Difference between revisions of "Curation Scenarios for new GO Model - GPAD and .ace Representations"
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GO_term "GO:0008406" Annotation_made_with "WBPhenotype:0000690" Inferred_automatically "Phenotype2GO Mappings" | GO_term "GO:0008406" Annotation_made_with "WBPhenotype:0000690" Inferred_automatically "Phenotype2GO Mappings" | ||
| − | ==IEA Annotations - InterPro2GO Pipeline== | + | ==IEA Annotations - InterPro2GO Pipeline (We would take this from WB mapping - but there are some differences?)== |
OLD .ACE FILE: | OLD .ACE FILE: | ||
| Line 434: | Line 434: | ||
CURRENT GO FILE: | 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 | ||
=For Reference= | =For Reference= | ||
Revision as of 21:52, 14 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? Also, specific isoform issue.)
- 1.14 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?)
- 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 some of these are likely to be IGI, rather than IMP annotations and also the 21uRNA annotations that come along with the mapping)
- 1.18 IEA Annotations - InterPro2GO Pipeline (We would take this from WB mapping - but there are some differences?)
- 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? 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 "RO:0002327" Assigned_by "Gene Ontology Consortium" 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" //Specific isoform is WP:CE05897. Would be great to automatically map. GO_term "GO:0005515" Annotation_made_with "WBGene00003150" Date_last_updated "2013-07-24" //Specific isoform is WP:CE05897. Would be great to automatically map.
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 "RO:0002327" Assigned_by "Gene Ontology Consortium" GO_term "GO:0005109" GO_code "ECO:0000318" Accession_evidence "Gene Ontology Consortium" "GO_REF:0000033" GO_term "GO:0005109" GO_code "ECO:0000318" Annotation_made_with "PANTHER:PTN000246517" GO_term "GO:0005109" GO_code "ECO:0000318" Date_last_updated "2013-03-29" 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" Assigned_by "Gene Ontology Consortium" 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
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" Assigned_by "Gene Ontology Consortium" GO_term "GO:0008406" GO_code "ECO:0000256" Paper_evidence "WBPaper00003386" GO_term "GO:0008406" GO_code "ECO:0000256" Date_last_updated "2013-08-13" GO_term "GO:0008406" GO_code "ECO:0000256" Inferred_automatically "Phenotype2GO Mappings" GO_term "GO:0008406" Annotation_made_with "WBVar00088333" Paper_evidence "WBPaper00003386" GO_term "GO:0008406" Annotation_made_with "WBVar00088333" Date_last_updated "2013-08-13" GO_term "GO:0008406" Annotation_made_with "WBVar00088333" Inferred_automatically "Phenotype2GO Mappings" GO_term "GO:0008406" Annotation_made_with "WBVar00088337" Paper_evidence "WBPaper00003386" GO_term "GO:0008406" Annotation_made_with "WBVar00088337" Date_last_updated "2013-08-13" GO_term "GO:0008406" Annotation_made_with "WBVar00088337" Inferred_automatically "Phenotype2GO Mappings" GO_term "GO:0008406" Annotation_made_with "WBVar00088347" Paper_evidence "WBPaper00003386" GO_term "GO:0008406" Annotation_made_with "WBVar00088347" Date_last_updated "2013-08-13" GO_term "GO:0008406" Annotation_made_with "WBVar00088347" Inferred_automatically "Phenotype2GO Mappings" 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" Inferred_automatically "Phenotype2GO Mappings"
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: 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 some of these are likely to be IGI, rather than IMP annotations and also the 21uRNA annotations that come along with the 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" Assigned_by "Gene Ontology Consortium" GO_term "GO:0008406" GO_code "ECO:0000256" Paper_evidence "WBPaper00003386" GO_term "GO:0008406" GO_code "ECO:0000256" Date_last_updated "2013-08-13" GO_term "GO:0008406" GO_code "ECO:0000256" Inferred_automatically "Phenotype2GO Mappings" GO_term "GO:0008406" Annotation_made_with "WBVar00088333" Paper_evidence "WBPaper00003386" GO_term "GO:0008406" Annotation_made_with "WBVar00088333" Date_last_updated "2013-08-13" GO_term "GO:0008406" Annotation_made_with "WBVar00088333" Inferred_automatically "Phenotype2GO Mappings" GO_term "GO:0008406" Annotation_made_with "WBVar00088337" Paper_evidence "WBPaper00003386" GO_term "GO:0008406" Annotation_made_with "WBVar00088337" Date_last_updated "2013-08-13" GO_term "GO:0008406" Annotation_made_with "WBVar00088337" Inferred_automatically "Phenotype2GO Mappings" GO_term "GO:0008406" Annotation_made_with "WBVar00088347" Paper_evidence "WBPaper00003386" GO_term "GO:0008406" Annotation_made_with "WBVar00088347" Date_last_updated "2013-08-13" GO_term "GO:0008406" Annotation_made_with "WBVar00088347" Inferred_automatically "Phenotype2GO Mappings" 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" Inferred_automatically "Phenotype2GO Mappings"
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
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
