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

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Different Types of GO Annotations

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:

GO_annotation : "00000001"
Gene "WBGene00001052" 
GO_term "GO:0007191" 
GO_code "IDA"
Annotation_relation "involved_in"
Reference "WBPaper00006389"
Date_last_updated "2007-05-22"

WormBase - manual annotation, IPI when entry in With/From column is a WBGene

OLD .ACE FILE:

Gene : "WBGene00004373"
GO_term "GO:0019904"   "IPI"  Paper_evidence "WBPaper00031193"
GO_term "GO:0019904"   "IPI"  Curator_confirmed "WBPerson1843"

CURRENT GO FILE:

UniProtKB Q9N5B7 enables GO:0019904 PMID:17997305 ECO:0000353 WB:WBGene00007010 20080623 WormBase		go_evidence=IPI|id=2113477100|curator_name=Kimberly Van Auken

NEW .ACE FILE:

GO_annotation : "00000002"
Gene "WBGene00004373"
GO_term "GO:0019904"
GO_code "IPI"
Annotation_relation "enables"
Interacting_entity "WBGene00000898"
Reference "WBPaper00031193"
Date_last_updated "2008-06-23"


WormBase - manual annotation, IPI when entry in With/From column is a UniProtKB protein ID

OLD .ACE FILE:

Gene : "WBGene00001978"
GO_term "GO:0008013"   "IPI"  Paper_evidence "WBPaper00004885"
GO_term "GO:0008013"   "IPI"  Curator_confirmed "WBPerson1843"


CURRENT GO FILE:

UniProtKB A5JYX3 enables GO:0008013 PMID:11560894 ECO:0000353 UniProtKB:O44326 20141208 WormBase		go_evidence=IPI|id=2113463757|curator_name=Kimberly Van Auken

NEW .ACE FILE:

GO_annotation : "00000003"
Gene "WBGene00001978"
GO_term "GO:0008013"
GO_code "IPI"
Annotation_relation "enables"
Interacting_entity "WBGene00001979"
Reference "WBPaper00004885"
Date_last_updated "2014-12-08"


WormBase - manual annotation, IPI when entry in With/From column is multiple WBGene IDs

OLD .ACE FILE:

Gene : "WBGene00002996"
GO_term "GO:0030674" Paper_evidence "WBPaper00003215"
GO_term "GO:0030674" Curator_confirmed "WBPerson1843"


CURRENT GO FILE:

UniProtKB A5PEX5 enables GO:0030674 PMID:9753323 ECO:0000353 WB:WBGene00002991|WB:WBGene00002999 20100609 WormBase go_evidence=IPI|id=2113463776|curator_name=Kimberly Van Auken


NEW .ACE FILE:

GO_annotation "00000004"
Gene "WBGene00002996"
GO_term "GO0030674"
GO_code "IPI"
Annotation_relation "enables"
Interacting_entity "WBGene00002991"
Interacting_entity "WBGene00002999"
Reference "WBPaper00003215"
Date_last_updated "2010-06-09"

WormBase - manual annotation, IPI when entry in With/From column is a WBGene ID and a rat UniProtKB ID not in WB

OLD .ACE FILE:

Gene: "WBGene00006594"
GO_term "GO:0031201" Paper_evidence "WBPaper00028364"
GO_term "GO:0031201" Curator_confirmed "WBPerson1843"

CURRENT GO FILE:

UniProtKB A8WFN4 part_of GO:0031201 PMID:16895441 ECO:0000353 UniProtKB:P60881|WB:WBGene00006798 20070719 WormBase		go_evidence=IPI|id=2113463891|curator_name=Kimberly Van Auken


NEW .ACE FILE:

GO_annotation "00000005"
Gene "WBGene00006594"
GO_term "GO:0031201"
GO_code "IPI"
Annotation_relation "enables"
Interacting_entity "WBGene00006798"
Interacting_entity_nonelegans "UniProtKB:P60881"
Reference "WBPaper00028364"
Date_last_updated "2007-07-19"

