Curation Scenarios for new GO Model - GPAD and .ace Representations

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Revision as of 20:06, 15 August 2013 by Vanaukenk (talk | contribs) (/* Phenotype2GO Pipeline - RNAi Phenotype2GO (Notes: Need to decide how best to populate Assigned_by. Also, can we have both a Paper reference and a GO_REF that describes the methodology for Phenotype2GO Mappings? In the future, remove results from)
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Contents

Different Types of GO Annotations

GO Annotation Model

WormBase - manual annotation, no extra information

OLD .ACE FILE:

Gene : "WBGene00001052"
GO_term "GO:0007191"    "IDA"   Paper_evidence  "WBPaper00006389"
GO_term "GO:0007191"    "IDA"   Curator_confirmed   "WBPerson1843"

CURRENT GO FILE:

UniProtKB  Q86ME3  involved_in  GO:0007191  PMID:14739932  ECO:0000314  20070522  WormBase  go_evidence=IDA|id=2113475183|curator_name=Kimberly Van Auken			

NEW .ACE FILE:

Gene : "WBGene00001052"
GO_term	"GO:0007191"	Relation "involved_in"  Paper_evidence "WBPaper00006389"
GO_term	"GO:0007191"	Relation "involved_in"	Assigned_by "Gene Ontology Consortium"
GO_term	"GO:0007191"	Relation "involved_in"  Date_last_updated "2007-05-22"
GO_term	"GO:0007191"	GO_code "ECO:0000314"	Paper_evidence "WBPaper00006389"
GO_term	"GO:0007191"	GO_code "ECO:0000314"	Curator_confirmed "WBPerson1843"
GO_term	"GO:0007191"	GO_code "ECO:0000314"   Date_last_updated "2007-05-22"

WormBase - manual annotation, entry in With/From column

OLD .ACE FILE:

Gene : "WBGene00000912"
GO_term "GO:0040024"   "IGI"  Paper_evidence "WBPaper00004702"
GO_term "GO:0040024"   "IGI"  Curator_confirmed "WBPerson1843"

CURRENT GO FILE:

UniProtKB  O16850  involved_in  GO:0040024  PMID:11381260  ECO:0000316  WB:WBGene00000898  20060203  WormBase  go_evidence=IGI|id=2113469094|curator_name=Kimberly Van Auken

NEW .ACE FILE:

Gene : "WBGene00000912"
GO_term     "GO:0040024"  Relation "involved_in" Paper_evidence "WBPaper00004702" 
GO_term     "GO:0040024"  Relation "involved_in" Assigned_by "Gene Ontology Consortium"
GO_term     "GO:0040024"  Relation "involved_in" Date_last_updated "2006-02-03"
GO_term     "GO:0040024"  GO_code "ECO:0000316"  Paper_evidence "WBPaper00004702"
GO_term     "GO:0040024"  GO_code "ECO:0000316"  Curator_confirmed "WBPerson1843"
GO_term     "GO:0040024"  GO_code "ECO:0000316"  Date_last_updated "2006-02-03"
GO_term     "GO:0040024"  Annotation_made_with  "WBGene00000898"  Paper_evidence "WBPaper00004702"
GO_term     "GO:0040024"  Annotation_made_with  "WBGene00000898"  Curator_confirmed "WBPerson1843"
GO_term     "GO:0040024"  Annotation_made_with  "WBGene00000898"  Date_last_updated "2006-02-03"

WormBase - manual annotation, entry in Annotation Extension column

OLD .ACE FILE:

Gene : "WBGene00020999"
GO_term     "GO:0005783" "IDA" Paper_evidence "WBPaper00038444"
GO_term     "GO:0005783" "IDA" Curator_confirmed "WBPerson1843"

CURRENT GO FILE:

UniProtKB  O16999  part_of  GO:0005783  PMID:21611156  ECO:0000314  20120727  WormBase  part_of(WBbt:0006804)  go_evidence=IDA|id=2113469099|curator_name=Kimberly Van Auken

NEW .ACE FILE:

