> 	GeneFeature
> 	gene
> 	snRNA
> 	tRNA
> HexamerFeature
> 	hexamer
> Immunoglobulin
> 	C-region
> 	D_segment
> 	J_segment
> 	N_region
> 	S_region
> 	V_region
> 	V_segment
> 	iDNA
> LowComplexityNAFeature
> 	low complexity sequence
> Miscellaneous
> 	misc_binding
> 	misc_feature
> 	misc_signal
> 	protein_bind
> 	stem_loop
> 	unsure
> PolyAFeature
> 	PolyAFeature
> PromoterFeature
> 	PromoterFeature
> 	various promoter sets
> ProteinFeature=09
> 	mat_peptide
> 	sig_peptide
> 	transit_peptide
> RNAFeature
> 	PREDICTED REFSEQ
> 	PROVISIONAL REFSEQ
> 	REFSEQ
> 	REVIEWED REFSEQ
> 	RNAFeature
> 	assembly
> 	mRNA
> RNAStructure
> 	RBS
> 	misc_RNA
> RNAType
> 	rRNA
> 	scRNA
> 	snRNA
> 	tRNA
> <Repeats: names of repeats>
> RestrictionFragmentFeature
> 	RestrictionFragmentFeature
> <SAGETagFeature: locations on chromosomes>
> STS
> 	STS
> ScaffoldGapFeature
> 	assembly gap
> SeqVariation
> 	SNP
> 	allele
> 	conflict
> 	misc_difference
> 	misc_recomb
> 	modified_base
> 	mutation
> 	old_sequence
> 	variation
> Source
> 	source
> TandemRepeatFeature
> 	tandem repeat
> TelomereFeature
> 	predicted telomere
> Transcript
> 	3'UTR
> 	3'clip
> 	5'UTR
> 	5'clip
> 	CDS
> 	exon
> 	intron
> 	mRNA
> 	polyA_signal
> 	precursor_RNA
> 	prim_transcript
>=20
>=20