WormBase - manual annotation, cross-species complementation assay

OLD .ACE FILE:

Gene : "WBGene00003960"
GO_term "GO:0071585"   "IGI"  Paper_evidence "WBPaper00004738"
GO_term "GO:0071585"   "IGI"  Curator_confirmed "WBPerson1843"


CURRENT GO FILE:

UniProtKB  A5JYS0  involved_in	 GO:0071585  PMID:11313333  ECO:0000316	 SGD:S000002542	 20100312  WormBase		go_evidence=IGI|id=2113463736|curator_name=Kimberly Van Auken


NEW .ACE FILE:

GO_annotation : "WBGO00000003"
Gene_rel "WBGene0003960" "GO"0071585" involved_in "IGI"
Database "SGD" "SGD" "S000002542"
Reference "WBPaper00004738"
Date_last_updated "2010-03-12"


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:

GO_annotation : "WBGO00000004"
Gene_rel "WBGene00020999" "GO:0005783" part_of "IDA"
Anatomy_relation "part_of" "WBbt:0006804"
Reference "WBPaper00038444"
Date_last_updated "2012-07-27"

WormBase - manual annotation, isoform-specific annotation (Need to map specific protein 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

GO_annotation : "WBGO00000005"
Gene_rel "WBGene00006604" "GO:0043565" enables "IDA"
Annotation_isoform "UniProtKB:P34708-1"
Reference "WBPaper00001790"
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

GO_annotation : "WBGO00000006"
Gene_rel "WBGene00003561" "GO:0003674" enables "ND"
GO_reference "Gene Ontology" "GO_REF" "0000015"
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:

GO_annotation : "WBGO00000007"
Gene_rel "WBGene00003822" "GO:0050829" involved_in "IMP"
Interacting_strain "PA14"
Reference "WBPaper00005370"
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:

GO_annotation : "WBGO00000008"
Gene_rel "WBGene00003183" "GO:0005819" part_of "IDA"
Reference "WBPaper00001977"
Date_last_updated "2005-07-08"
GO_annotation : "WBGO00000009"
Gene_rel "WBGene00003183" "GO:0005819" part_of "IDA"
Reference "WBPaper00005914"
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:

GO_annotation : "WBGO00000010"
Gene_rel "WBGene00003183" "GO:0007143" involved_in "IMP"
Variation "WBVar00054422"
Reference "WBPaper00001977"
Date_last_updated "2006-05-01"
GO_annotation : "WBGO00000011"
Gene_rel "WBGene00003183" "GO:0000922" part_of "IDA"
Reference "WBPaper00001977"
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:

GO_annotation : "WBGO00000012"
Gene_rel "WBGene00003183" "GO:0000785" colocalizes_with "IDA"
Reference "WBPaper00001977"
Date_last_updated "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

GO_annotation : "WBGO00000013"
Gene_rel "WBGene00006805" "GO:00035022" involved_in "IC"
Inferred_GO_term "GO:0030676"
Gene_relation "has_regulation_target" "WBGene00000424"
Reference "WBPaper00005495"
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:

GO_annotation : "WBGO00000015"
Gene_rel "WBGene00006772" "GO:00005245" enables "IDA"
Reference "WBPaper00027747"
Contributed_by "UniProt_GOA"
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:

GO_annotation : "WBGO00000016"
Gene_rel "WBGene00002998" "GO:0070176" part_of "IDA"
Reference "WBPaper00028753"
Contributed_by "UniProt_GOA"
Date_last_updated "2008-12-15"
GO_annotation : "WBGO00000017"
Gene_rel "WBGene00002998" "GO:0070176" part_of "IDA"
Reference "WBPaper00028753"
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:

