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Draft evidence code ontology

Michael Ashburner (Genetics) ma11 at gen.cam.ac.uk
Fri Feb 27 05:35:59 PST 2004


Thanks for the input. I have - I hope - taken account of the
suggestions.

1. Now always 'inferred from', except 'inferred by curator'
2. ISS corrected
3.     @is_a at inferred from overexpression ; EV:0000016
  removed
4. Becky: 'There are several evidence codes under 'inferred from direct assay', 
which I think should not be, and should be 
moved up a level.
inferred from genetic interaction
inferred from mutant phenotype
inferred sequence similarity
inferred from expression pattern'

Midori made the same point.
.. I disagree, these are all direct assays

5: Becky: 5. 'inferred from protein binding ; EV:0000024' and 'inferred from 
ligand binding ; EV:0000023' sound very broad. 
Since we already have inferred from co-purification and inferred from 2-hybrid 
interaction, do we need EV:0000023 and 
EV:0000024?

.. yes ligand is broader than protein, could be a calcium-binding assay for 
example

6: Becky: 6. I think it may be nice to have a general 'inferred from experiment' 
evidence code for all the IDA, IPI, IGI, IEP 
and IMPs?
.. I think IDA _is_ inferred from experiment

7: Gillian: would this apply to both loss of function and gain of function 
mutants
made eg. by EMS, X ray etc. i.e. any non-transgenic mutation made in an
organism ? or just loss of function, to contrast with "inferred from
ectopic expression"

. have added

    @is_a at inferred from loss-of-function mutant phenotype ; EV:0000016
    @is_a at inferred from gain-of-function mutant phenotype ; EV:0000042

>From David S: 1. Should 2 hybrid and protein binding be under ligand binding?

.. yes, I think so.

8. From David S: 2. The subdivision of IGI seems a bit odd.  Would enhancement 
and suppression 

.. yes I agree, changed, now:

   @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
    
9. From David S: 3. I may be being pedantic, but should sequence similarity and 
its children be 

I have created a new parent

 @is_a at inferred from in-silico analysis ; EV:0000043

with
  @is_a at inferred from electronic annotation ; EV:0000036 ; synonym:IEA
   @is_a at inferred from sequence or structural similarity ; EV:0000041 ; 
synonym:ISS @is_a@ inferred from in-silico analysis ; EV:0000043

as kids



Updates attached in GO f/file and obo formats.

Michael

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format-version: 1.0
date: 27:02:2004 13:32
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\:                 Thu Feb 26 17\:10\:28 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:0000041

[Term]
id: EV:0000039
name: inferred from protein assay
is_a: EV:0000002

[Term]
id: EV:0000007
name: inferred from immunofluorescence
is_a: EV:0000002

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

[Term]
id: EV:0000002
name: inferred from direct assay
synonym: "IDA" []
is_a: EV:0000033

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

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

[Term]
id: EV:0000041
name: inferred from sequence or structural similarity
synonym: "ISS" []
is_a: EV:0000002
is_a: EV:0000043

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

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

[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:0000010
name: inferred from protein expression
is_a: EV:0000008

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

[Term]
id: EV:0000026
name: inferred from nucleic acid hybridization
is_a: EV:0000002
is_a: EV:0000041

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

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

[Term]
id: EV:0000004
name: inferred from cell fractionation
is_a: EV:0000002

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

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

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

[Term]
id: EV:0000003
name: inferred from reconstitution assay
is_a: EV:0000002

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

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

[Term]
id: EV:0000028
name: inferred from motif similarity
is_a: EV:0000041

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

[Term]
id: EV:0000012
name: inferred from functional complementation
is_a: EV:0000002

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

[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:0000002

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

[Term]
id: EV:0000000
name: Evidence_Codes_Ontology

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

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

[Term]
id: EV:0000008
name: inferred from expression pattern
synonym: "IEP" []
is_a: EV:0000002

[Term]
id: EV:0000011
name: inferred from genetic interaction
synonym: "IGI" []
is_a: EV:0000002

