Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

Draft evidence code ontology

Judith Blake jblake at informatics.jax.org
Fri Feb 27 08:05:44 PST 2004


yes I agree with Harold, ISS is better (in confidence level) than IEA in 
that a curator has assessed the sequence similarity , but it is not a 
'direct assay' that demonstrates that a certain function is performed by 
the protein in question.

judy


At 10:39 AM 2/27/2004, Harold Drabkin wrote:
>Hi all
>
>I have a problem with an ISS being thought of as a type of IDA or
>experiment. It is very important to make a distinction between something
>with experiments behind them.
>For example, suppose two proteins are similar except for one amino acid, and
>the identity of the amino acid determines whether or not the protein
>functions as a kinase.
>ISS would predict that one was a kinase based on similarity to the other,
>but the real experiment (IDA) would demonstrate that one did NOT have kinase
>activity.
>
>hjd
>
>On 2/27/04 6:13 AM, "David Sutherland" <djs93 at gen.cam.ac.uk> wrote:
>
> >
> > Hi Michael,
> >
> > Here's my penneth:
> > 1. Should 2 hybrid and protein binding be under ligand binding?
> >
> > 2. The subdivision of IGI seems a bit odd.  Would enhancement and 
> suppression
> > better terms than rescue?  To use rescue seems at odds with FlyBase 
> phenotype
> > curation, (where as you know it is currently reserved for suppression of a
> > phenotype by alleles/transgenes of the same gene).  The same argument could
> > apply to functional complementation - currently in use by FlyBase for cross
> > species rescue by "homologues".  Functional complementation in this 
> sense is
> > clearly a useful form of evidence for assigning GO terms, but it seems 
> quite
> > distinct from the usual usage of 'genetic interaction'.
> >
> >
> > 3. I may be being pedantic, but should sequence similarity and its 
> children be
> > under 'inferred from direct assay'?  I guess one could consider them in 
> silico
> > assays (?).
> >
> > Dave
> >
> >> Envelope-to: djs93 at gen.cam.ac.uk
> >> Delivery-date: Thu, 26 Feb 2004 18:23:31 +0000
> >> X-Authentication-Warning: fafner.Stanford.EDU: majordom set sender to
> > owner-gofriends at genome-mail.stanford.edu using -f
> >> Date: Thu, 26 Feb 2004 18:14:42 +0000 (GMT)
> >> From: "Michael Ashburner (Genetics)" <ma11 at gen.cam.ac.uk>
> >> Subject: Draft evidence code ontology
> >> To: gofriends at genome.stanford.edu
> >> MIME-Version: 1.0
> >> Content-MD5: mry4eReiFy7MRqA8F9KmeQ==
> >> X-Cam-AntiVirus: No virus found
> >> X-Cam-SpamDetails: Not scanned
> >> X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/
> >> X-Cam-AntiVirus: No virus found
> >> X-Cam-SpamDetails: scanned, SpamAssassin (score=-0.4, FROM_CRSID -0.74,
> > FROM_ENDS_IN_NUMS 0.74, X_AUTH_WARNING -0.40)
> >>
> >>
> >>
> >> Folks - here is a very drafty evidence codes ontology (w/out definitions).
> >> Feedback please on all of its particulars.
> >>
> >> Michael
> >>
> >> !autogenerated-by:     DAG-Edit version 1.409-beta-4
> >> !saved-by:             ma11
> >> !date:                 Thu Feb 26 17:10:28 GMT 2004
> >> !version: $Revision: 1.23 $
> >> !type: @is_a@ is_a is a
> >> $Evidence_Codes_Ontology ; EV:0000000
> >>  @is_a at inferred by curator ; EV:0000001 ; synonym:IC
> >>  @is_a at inferred by electronic annotation ; EV:0000036 ; synonym:IEA
> >>  @is_a at no biological data ; EV:0000035 ; synonym:ND
> >>  @is_a at non-traceable author statement ; EV:0000034 ; synonym:NAS
> >>  @is_a at not_recorded ; EV:0000037 ; synonym:NR
> >>  @is_a at traceable author statement ; EV:0000033 ; synonym:TAS
> >>   @is_a at inferred from direct assay ; EV:0000002 ; synonym:IDA
> >>    @is_a at inferred by cell fractionation ; EV:0000004
> >>    @is_a at inferred by immunofluorescence ; EV:0000007
