[Gusdev-gusdev] Re: GUS features

[Chris S. <sto...@pc...>]

Matt,
Thanks! Looks like there are a number of direct mappings which is 
great. I've been working on the MGED ontology this week while Helen 
Parkinson has been visiting but will get back to this tomorrow and try 
to fill in gaps and address questions.
Cheers,
Chris

On Tuesday, December 3, 2002, at 02:21  PM, Matthew Berriman wrote:

> Chris
> 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			
> <BindingSiteFeature: names of binding sites>			
> CentromereFeature:			
>  	predicted centromere 	????	SO:0000577	centromere
> DNARegulatory:			
>  	-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:			
>  	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			
>  	ExonFeature 		SO:0000147	exon *
> GeneFeature			
>  	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			
>  	hexamer 	????		
> 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 	????		
>  	S_region 	????		
>  	V_region 	????	SO:0000466	V-gene
>  	V_segment 	????		
>  	iDNA 	????		
> LowComplexityNAFeature			
>  	low complexity sequence 	????		
> Miscellaneous			
>  	misc_binding 	????		
>  	misc_feature 	????		
>  	misc_signal 	????		
>  	protein_bind 	????		
>  	stem_loop 		SO:0000313	stem loop
>  	unsure 	????		
> PolyAFeature			
>  	PolyAFeature 	????	SO:0000610	polyA sequence
> 	????	SO:0000553	polyA site
> PromoterFeature			
>  	PromoterFeature 	???? How does this differ from
> DNARegulatory>Promoter ?		differ from
> DNARegulatory>Promoter ?
>  	various promoter sets 	????		
>  ProteinFeature	 			
>  	mat_peptide 	???? N/A		
>  	sig_peptide 	???? N/A		
>  	transit_peptide 	???? N/A		
> RNAFeature			
>  	PREDICTED REFSEQ 	????		
>  	PROVISIONAL REFSEQ 	????		
>  	REFSEQ 	????		
>  	REVIEWED REFSEQ 	????		
>  	RNAFeature 	????	SO:0000184	transcript region
>  	assembly 	????		
>  	mRNA 		SO:0000234	messenger RNA
> RNAStructure			
>  	RBS 		SO:0000552	5'-ribosome binding site
>  	misc_RNA 	????		
> RNAType			
>  	rRNA 	???? is this different to the GeneFeature>rRNA?		
>  	scRNA 	????		
>  	snRNA 	???? is this different to the GeneFeature>rRNA?		
>  	tRNA 	???? is this different to the GeneFeature>rRNA?		
> <Repeats: names of repeats>			
> RestrictionFragmentFeature			
>  	RestrictionFragmentFeature 	???? Is this to describe the DNA
> source?		
> <SAGETagFeature: locations on chromosomes>			
> STS			
>  	STS 	????		
> ScaffoldGapFeature			
>  	assembly gap 	????		
> SeqVariation			
>  	SNP 		SO:0000694	single nucleotide polymorphism
>  	allele 	????		
>  	conflict 	????		
>  	misc_difference 	????		
>  	misc_recomb 	????		
>  	modified_base 		SO:0000199	modified DNA base
> feature
>  	mutation 	????	SO:1000170	uncharacterised
> chromosomal mutation
>  	old_sequence 	????		
>  	variation 		SO:1000128	sequence variation
> feature
> Source			
>  	source 	????		
> TandemRepeatFeature			
>  	tandem repeat 		SO:0000705	tandem repeat
> TelomereFeature			
>  	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 	????		
>  	prim_transcript 		SO:0000185	primary
> transcript
>
>> -----Original Message-----
>> From: Chris Stoeckert [mailto:sto...@pc...]
>> Sent: 26 November 2002 19:37
>> To: Matthew Berryman
>> Cc: gusdev-gusdev
>> Subject: Re: GUS features
>>
>>
>> Hi Matt,
>> I've generated a list of the 26 subclass views of NAFeatureImp and
>> looked at the distinct names associated with. These are given below.
>> Will now start looking at the SO and SO lite for these.
>> Chris
>>
>> On Friday, November 22, 2002, at 12:59  PM, Matt Berriman wrote:
>>
>>> 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
>> everything is
>>> represented.
>>>
>>> cheers
>>> Matt
>>
>> 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	
>> 	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
>>
>>
> <GUS2SO.txt>