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

From WormBaseWiki
Jump to navigationJump to search

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

WormBase - manual annotation, use of ND evidence code and GO_REF

WormBase - manual annotation, including 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

Retrieved from "https://wiki.wormbase.org/index.php?title=Curation_Scenarios_for_new_GO_Model_-_GPAD_and_.ace_Representations&oldid=19601"