> >>    @is_a at inferred by physical interaction ; EV:0000021 ; synonym:IPI
> >>     @is_a at inferred from co-purification ; EV:0000022
> >>     @is_a at inferred from ligand binding ; EV:0000023
> >>      @is_a at inferred from 2-hybrid interaction ; EV:0000025
> >>      @is_a at inferred from protein binding ; EV:0000024 @is_a@ inferred by
> > protein
> >> assay ; EV:0000039
> >>    @is_a at inferred by protein assay ; EV:0000039
> >>     @is_a at inferred by enzyme assay ; EV:0000005
> >>     @is_a at inferred by immunological assay ; EV:0000040
> >>     @is_a at inferred from protein binding ; EV:0000024 @is_a@ inferred from
> > ligand
> >> binding ; EV:0000023
> >>    @is_a at inferred by reconstitution assay ; EV:0000003
> >>    @is_a at inferred from expression pattern ; EV:0000008 ; synonym:IEP
> >>     @is_a at inferred from protein expression ; EV:0000010
> >>     @is_a at inferred from transcript expression ; EV:0000009
> >>    @is_a at inferred from genetic interaction ; EV:0000011 ; synonym:IGI
> >>     @is_a at inferred from functional complementation ; EV:0000012
> >>     @is_a at inferred from transgenic rescue ; EV:0000013
> >>     @is_a at inferred from transient rescue ; EV:0000038
> >>    @is_a at inferred from mutant phenotype ; EV:0000014 ; synonym:IMP
> >>     @is_a at inferred from anti-sense experiment ; EV:0000018
> >>     @is_a at inferred from ectopic expression ; EV:0000017
> >>     @is_a at inferred from gene mutation ; EV:0000015
> >>     @is_a at inferred from overexpression ; EV:0000016
> >>     @is_a at inferred from RNAi experiment ; EV:0000019
> >>    @is_a at inferred from nucleic acid hybridization ; EV:0000026 @is_a@
> >> inferred
> >> sequence similarity ; EV:0000041
> >>    @is_a at inferred from specific protein inhibition ; EV:0000020
> >>    @is_a at inferred sequence similarity ; EV:0000041 ; synonym:ISS
> >>     @is_a at inferred from curated BLAST match ; EV:0000030
> >>      @is_a at inferred from curated BLAST match to nucleic acid ; EV:0000032
> >>      @is_a at inferred from curated BLAST match to protein ; EV:0000031
> >>     @is_a at inferred from motif similarity ; EV:0000028
> >>      @is_a at inferred from InterPro motif similarity ; EV:0000029
> >>     @is_a at inferred from nucleic acid hybridization ; EV:0000026 @is_a@
> > inferred
> >> from direct assay ; EV:0000002
> >>     @is_a at inferred from structural similarity ; EV:0000027
> >>
> >>
> >>
> >> --
> >> This message is from the GOFriends moderated mailing list.  A list of 
> public
> >> announcements and discussion of the Gene Ontology (GO) project.
> >> Problems with the list?           E-mail: owner-gofriends at geneontology.org
> >> Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
> >> Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
> >> Web:          http://www.geneontology.org/
> >
> >
> >
> > --
> > This message is from the GOFriends moderated mailing list.  A list of 
> public
> > announcements and discussion of the Gene Ontology (GO) project.
> > Problems with the list?           E-mail: owner-gofriends at geneontology.org
> > Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
> > Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
> > Web:          http://www.geneontology.org/
>
>
>--
>This message is from the GOFriends moderated mailing list.  A list of public
>announcements and discussion of the Gene Ontology (GO) project.
>Problems with the list?           E-mail: owner-gofriends at geneontology.org
>Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
>Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
>Web:          http://www.geneontology.org/


--
This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
Web:          http://www.geneontology.org/



More information about the go-friends mailing list