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Draft evidence code ontology

Michael Ashburner (Genetics) ma11 at gen.cam.ac.uk
Mon May 31 06:11:32 PDT 2004


I would like to revisit the evidence codes ontology, perhaps
with the idea of some discussion about it during the annotation
workshop in 2 weeks time.

I attach a new version. The major change is:

inferred from experiment added as a parent to ida (and its children)

I also added some new terms. I am still awaiting the TAIR codes
for inclusion.

Michael
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format-version: 1.0
date: 31:05:2004 14:08
saved-by: ma11
auto-generated-by: DAG-Edit 1.409-beta-4
default-namespace: evidence_codes.ontology
remark: autogenerated-by\:     DAG-Edit version 1.409-beta-4\nsaved-by\:             ma11\ndate\:                 Fri Feb 27 16\:10\:50 GMT 2004\nversion\: $Revision\: 1.23 $

[Term]
id: EV:0000017
name: inferred from ectopic expression
is_a: EV:0000014

[Term]
id: EV:0000030
name: inferred from curated BLAST match
is_a: EV:0000044

[Term]
id: EV:0000007
name: inferred from immunofluorescence
is_a: EV:0000006

[Term]
id: EV:0000002
name: inferred from direct assay
synonym: "IDA" []
is_a: EV:0000006

[Term]
id: EV:0000031
name: inferred from curated BLAST match to protein
is_a: EV:0000030

[Term]
id: EV:0000041
name: inferred from similarity
synonym: "ISS" []
is_a: EV:0000043
is_a: EV:0000033

[Term]
id: EV:0000032
name: inferred from curated BLAST match to nucleic acid
is_a: EV:0000030

[Term]
id: EV:0000040
name: inferred from immunological assay
is_a: EV:0000023
is_a: EV:0000039

[Term]
id: EV:0000018
name: inferred from anti-sense experiment
is_a: EV:0000014

[Term]
id: EV:0000049
name: inferred from reporter gene assay
is_a: EV:0000006

[Term]
id: EV:0000046
name: inferred from level of protein expression
is_a: EV:0000010

[Term]
id: EV:0000023
name: inferred from ligand binding
is_a: EV:0000021

[Term]
id: EV:0000028
name: inferred from motif similarity
is_a: EV:0000044

[Term]
id: EV:0000035
name: no biological data
synonym: "ND" []
is_a: EV:0000000

[Term]
id: EV:0000013
name: inferred from transgenic rescue
is_a: EV:0000012

[Term]
id: EV:0000012
name: inferred from functional complementation
is_a: EV:0000006

[Term]
id: EV:0000048
name: inferred from level of transcript expression
is_a: EV:0000009

[Term]
id: EV:0000009
name: inferred from transcript expression
is_a: EV:0000008

[Term]
id: EV:0000029
name: inferred from InterPro motif similarity
is_a: EV:0000028

[Term]
id: EV:0000022
name: inferred from co-purification
is_a: EV:0000021

[Term]
id: EV:0000008
name: inferred from expression pattern
synonym: "IEP" []
is_a: EV:0000006

[Term]
id: EV:0000036
name: inferred from electronic annotation
synonym: "IEA" []
is_a: EV:0000043

[Term]
id: EV:0000014
name: inferred from mutant phenotype
synonym: "IMP" []
is_a: EV:0000006

[Term]
id: EV:0000011
name: inferred from genetic interaction
synonym: "IGI" []
is_a: EV:0000006

[Term]
id: EV:0000039
name: inferred from protein assay
is_a: EV:0000006

[Term]
id: EV:0000024
name: inferred from protein binding
is_a: EV:0000023
is_a: EV:0000039

[Term]
id: EV:0000045
name: inferred from spatial pattern of protein expression
is_a: EV:0000010

[Term]
id: EV:0000047
name: inferred from spatial pattern of transcript expression
is_a: EV:0000009

[Term]
id: EV:0000027
name: inferred from structural similarity
is_a: EV:0000041

[Term]
id: EV:0000038
name: inferred from transient rescue
is_a: EV:0000012

[Term]
id: EV:0000044
name: inferred from sequence similarity
is_a: EV:0000041

[Term]
id: EV:0000016
name: inferred from loss-of-function mutant phenotype
is_a: EV:0000015

[Term]
id: EV:0000005
name: inferred from enzyme assay
is_a: EV:0000039

[Term]
id: EV:0000037
name: not_recorded
synonym: "NR" []
is_a: EV:0000000

[Term]
id: EV:0000026
name: inferred from nucleic acid hybridization
is_a: EV:0000041
is_a: EV:0000006

[Term]
id: EV:0000015
name: inferred from gene mutation
is_a: EV:0000014

[Term]
id: EV:0000010
name: inferred from protein expression
is_a: EV:0000008
is_a: EV:0000039