[Term]
id: EV:0000014
name: inferred from mutant phenotype
synonym: "IMP" []
is_a: EV:0000002

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

-------------- next part --------------
!autogenerated-by:     DAG-Edit version 1.409-beta-4
!saved-by:             ma11
!date:                 Fri Feb 27 13:34:28 GMT 2004
!version: $Revision: 1.23 $
!type: % is_a is a
$Evidence_Codes_Ontology ; EV:0000000
 %inferred by curator ; EV:0000001 ; synonym:IC
 %inferred from in-silico analysis ; EV:0000043
  %inferred from electronic annotation ; EV:0000036 ; synonym:IEA
  %inferred from sequence or structural similarity ; EV:0000041 ; synonym:ISS % inferred from direct assay ; EV:0000002
   %inferred from curated BLAST match ; EV:0000030
    %inferred from curated BLAST match to nucleic acid ; EV:0000032
    %inferred from curated BLAST match to protein ; EV:0000031
   %inferred from motif similarity ; EV:0000028
    %inferred from InterPro motif similarity ; EV:0000029
   %inferred from nucleic acid hybridization ; EV:0000026 % inferred from direct assay ; EV:0000002
   %inferred from structural similarity ; EV:0000027
 %no biological data ; EV:0000035 ; synonym:ND
 %non-traceable author statement ; EV:0000034 ; synonym:NAS
 %not_recorded ; EV:0000037 ; synonym:NR
 %traceable author statement ; EV:0000033 ; synonym:TAS
  %inferred from direct assay ; EV:0000002 ; synonym:IDA
   %inferred from cell fractionation ; EV:0000004
   %inferred from expression pattern ; EV:0000008 ; synonym:IEP
    %inferred from protein expression ; EV:0000010
    %inferred from transcript expression ; EV:0000009
   %inferred from functional complementation ; EV:0000012
    %inferred from transgenic rescue ; EV:0000013
    %inferred from transient rescue ; EV:0000038
   %inferred from genetic interaction ; EV:0000011 ; synonym:IGI
   %inferred from immunofluorescence ; EV:0000007
   %inferred from mutant phenotype ; EV:0000014 ; synonym:IMP
    %inferred from anti-sense experiment ; EV:0000018
    %inferred from ectopic expression ; EV:0000017
    %inferred from gene mutation ; EV:0000015
     %inferred from gain-of-function mutant phenotype ; EV:0000042
     %inferred from loss-of-function mutant phenotype ; EV:0000016
    %inferred from RNAi experiment ; EV:0000019
   %inferred from nucleic acid hybridization ; EV:0000026 % inferred from sequence or structural similarity ; EV:0000041
   %inferred from physical interaction ; EV:0000021 ; synonym:IPI
    %inferred from co-purification ; EV:0000022
    %inferred from ligand binding ; EV:0000023
     %inferred from 2-hybrid interaction ; EV:0000025
     %inferred from immunological assay ; EV:0000040 % inferred from protein assay ; EV:0000039
     %inferred from protein binding ; EV:0000024 % inferred from protein assay ; EV:0000039
   %inferred from protein assay ; EV:0000039
    %inferred from enzyme assay ; EV:0000005
    %inferred from immunological assay ; EV:0000040 % inferred from ligand binding ; EV:0000023
    %inferred from protein binding ; EV:0000024 % inferred from ligand binding ; EV:0000023
    %inferred from specific protein inhibition ; EV:0000020
   %inferred from reconstitution assay ; EV:0000003
   %inferred from sequence or structural similarity ; EV:0000041 ; synonym:ISS % inferred from in-silico analysis ; EV:0000043
    %inferred from curated BLAST match ; EV:0000030
     %inferred from curated BLAST match to nucleic acid ; EV:0000032
     %inferred from curated BLAST match to protein ; EV:0000031
    %inferred from motif similarity ; EV:0000028
     %inferred from InterPro motif similarity ; EV:0000029
    %inferred from nucleic acid hybridization ; EV:0000026 % inferred from direct assay ; EV:0000002
    %inferred from structural similarity ; EV:0000027


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