Gene : "WBGene00020999"
GO_term     "GO:0005783"  Relation  "part_of" Paper_evidence "WBPaper00038444" 
GO_term     "GO:0005783"  Relation  "part_of" Assigned_by "Gene Ontology Consortium"
GO_term     "GO:0005783"  Relation  "part_of" Date_last_updated "2012-07-27" 
GO_term     "GO:0005783"  GO_code "ECO:0000314" Paper_evidence "WBPaper00038444"
GO_term     "GO:0005783"  GO_code "ECO:0000314" Curator_confirmed "WBPerson1843"
GO_term     "GO:0005783"  GO_code "ECO:0000314" Date_last_updated "2012-07-27"
GO_term     "GO:0005783"  Annotation_extension "part_of" "WBbt:0006804"  Paper_evidence "WBPaper00038444"
GO_term     "GO:0005783"  Annotation_extension "part_of" "WBbt:0006804"  Curator_confirmed "WBPerson1843"
GO_term     "GO:0005783"  Annotation_extension "part_of" "WBbt:0006804"  Date_last_updated "2012-07-27"

WormBase - manual annotation, isoform-specific annotation (Question: Should we map specific isoforms in UniProt to WP:CE ids?)

OLD .ACE FILE

Gene : "WBGene00006604"
GO_term     "GO:0043565" "IDA" Paper_evidence "WBPape00001790"
GO_term     "GO:0043565" "IDA" Curator_confirmed "WBPerson1843"

CURRENT GO FILE:

UniProtKB  P34708-1  enables  GO:0043565  PMID:8367286  ECO:0000314  20130424  WormBase go_evidence=IDA|id=2113490855|curator_name=Kimberly Van Auken

NEW .ACE FILE

Gene : "WBGene00006604"
GO_term     "GO:0043565"     Relation "enables"    Paper_evidence "WBPaper00001790"
GO_term     "GO:0043565"     Relation "enables"    Assigned_by "Gene Ontology Consortium"
GO_term     "GO:0043565"     Relation "enables"    Date_last_updated "2013-04-24"
GO_term     "GO:0043565"     GO_code "ECO:0000314" Paper_evidence "WBPaper00001790"
GO_term     "GO:0043565"     GO_code "ECO:0000314" Curator_confirmed "WBPerson1843"
GO_term     "GO:0043565"     GO_code "ECO:0000314" Date_last_updated "2013-04-24"
GO_term     "GO:0043565"     Annotation_isoform "UniProtKB" "UniProtAcc" "P34708-1" Paper_evidence "WBPaper00001790"
GO_term     "GO:0043565"     Annotation_isoform "UniProtKB" "UniProtAcc" "P34708-1" Curator_confirmed "WBPerson1843" 
GO_term     "GO:0043565"     Annotation_isoform "UniProtKB" "UniProtAcc" "P34708-1" Date_last_updated "2013-04-24"

WormBase - manual annotation, use of ND evidence code which requires use of a GO_REF for evidence

OLD .ACE FILE

 Gene : "WBGene00003561"
 GO_term     "GO:0003674" "ND" Curator_confirmed "WBPerson1843"

CURRENT GO FILE:

UniProtKB  Q19127  enables  GO:0003674  GO_REF:0000015  ECO:0000307  20041019  WormBase go_evidence=ND|id=2113472633|curator_name=Kimberly Van Auken

NEW .ACE FILE

Gene : "WBGene00003561"
GO_term	"GO:0003674"	Relation "enables" Accession_evidence "Gene Ontology Consortium" "GO_REF:0000015" 
GO_term	"GO:0003674"	Relation "enables" Assigned_by "Gene Ontology Consortium"
GO_term	"GO:0003674"	Relation "enables" Date_last_updated "2004-10-19"
GO_term	"GO:0003674"	GO_code "ECO:0000307" Accession_evidence "Gene Ontology Consortium" "GO_REF:0000015"
GO_term	"GO:0003674"	GO_code "ECO:0000307" Curator_confirmed "WBPerson1843"
GO_term	"GO:0003674"	GO_code "ECO:0000307" Date_last_updated "2004-10-19"

WormBase - manual annotation, including interacting taxon

OLD .ACE FILE

Gene : "WBGene00003822"
GO_term     "GO:0050829"  "IMP" Paper_evidence "WBPaper00005370"
GO_term     "GO:0050829"  "IMP" Curator_confirmed "WBPerson1843"