GO_annotation : "WBGO00000018"
Gene_rel "WBGene00003183" "GO:0005515" enables "IPI"
Interacting_protein "UniProtKB:Q94420"
Reference "WBPaper00032484"
Contributed_by "IntAct"
Date_last_updated "2014-12-01"

PAINT - annotation from phylogenetic inference (The supporting evidence in the With/From column is an identifier for a Panther Tree Node (PTN)

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:

GO_annotation : "WBGO00000019"
Gene_rel "WBGene00000857" "GO:0005109" enables "IBA"
Database "Panther" "PTN" "000246517"
GO_reference "Gene Ontology" "GO_REF" "0000033"
Contributed_by "GO_Central"
Date_last_updated "2014-07-30"

Function-Process Links - annotations inferred by GOC based on inter-ontology relationships (would like to see the appropriate GO_REF included, as well, will need to talk to Tony S. (GO_REF:0000032 Inference of Biological Process annotations from inter-ontology links)

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:

GO_annotation : "WBGO00000020"
Gene_rel "WBGene00003963" "GO:0006457" involved_in "IDA"
Reference "WBPaper00005704"
Contributed_by "GOC_Inter-Ontology_Links"
Date_last_updated "2013-07-20"

Phenotype2GO Pipeline - Variation Phenotype2GO (Would like to also have 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"

CURRENT GO FILE:

n/a

NEW .ACE FILE: Evidence code changed to IEA to reflect annotation process correctly.

GO_annotation : "WBGO00000021"
Gene_rel "WBGene00001182" "GO:0008406" involved_in "IEA"
Variation "WBVar00088333"
Phenotype "WBPhenotype:0000690"
Reference "WBPaper00003386"
Date_last_updated "2013-08-13"
GO_annotation : "WBGO00000022"
Gene_rel "WBGene00001182" "GO:0008406" involved_in "IEA"
Variation "WBVar00088337"
Phenotype "WBPhenotype:0000690"
Reference "WBPaper00003386"
Date_last_updated "2013-08-13"

Phenotype2GO Pipeline - RNAi Phenotype2GO (Notes: Would like to 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, how best to handle 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: Evidence code changed to IEA

GO_annotation : "WBGO00000023"
Gene_rel "WBGene00001182" "GO:0000003" involved_in "IEA"
RNAi_result "WBRNAi00027490"
Phenotype "WBPhenotype:0001037"
Reference "WBPaper00003386"
Date_last_updated "2013-08-13"

IEA Annotations - UniProtKB Keyword Mapping

OLD .ACE FILE:

na

CURRENT GO FILE:

UniProtKB	A5JYS3	part_of	GO:0016020	GO_REF:0000038	ECO:0000323	UniProtKB-KW:KW-0472		20141129	UniProt		go_evidence=IEA

NEW .ACE FILE:

Gene : "WBGene00006543"
GO_term "GO:0005634"    GO_code "IEA"   Accession_evidence "Gene Ontology Consortium" "GO_REF:0000002"
GO_term "GO:0005634"    GO_code "IEA"   Date_last_updated "2013-07-20"
GO_term "GO:0005634"    Annotation_relation "part_of"   Accession_evidence "Gene Ontology Consortium" "GO_REF:0000002"
GO_term "GO:0005634"    Annotation_relation "part_of"   Date_last_updated "2013-07-20"
GO_term "GO:0005634"    Database "INTERPRO" "INTERPRO_ID" "IPR001699"   Accession_evidence "Gene Ontology Consortium" "GO_REF:0000002"
GO_term "GO:0005634"    Database "INTERPRO" "INTERPRO_ID" "IPR001699"   Date_last_updated "2013-07-20"
GO_term "GO:0005634"    Database "INTERPRO" "INTERPRO_ID" "IPR002070"   Accession_evidence "Gene Ontology Consortium" "GO_REF:0000002"
GO_term "GO:0005634"    Database "INTERPRO" "INTERPRO_ID" "IPR002070"   Date_last_updated "2013-07-20"

For Reference

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