Difference between revisions of "Curation Scenarios for new GO Model - GPAD and .ace Representations"
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| − | =Different Types of GO Annotations | + | =Different Types of GO Annotations= |
==WormBase - manual annotation, no extra information== | ==WormBase - manual annotation, no extra information== | ||
Revision as of 20:46, 8 August 2013
Contents
- 1 Different Types of GO Annotations
- 1.1 WormBase - manual annotation, no extra information
- 1.2 WormBase - manual annotation, entry in With/From column
- 1.3 WormBase - manual annotation, entry in Annotation Extension column
- 1.4 WormBase - manual annotation, isoform-specific annotation (Question: Should we map specific isoforms in UniProt to WP:CE ids?)
- 1.5 WormBase - manual annotation, use of ND evidence code and GO_REF
- 1.6 WormBase - manual annotation, including interacting taxon
- 1.7 WormBase - manual annotation, same GO term and evidence code but different papers
- 1.8 WormBase - manual annotation, multiple annotations from a single paper (also includes an entry in the With/From column)
- 1.9 WormBase - manual annotation, use of qualifier (Double-check capitalization of Not)
- 1.10 WormBase - manual annotation, multiple additional columns (e.g., With/From and Annotation Extension - need to check about has_regulation_target in RO file. If not there, switch this tag to a text value?)
- 1.11 UniProtKB - manual annotation, no extra information
- 1.12 WormBase and UniProtKB - exact same manual annotation
- 1.13 IntAct - manual protein binding annotation (Question: How many of these annotations have a more granular annotation from WB?)
- 1.14 PAINT - annotation from phylogenetic inference
- 1.15 Function-Process Links - annotations inferred by GOC based on inter-ontology relationships
- 1.16 Phenotype2GO Pipeline - Variation Phenotype2GO
- 1.17 Phenotype2GO Pipeline - RNAi Phenotype2GO (Notes: in the future, remove secondary targets (or change how we're handling them i.e., use a GO_Ref) and also remove non-WT background as these are likely to be IGI, rather than IMP annotations?)
- 2 For Reference
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:
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 "BFO: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 "BFO:0000050" "WBbt:0006804" Paper_evidence "WBPaper00038444" GO_term "GO:0005783" Annotation_extension "BFO:0000050" "WBbt:0006804" Curator_confirmed "WBPerson1843" GO_term "GO:0005783" Annotation_extension "BFO: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:652611 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 "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 "BFO:0000050" Assigned_by "Gene Ontology Consortium" 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" 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 "RO:0002331" Assigned_by "Gene Ontology Consortium" 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 "BFO:0000050" Assigned_by "Gene Ontology Consortium" 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 (Double-check capitalization of Not)
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 "BFO:0000050" Assigned_by "Gene Ontology Consortium" 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_update "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 - need to check about has_regulation_target in RO file. If not there, switch this tag to a text value?)
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 "RO:0002331" Assigned_by "Gene Ontology Consortium" 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 "RO:nnnnnnn" "WBGene00000424" Paper_evidence "WBPaper00005495" //has_regulation_target does not exist in the RO yet GO_term "GO:0035022" Annotation_extension "RO:nnnnnnn" "WBGene00000424" Curator_confirmed "WBPerson1843" //has_regulation_target does not exist in the RO yet GO_term "GO:0035022" Annotation_extension "RO:nnnnnnn" "WBGene00000424" Date_last_updated "2012-08-10" //has_regulation_target does not exist in the RO yet GO_term "GO:0035022" Annotation_extension "RO:nnnnnnn" "WBGene00003239" Paper_evidence "WBPaper00005495" //has_regulation_target does not exist in the RO yet GO_term "GO:0035022" Annotation_extension "RO:nnnnnnn" "WBGene00003239" Curator_confirmed "WBPerson1843" //has_regulation_target does not exist in the RO yet GO_term "GO:0035022" Annotation_extension "RO:nnnnnnn" "WBGene00003239" Date_last_updated "2012-08-10" //has_regulation_target does not exist in the RO yet
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 "RO:0002327" Assigned_by "Gene Ontology Consortium" 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 "BFO:0000050" Assigned_by "Gene Ontology Consortium" 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" 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?)
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: in the future, remove secondary targets (or change how we're handling them i.e., use a GO_Ref) and also remove non-WT background as these are likely to be IGI, rather than IMP annotations?)
For Reference
- http://wiki.geneontology.org/index.php/Final_GPAD_and_GPI_file_format
- http://wiki.geneontology.org/index.php/Evidence_Code_Ontology_%28ECO%29
- http://www.geneontology.org/cgi-bin/references.cgi
- http://obo-relations.googlecode.com/svn/trunk/src/ontology/ro.obo
- http://evidenceontology.googlecode.com/svn/trunk/eco.obo
- ftp://ftp.ebi.ac.uk/pub/contrib/goa/
Back to Gene Ontology