CURRENT GO FILE:

UniProtKB  Q21029  involved_in  GO:0050829  PMID:12142542  ECO:0000315  taxon:652611  20130619  WormBase	go_evidence=IMP|id=2113495147|curator_name=Kimberly Van Auken

NEW .ACE FILE:

Gene : "WBGene00003822"
GO_term     "GO:0050829" Relation "involved_in" Paper_evidence "WBPaper00005370"
GO_term     "GO:0050829" Relation "involved_in" Assigned_by "Gene Ontology Consortium"
GO_term     "GO:0050829" Relation "involved_in" Date_last_updated "2013-06-19"
GO_term     "GO:0050829" GO_code "ECO:0000315" Paper_evidence "WBPaper00005370"
GO_term     "GO:0050829" GO_code "ECO:0000315" Curator_confirmed "WBPerson1843"
GO_term     "GO:0050829" GO_code "ECO:0000315" Date_last_updated "2013-06-19"
GO_term     "GO:0050829" Interacting_taxon "652611" Paper_evidence "WBPaper00005370"
GO_term     "GO:0050829" Interacting_taxon "652611" Curator_confirmed "WBPerson1843" 
GO_term     "GO:0050829" Interacting_taxon "652611" Date_last_updated "2013-06-19"

WormBase - manual annotation, same GO term and evidence code but different papers

OLD .ACE FILE:

Gene : "WBGene00003183"
GO_term "GO:0005819" "IDA" Paper_evidence "WBPaper00001977"
GO_term "GO:0005819" "IDA" Curator_confirmed "WBPerson1843"
GO_term "GO:0005819" "IDA" Paper_evidence "WBPaper00005914"
GO_term "GO:0005819" "IDA" Curator_confirmed "WBPerson1843"

CURRENT GO FILE:

UniProtKB  P34808  part_of  GO:0005819  PMID:12781129  ECO:0000314  20050708  WormBase  go_evidence=IDA|id=2113470647|curator_name=Kimberly Van Auken
UniProtKB  P34808  part_of  GO:0005819  PMID:8027178  ECO:0000314  20050708  WormBase		go_evidence=IDA|id=2113470646|curator_name=Kimberly Van Auken

NEW .ACE FILE:

Gene : "WBGene00003183"
GO_term "GO:0005819" Relation "part_of" Paper_evidence "WBPaper00001977"
GO_term "GO:0005819" Relation "part_of" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0005819" Relation "part_of" Date_last_updated "2005-07-08"
GO_term "GO:0005819" GO_code "ECO:0000314" Paper_evidence "WBPaper00001977"
GO_term "GO:0005819" GO_code "ECO:0000314" Curator_confirmed "WBPerson1843"
GO_term "GO:0005819" GO_code "ECO:0000314" Date_last_updated "2005-07-08"
GO_term "GO:0005819" Relation "part_of" Paper_evidence "WBPaper00005914"
GO_term "GO:0005819" Relation "part_of" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0005819" Relation "part_of" Date_last_updated "2005-07-08"
GO_term "GO:0005819" GO_code "ECO:0000314" Paper_evidence "WBPaper00005914"
GO_term "GO:0005819" GO_code "ECO:0000314" Curator_confirmed "WBPerson1843"
GO_term "GO:0005819" GO_code "ECO:0000314" Date_last_updated "2005-07-08"

WormBase - manual annotation, multiple annotations from a single paper (also includes an entry in the With/From column)

OLD .ACE FILE:

Gene : "WBGene00003183"
GO_term "GO:0007143" "IMP" Paper_evidence "WBPaper00001977"
GO_term "GO:0007143" "IMP" Curator_confirmed "WBPerson1843"
GO_term "GO:0000922" "IDA" Paper_evidence "WBPaper00001977"
GO_term "GO:0000922" "IDA" Curator_confirmed "WBPerson1843"

CURRENT GO FILE:

