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

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Different Types of GO Annotations in GPAD File from UniProtKB

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 "RO:0002331"	Assigned_by "Gene Ontology Consortium"
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 "RO:0002331"  Assigned_by "Gene Ontology Consortium"
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  "RO:0000050"  Assigned_by "Gene Ontology Consortium"
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 "RO:0000050" "WBbt:0006804"  Paper_evidence "WBPaper00038444"
GO_term     "GO:0005783"  Annotation_extension "RO:0000050" "WBbt:0006804"  Curator_confirmed "WBPerson1843"
GO_term     "GO:0005783"  Annotation_extension "RO:0000050" "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 "RO:0002327"	Assigned_by "Gene Ontology Consortium"
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_update "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 and GO_REF

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 "RO:0002327" Assigned_by "Gene Ontology Consortium"
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"
GO_term	"GO:0003674"	GO_code "ECO:0000307" Accession_evidence "Gene Ontology Consortium" "GO_REF:0000015"

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:6526111  20130619  WormBase	go_evidence=IMP|id=2113495147|curator_name=Kimberly Van Auken

NEW .ACE FILE: 

Gene : "WBGene00003822"
GO_term     "GO:0050829" Relation "RO:0002331"  Assigned_by "Gene Ontology Consortium"
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


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

WormBase - manual annotation, multiple annotations from a single paper

WormBase - manual annotation, use of qualifier

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

UniProtKB - manual annotation, no extra information

WormBase and UniProtKB - exact same manual annotation

IntAct - manual protein binding annotation (Question: How many of these annotations have a more granular annotation from WB?)

PAINT - annotation from phylogenetic inference

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

Phenotype2GO Pipeline - Variation Phenotype2GO

Phenotype2GO Pipeline - RNAi Phenotype2GO (Notes: remove secondary targets, remove non-WT background as these are likely to be IGI, rather than IMP annotations?)

For Reference

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