[Term]
id: EV:0000004
name: inferred from cell fractionation
is_a: EV:0000006

[Term]
id: EV:0000025
name: inferred from 2-hybrid interaction
is_a: EV:0000023

[Term]
id: EV:0000003
name: inferred from reconstitution assay
is_a: EV:0000006

[Term]
id: EV:0000034
name: non-traceable author statement
synonym: "NAS" []
is_a: EV:0000000

[Term]
id: EV:0000001
name: inferred by curator
synonym: "IC" []
is_a: EV:0000000

[Term]
id: EV:0000006
name: inferred from experiment
is_a: EV:0000033

[Term]
id: EV:0000042
name: inferred from gain-of-function mutant phenotype
is_a: EV:0000015

[Term]
id: EV:0000020
name: inferred from specific protein inhibition
is_a: EV:0000039

[Term]
id: EV:0000019
name: inferred from RNAi experiment
is_a: EV:0000014

[Term]
id: EV:0000021
name: inferred from physical interaction
synonym: "IPI" []
is_a: EV:0000006

[Term]
id: EV:0000033
name: traceable author statement
synonym: "TAS" []
is_a: EV:0000000

[Term]
id: EV:0000000
name: Evidence_Codes_Ontology

[Term]
id: EV:0000043
name: inferred from in-silico analysis
is_a: EV:0000000

[Term]
id: EV:0000051
name: inferred from gain of function mutant phenotype
is_obsolete: true

[Term]
id: EV:0000050
name: inferred from loss of function mutant phenotype
is_obsolete: true

-------------- next part --------------
!autogenerated-by:     DAG-Edit version 1.409-beta-4
!saved-by:             ma11
!date:                 Mon May 31 14:07:42 BST 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 from in-silico analysis ; EV:0000043
  @is_a at inferred from electronic annotation ; EV:0000036 ; synonym:IEA
  @is_a at inferred from similarity ; EV:0000041 ; synonym:ISS @is_a@ traceable author statement ; EV:0000033
   @is_a at inferred from nucleic acid hybridization ; EV:0000026 @is_a@ inferred from experiment ; EV:0000006
   @is_a at inferred from sequence similarity ; EV:0000044
    @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 structural similarity ; EV:0000027
 @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 experiment ; EV:0000006
   @is_a at inferred from cell fractionation ; EV:0000004
   @is_a at inferred from direct assay ; EV:0000002 ; synonym:IDA
   @is_a at inferred from expression pattern ; EV:0000008 ; synonym:IEP
    @is_a at inferred from protein expression ; EV:0000010 @is_a@ inferred from protein assay ; EV:0000039
     @is_a at inferred from level of protein expression ; EV:0000046
     @is_a at inferred from spatial pattern of protein expression ; EV:0000045
    @is_a at inferred from transcript expression ; EV:0000009
     @is_a at inferred from level of transcript expression ; EV:0000048
     @is_a at inferred from spatial pattern of transcript expression ; EV:0000047
   @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 genetic interaction ; EV:0000011 ; synonym:IGI
   @is_a at inferred from immunofluorescence ; EV:0000007
   @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 gain-of-function mutant phenotype ; EV:0000042
     @is_a at inferred from loss-of-function mutant phenotype ; EV:0000016
    @is_a at inferred from RNAi experiment ; EV:0000019
   @is_a at inferred from nucleic acid hybridization ; EV:0000026 @is_a@ inferred from similarity ; EV:0000041
   @is_a at inferred from 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 immunological assay ; EV:0000040 @is_a@ inferred from protein assay ; EV:0000039
     @is_a at inferred from protein binding ; EV:0000024 @is_a@ inferred from protein assay ; EV:0000039
   @is_a at inferred from protein assay ; EV:0000039
    @is_a at inferred from enzyme assay ; EV:0000005
    @is_a at inferred from immunological assay ; EV:0000040 @is_a@ inferred from ligand binding ; EV:0000023
    @is_a at inferred from protein binding ; EV:0000024 @is_a@ inferred from ligand binding ; EV:0000023
    @is_a at inferred from protein expression ; EV:0000010 @is_a@ inferred from expression pattern ; EV:0000008
     @is_a at inferred from level of protein expression ; EV:0000046
     @is_a at inferred from spatial pattern of protein expression ; EV:0000045
    @is_a at inferred from specific protein inhibition ; EV:0000020
   @is_a at inferred from reconstitution assay ; EV:0000003
   @is_a at inferred from reporter gene assay ; EV:0000049
  @is_a at inferred from similarity ; EV:0000041 ; synonym:ISS @is_a@ inferred from in-silico analysis ; EV:0000043
   @is_a at inferred from nucleic acid hybridization ; EV:0000026 @is_a@ inferred from experiment ; EV:0000006
   @is_a at inferred from sequence similarity ; EV:0000044
    @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 structural similarity ; EV:0000027


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