UniProtKB  P34808  involved_in  GO:0007143  PMID:8027178  ECO:0000315	WB:WBVar00054422  20060501  WormBase  go_evidence=IMP|id=2113470648|curator_name=Kimberly Van Auken
UniProtKB  P34808  part_of  GO:0000922  PMID:8027178  ECO:0000314  20050707  WormBase  go_evidence=IDA|id=2113470644|curator_name=Kimberly Van Auken

NEW .ACE FILE:

Gene : "WBGene00003183"
GO_term "GO:0007143" Relation  "involved_in" Paper_evidence "WBPaper00001977"
GO_term "GO:0007143" Relation  "involved_in" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0007143" Relation  "involved_in" Date_last_updated "2006-05-01"
GO_term "GO:0007143" GO_code "ECO:0000315" Paper_evidence "WBPaper00001977"
GO_term "GO:0007143" GO_code "ECO:0000315" Curator_confirmed "WBPerson1843"
GO_term "GO:0007143" GO_code "ECO:0000315" Date_last_updated "2006-05-01"
GO_term "GO:0007143" Annotation_made_with  "WBVar00054422"  Paper_evidence "WBPaper00001977"
GO_term "GO:0007143" Annotation_made_with  "WBVar00054422"  Curator_confirmed "WBPerson1843"
GO_term "GO:0007143" Annotation_made_with  "WBVar00054422"  Date_last_updated "2006-05-01" 
GO_term "GO:0000922" Relation  "part_of" Paper_evidence "WBPaper00001977"
GO_term "GO:0000922" Relation  "part_of" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0000922" Relation  "part_of" Date_last_updated "2005-07-07"
GO_term "GO:0000922" GO_code "ECO:0000314" Paper_evidence "WBPaper00001977"
GO_term "GO:0000922" GO_code "ECO:0000314" Curator_confirmed "WBPerson1843"
GO_term "GO:0000922" GO_code "ECO:0000314" Date_last_updated "2005-07-07"

WormBase - manual annotation, use of qualifier

OLD .ACE FILE:

Gene : "WBGene00003183"
GO_term "GO:0000785" "IDA" Paper_evidence "WBPaper00001977"
GO_term "GO:0000785" "IDA" Curator_confirmed "WBPerson1843"

CURRENT GO FILE:

UniProtKB  P34808  colocalizes_with  GO:0000785  PMID:8027178  ECO:0000314  20050707  WormBase  go_evidence=IDA|id=2113470643|curator_name=Kimberly Van Auken

NEW .ACE FILE:

Gene : "WBGene00003183"
GO_term "GO:0000785" Relation "part_of" Paper_evidence "WBPaper00001977"
GO_term "GO:0000785" Relation "part_of" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0000785" Relation "part_of" Date_last_updated "2005-07-07"
GO_term "GO:0000785" GO_code "ECO:0000314" Paper_evidence "WBPaper00001977"
GO_term "GO:0000785" GO_code "ECO:0000314" Curator_confirmed "WBPerson1843"
GO_term "GO:0000785" GO_code "ECO:0000314" Date_last_updated "2005-07-07"
GO_term "GO:0000785" Annotation_qualifier "colocalizes_with" Paper_evidence "WBPaper00001977"
GO_term "GO:0000785" Annotation_qualifier "colocalizes_with" Curator_confirmed "WBPerson1843"
GO_term "GO:0000785" Annotation_qualifier "colocalizes_with" Date_last_update "2005-07-07"

WormBase - manual annotation, multiple additional columns (e.g., With/From and Annotation Extension)

OLD .ACE FILE:

Gene : "WBGene00006805"
GO_term "GO:0035022"  "IC" Paper_evidence "WBPaper00005495"
GO_term "GO:0035022"  "IC" Curator_confirmed "WBPerson1843"


CURRENT GO FILE:

UniProtKB  Q7JNG4  involved_in  GO:0035022  PMID:12297102  ECO:0000305  GO:0030676  20120810  WormBase  has_regulation_target(WB:WBGene00000424)|has_regulation_target(WB:WBGene00003239)  go_evidence=IC|id=2113474833|curator_name=Kimberly Van Auken


