[MOBY-dev] attn. especially Heiko
Mark Wilkinson
markw at illuminae.com
Mon May 31 19:12:49 UTC 2004
Heiko,
this might have consequences for the new Xref block...
M
-----Forwarded Message-----
> From: Michael Ashburner (Genetics) <ma11 at gen.cam.ac.uk>
> To: ma11 at gen.cam.ac.uk, midori at ebi.ac.uk
> Cc: gofriends at genome.stanford.edu, ref26 at gen.cam.ac.uk
> Subject: [GO] Re: Draft evidence code ontology
> Date: Mon, 31 May 2004 14:11:32 +0100
>
> 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
>
> ______________________________________________________________________
> 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
>
>
> ______________________________________________________________________
> !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
--
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre
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