NEW .ACE FILE

Gene : "WBGene00006805"
GO_term  "GO:0035022"	Relation "involved_in" Paper_evidence "WBPaper00005495"
GO_term  "GO:0035022"	Relation "involved_in" Assigned_by "Gene Ontology Consortium"
GO_term  "GO:0035022"	Relation "involved_in" Date_last_updated "2012-08-10"
GO_code  "GO:0035022"	GO_code "ECO:0000305" Paper_evidence "WBPaper00005495"
GO_term  "GO:0035022"	GO_code "ECO:0000305" Curator_confirmed "WBPerson1843"
GO_term  "GO:0035022"	GO_code "ECO:0000305" Date_last_updated "2012-08-10"
GO_term  "GO:0035022"	Annotation_made_with "GO:0030676" Paper_evidence "WBPaper0005495"
GO_term  "GO:0035022"	Annotation_made_with "GO:0036076" Curator_confirmed "WBPerson1843"
GO_term  "GO:0035022"	Annotation_made_with "GO:0036076" Date_last_updated "2012-08-10
GO_term  "GO:0035022"	Annotation_extension "has_regulation_target" "WBGene00000424"  Paper_evidence "WBPaper00005495"  
GO_term  "GO:0035022"	Annotation_extension "has_regulation_target" "WBGene00000424"  Curator_confirmed "WBPerson1843"  
GO_term  "GO:0035022"	Annotation_extension "has_regulation_target" "WBGene00000424"  Date_last_updated  "2012-08-10"  
GO_term  "GO:0035022"	Annotation_extension "has_regulation_target" "WBGene00003239"  Paper_evidence "WBPaper00005495" 
GO_term  "GO:0035022"	Annotation_extension "has_regulation_target" "WBGene00003239"  Curator_confirmed "WBPerson1843" 
GO_term  "GO:0035022"	Annotation_extension "has_regulation_target" "WBGene00003239"  Date_last_updated  "2012-08-10"

UniProtKB - manual annotation, no extra information

OLD .ACE FILE:

n/a

CURRENT GO FILE:

UniProtKB  P34374  enables  GO:0005245  PMID:16838374  ECO:0000314  20110523  UniProt  go_evidence=IDA

NEW .ACE FILE:

Gene : "WBGene00006772"
GO_term "GO:0005245" Relation "enables" Paper_evidence "WBPaper00027747"
GO_term "GO:0005245" Relation "enables" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0005245" Relation "enables" Date_last_updated  "2011-05-23"
GO_term "GO:0005245" GO_code "ECO:0000314" Paper_evidence "WBPaper00027747"
GO_term "GO:0005245" GO_code "ECO:0000314" Assigned_by "UniProt"
GO_term "GO:0005245" GO_code "ECO:0000314" Date_last_updated  "2011-05-23"

WormBase and UniProtKB - exact same manual annotation

OLD .ACE FILE:

Gene : "WBGene00002998"
GO_term "GO:0070176" "IDA" Paper_evidence "WBPaper00028753"
GO_term "GO:0070176" "IDA" Curator_confirmed "WBPerson1843"

CURRENT GO FILE:

UniProtKB  P30630  part_of  GO:0070176  PMID:17075059  ECO:0000314  20081215  UniProt  go_evidence=IDA
UniProtKB  P30630  part_of  GO:0070176	 PMID:17075059	ECO:0000314  20110614  WormBase  go_evidence=IDA|id=2113470216|curator_name=Kimberly Van Auken

NEW .ACE FILE:

Gene : "WBGene00002998"
GO_term "GO:0070176" Relation "part_of" Paper_evidence "WBPaper00028753"  
GO_term "GO:0070176" Relation "part_of" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0070176" Relation "part_of" Date_last_updated "2011-06-14"
GO_term "GO:0070176" GO_code "ECO:0000314"  Paper_evidence "WBPaper00028753" 
GO_term "GO:0070176" GO_code "ECO:0000314"  Assigned_by "UniProt"
GO_term "GO:0070176" GO_code "ECO:0000314"  Date_last_updated "2008-12-15"
GO_term "GO:0070176" GO_code "ECO:0000314"  Paper_evidence "WBPaper00028753" //Do we need to repeat this?
GO_term "GO:0070176" GO_code "ECO:0000314"  Curator_confirmed "WBPerson1843"
GO_term "GO:0070176" GO_code "ECO:0000314"  Date_last_updated "2011-06-14"

IntAct - manual protein binding annotation (Question: How many of these annotations have a more granular annotation from WB? Also, specific isoform issue.)

OLD .ACE FILE:

n/a


CURRENT GO FILE:

UniProtKB P34808 enables GO:0005515 PMID:19879842 ECO:0000021 UniProtKB:Q9XTF3-2 20130724 IntAct  go_evidence=IPI


NEW .ACE FILE:

Gene : "WBGene00003183"
GO_term "GO:0005515" Relation "enables" Paper_evidence "WBPaper00035427"
GO_term "GO:0005515" Relation "enables" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0005515" Relation "enables" Date_last_updated "2013-07-24"
GO_term "GO:0005515" GO_code "ECO:0000021"  Paper_evidence "WBPaper00035427"
GO_term "GO:0005515" GO_code "ECO:0000021"  Assigned_by "IntAct"
GO_term "GO:0005515" GO_code "ECO:0000021"  Date_last_updated "2013-07-24"
GO_term "GO:0005515" Annotation_made_with "WBGene00003150"  Paper_evidence "WBPaper00035427" //Specific isoform is WP:CE05897.  Would be great to automatically map.
GO_term "GO:0005515" Annotation_made_with "WBGene00003150"  Assigned_by "IntAct" 
GO_term "GO:0005515" Annotation_made_with "WBGene00003150"  Date_last_updated "2013-07-24"

PAINT - annotation from phylogenetic inference (These are based on PANTHER families - do we have these in WB and if so, what type of object are they?)

OLD .ACE FILE:

n/a

CURRENT GO FILE:

UniProtKB  P34888  enables  GO:0005109  GO_REF:0000033  ECO:0000318  PANTHER:PTN000246517  20130329  RefGenome  go_evidence=IBA

NEW .ACE FILE:

Gene : "WBGene00000857"
GO_term "GO:0005109"  Relation "enables" Accession_evidence "Gene Ontology Consortium" "GO_REF:0000033"
GO_term "GO:0005109"  Relation "enables" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0005109"  Relation "enables" Date_last_updated "2013-03-29"
GO_term "GO:0005109"  GO_code "ECO:0000318"  Accession_evidence "Gene Ontology Consortium" "GO_REF:0000033"
GO_term "GO:0005109"  GO_code "ECO:0000318"  Assigned_by "Gene Ontology Consortium"
GO_term "GO:0005109"  GO_code "ECO:0000318"  Date_last_updated "2013-03-29"
GO_term "GO:0005109"  Annotation_made_with "PANTHER:PTN000246517" Accession_evidence "Gene Ontology Consortium" "GO_REF:0000033"
GO_term "GO:0005109"  Annotation_made_with "PANTHER:PTN000246517" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0005109"  Annotation_made_with "PANTHER:PTN000246517" Date_last_updated "2013-03-29"
GO_term "GO:0005109"  Gene_product_properties "RefGenome" Accession_evidence "Gene Ontology Consortium" "GO_REF:0000033"
GO_term "GO:0005109"  Gene_product_properties "RefGenome" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0005109"  Gene_product_properties "RefGenome" Date_last_updated "2013-03-29"

Function-Process Links - annotations inferred by GOC based on inter-ontology relationships

OLD .ACE FILE:

Gene : "WBGene00003963"
GO_term "GO:0006457" "IDA" Paper_evidence "WBPaper00005704"
GO_term "GO:0006457" "IDA" Curator_confirmed "WBPerson1843"

CURRENT GO FILE:

UniProtKB  A3RMS2  involved_in  GO:0006457  PMID:12424233  ECO:0000314  20130720  GOC  go_evidence=IDA

NEW .ACE FILE:

Gene : "WBGene00003963"
GO_term "GO:0006457" Relation "involved_in" Paper_evidence "WBPaper00005704"
GO_term "GO:0006457" Relation "involved_in" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0006457" Relation "involved_in" Date_last_updated "2013-07-20"
GO_term "GO:0006457" Evidence_code "ECO:0000314" Paper_evidence "WBPaper00005704"
GO_term "GO:0006457" Evidence_code "ECO:0000314" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0006457" Evidence_code "ECO:0000314" Date_last_updated "2013-07-20"

Phenotype2GO Pipeline - Variation Phenotype2GO (Need to decide how best to populate Assigned_by. Also, can we have both a Paper reference and a GO_REF that describes the methodology for Phenotype2GO Mappings? To be consistent with RNAi-based Phenotype2GO annotations we should include the WBPhenotype, as well.)

OLD .ACE FILE:

Gene : "WBGene00001182"
GO_term "GO:0008406" "IMP" Paper_evidence "WBPaper00003386"
GO_term "GO:0008406" "IMP" Variation_evidence "WBVar00088333"
GO_term "GO:0008406" "IMP" Paper_evidence "WBPaper00003386"
GO_term "GO:0008406" "IMP" Variation_evidence "WBVar00088337"
GO_term "GO:0008406" "IMP" Paper_evidence "WBPaper00003386"
GO_term "GO:0008406" "IMP" Variation_evidence "WBVar00088347"

CURRENT GO FILE:

n/a

NEW .ACE FILE:

Gene : "WBGene00001182"
GO_term "GO:0008406" Relation "involved_in" Paper_evidence "WBPaper00003386"
GO_term "GO:0008406" Relation "involved_in" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0008406" Relation "involved_in" Date_last_updated "2013-08-13"
GO_term "GO:0008406" GO_code "ECO:0000256" Paper_evidence "WBPaper00003386"
GO_term "GO:0008406" GO_code "ECO:0000256" Assigned_by "WormBase"
GO_term "GO:0008406" GO_code "ECO:0000256" Date_last_updated "2013-08-13" 
GO_term "GO:0008406" Annotation_made_with "WBVar00088333" Paper_evidence "WBPaper00003386" 
GO_term "GO:0008406" Annotation_made_with "WBVar00088333" Assigned_by "WormBase"
GO_term "GO:0008406" Annotation_made_with "WBVar00088333" Date_last_updated "2013-08-13"
GO_term "GO:0008406" Annotation_made_with "WBVar00088337" Paper_evidence "WBPaper00003386" 
GO_term "GO:0008406" Annotation_made_with "WBVar00088337" Assigned_by "WormBase"
GO_term "GO:0008406" Annotation_made_with "WBVar00088337" Date_last_updated "2013-08-13" 
GO_term "GO:0008406" Annotation_made_with "WBVar00088347" Paper_evidence "WBPaper00003386"
GO_term "GO:0008406" Annotation_made_with "WBVar00088347" Assigned_by "WormBase"
GO_term "GO:0008406" Annotation_made_with "WBVar00088347" Date_last_updated "2013-08-13" 
GO_term "GO:0008406" Annotation_made_with "WBPhenotype:0000690" Paper_evidence "WBPaper00003386" 
GO_term "GO:0008406" Annotation_made_with "WBPhenotype:0000690" Date_last_updated "2013-08-13"  
GO_term "GO:0008406" Annotation_made_with "WBPhenotype:0000690" Assigned_by "WormBase"


NEW GO FILE:

UniProtKB  Q23045  involved_in  GO:0008406  PMID:9834196  ECO:0000256	WB:WBVar00088333|WB:WBVar00088337|WB:WBVar00088347|WBPhenotype:0000690"  20130813  WormBase  go_evidence=IEA|id=tbd|curator_name=Does this need to be filled in?

Phenotype2GO Pipeline - RNAi Phenotype2GO (Notes: Need to decide how best to populate Assigned_by. Also, can we have both a Paper reference and a GO_REF that describes the methodology for Phenotype2GO Mappings? In the future, remove results from secondary targets (or change how we're handling them i.e., use a GO_Ref that explains that these are predictions from WB based upon nucleotide sequence similarity). Also remove annotations from non-WT background as some of these are likely to be IGI. Also, what about the 21uRNA annotations that come along with the sequence mapping?)

OLD .ACE FILE (NOT SURE ABOUT THIS):

Gene : "WBGene00001182"
GO_term "GO:0000003" "IMP" Paper_evidence "WBPaper00003386"
GO_term "GO:0000003" "IMP" Inferred_automatically "(WBPhenotype:0001037|WBRNAi00027490)"
GO_term "GO:0000003" "IMP" Inferred_automatically "sterile progeny (WBPhenotype:0001037|WBRNAi00027490)"

CURRENT GO FILE:

WB	WBGene00001182	egl-13		GO:0040035	WB_REF:WBPaper00006395|PMID:14551910	IMP	WB:WBRNAi00026443|WB:WBPhenotype:0000697	P		T22B7.1	gene	taxon:6239	20130207

NEW .ACE FILE:

Gene : "WBGene00001182"
GO_term "GO:0008406" Relation "involved_in" Paper_evidence "WBPaper00003386"
GO_term "GO:0008406" Relation "involved_in" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0008406" Relation "involved_in" Date_last_updated "2013-08-13"
GO_term "GO:0008406" GO_code "ECO:0000256" Paper_evidence "WBPaper00003386"
GO_term "GO:0008406" GO_code "ECO:0000256" Assigned_by "WormBase"
GO_term "GO:0008406" GO_code "ECO:0000256" Date_last_updated "2013-08-13" 
GO_term "GO:0008406" Annotation_made_with "WBRNAi00026443" Paper_evidence "WBPaper00003386" 
GO_term "GO:0008406" Annotation_made_with "WBRNAi00026443" Assigned_by "WormBase" 
GO_term "GO:0008406" Annotation_made_with "WBRNAi00026443" Date_last_updated "2013-08-13"
GO_term "GO:0008406" Annotation_made_with "WBPhenotype:0000690" Paper_evidence "WBPaper00003386" 
GO_term "GO:0008406" Annotation_made_with "WBPhenotype:0000690" Assigned_by "WormBase"
GO_term "GO:0008406" Annotation_made_with "WBPhenotype:0000690" Date_last_updated "2013-08-13"

IEA Annotations - InterPro2GO Pipeline (We would take this from WB mapping - but there are some differences?)

OLD .ACE FILE:

Gene : "WBGene00006543"
GO_term "GO:0005634" "IEA" Inferred_automatically "INTERPRO:IPR001699"
GO_term "GO:0005634" "IEA" Inferred_automatically "INTERPRO:IPR002070"

CURRENT GO FILE:

UniProtKB  Q19691  part_of  GO:0005634  GO_REF:0000002  ECO:0000256  InterPro:IPR001699|InterPro:IPR002070|InterPro:IPR018186  20130720  InterPro  go_evidence=IEA

NEW .ACE FILE:

Gene : "WBGene00006543"
GO_term "GO:0005634" Relation "part_of" Accession_evidence "Gene Ontology Consortium" "GO_REF:0000002"
GO_term "GO:0005634" Relation "part_of" Assigned_by "Gene Ontology Consortium"
GO_term "GO:0005634" Relation "part_of" Date_last_updated "2013-07-20"
GO_term "GO:0005634" GO_code "ECO:0000256" Accession_evidence "Gene Ontology Consortium" "GO_REF:0000002"
GO_term "GO:0005634" GO_code "ECO:0000256" Assigned_by "WormBase"
GO_term "GO:0005634" GO_code "ECO:0000256" Date_last_updated "2013-07-20"
GO_term "GO:0005634" Annotation_made_with "InterPro:IPR001699" Accession_evidence "Gene Ontology Consortium" "GO_REF:0000002"
GO_term "GO:0005634" Annotation_made_with "InterPro:IPR001699" Assigned_by "WormBase"
GO_term "GO:0005634" Annotation_made_with "InterPro:IPR001699" Date_last_updated "2013-07-20"
GO_term "GO:0005634" Annotation_made_with "InterPro:IPR002070" Accession_evidence "Gene Ontology Consortium" "GO_REF:0000002"
GO_term "GO:0005634" Annotation_made_with "InterPro:IPR002070" Assigned_by "WormBase"
GO_term "GO:0005634" Annotation_made_with "InterPro:IPR002070" Date_last_updated "2013-07-20"

For Reference

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