Difference between revisions of "Curation Scenarios for new GO Model - GPAD and .ace Representations"
(/* Phenotype2GO Pipeline - RNAi Phenotype2GO (Notes: Need to decide how best to populate Assigned_by. Also, can we have both a Paper reference and a GO_REF that describes the methodology for Phenotype2GO Mappings? In the future, remove results from se...) |
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CURRENT GO FILE: | CURRENT GO FILE: | ||
− | UniProtKB Q86ME3 involved_in GO:0007191 PMID:14739932 ECO:0000314 20070522 WormBase | + | 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: | NEW .ACE FILE: | ||
− | + | GO_annotation : "00000001" | |
− | + | Gene "WBGene00001052" | |
− | GO_term "GO:0007191 | + | GO_term "GO:0007191" |
− | + | GO_code "IDA" | |
− | + | Annotation_relation "involved_in" | |
− | + | Reference "WBPaper00006389" | |
− | + | Date_last_updated "2007-05-22" | |
− | ==WormBase - manual annotation, entry in With/From column== | + | ==WormBase - manual annotation, IPI when entry in With/From column is a WBGene== |
OLD .ACE FILE: | OLD .ACE FILE: | ||
− | Gene : " | + | Gene : "WBGene00004373" |
− | GO_term "GO: | + | GO_term "GO:0019904" "IPI" Paper_evidence "WBPaper00031193" |
− | GO_term "GO: | + | GO_term "GO:0019904" "IPI" Curator_confirmed "WBPerson1843" |
CURRENT GO FILE: | CURRENT GO FILE: | ||
− | UniProtKB | + | 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: | NEW .ACE FILE: | ||
− | Gene | + | GO_annotation : "00000002" |
− | GO_term "GO: | + | Gene "WBGene00004373" |
− | GO_term "GO: | + | GO_term "GO:0019904" |
− | GO_term "GO: | + | GO_code "IPI" |
− | GO_term "GO: | + | Annotation_relation "enables" |
− | GO_term "GO: | + | Interacting_entity "WBGene00000898" |
− | GO_term "GO: | + | Reference "WBPaper00031193" |
− | GO_term "GO: | + | Date_last_updated "2008-06-23" |
− | GO_term "GO: | + | |
− | + | ||
+ | ==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== | ==WormBase - manual annotation, entry in Annotation Extension column== | ||
Line 62: | Line 160: | ||
NEW .ACE FILE: | 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)== | ==WormBase - manual annotation, isoform-specific annotation (Need to map specific protein isoforms in UniProt to WP:CE ids)== | ||
Line 87: | Line 180: | ||
NEW .ACE FILE | 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== | ==WormBase - manual annotation, use of ND evidence code which requires use of a GO_REF for evidence== | ||
Line 111: | Line 199: | ||
NEW .ACE FILE | 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== | ==WormBase - manual annotation, including interacting taxon== | ||
Line 133: | Line 218: | ||
NEW .ACE FILE: | 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== | ==WormBase - manual annotation, same GO term and evidence code but different papers== | ||
Line 161: | Line 241: | ||
NEW .ACE FILE: | 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)== | ==WormBase - manual annotation, multiple annotations from a single paper (also includes an entry in the With/From column)== | ||
Line 193: | Line 269: | ||
NEW .ACE FILE: | 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== | ==WormBase - manual annotation, use of qualifier== | ||
Line 224: | Line 294: | ||
NEW .ACE FILE: | 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)== | ==WormBase - manual annotation, multiple additional columns (e.g., With/From and Annotation Extension)== | ||
Line 248: | Line 315: | ||
NEW .ACE FILE | 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== | ==UniProtKB - manual annotation, no extra information== | ||
Line 277: | Line 334: | ||
NEW .ACE FILE: | 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== | ==WormBase and UniProtKB - exact same manual annotation== | ||
Line 298: | Line 353: | ||
UniProtKB P30630 part_of GO:0070176 PMID:17075059 ECO:0000314 20110614 WormBase go_evidence=IDA|id=2113470216|curator_name=Kimberly Van Auken | 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: | + | 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.)== | ==IntAct - manual protein binding annotation (Question: How many of these annotations have a more granular annotation from WB? Also, specific isoform issue.)== | ||
Line 326: | Line 380: | ||
NEW .ACE FILE: | 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 ( | + | ==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: | OLD .ACE FILE: | ||
Line 348: | Line 398: | ||
NEW .ACE FILE: | NEW .ACE FILE: | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | ==Function-Process Links - annotations inferred by GOC based on inter-ontology relationships== | + | 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: | OLD .ACE FILE: | ||
Line 371: | Line 418: | ||
UniProtKB A3RMS2 involved_in GO:0006457 PMID:12424233 ECO:0000314 20130720 GOC go_evidence=IDA | UniProtKB A3RMS2 involved_in GO:0006457 PMID:12424233 ECO:0000314 20130720 GOC go_evidence=IDA | ||
− | NEW .ACE FILE: | + | 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 ( | + | ==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: | OLD .ACE FILE: | ||
Line 390: | Line 435: | ||
GO_term "GO:0008406" "IMP" Paper_evidence "WBPaper00003386" | GO_term "GO:0008406" "IMP" Paper_evidence "WBPaper00003386" | ||
GO_term "GO:0008406" "IMP" Variation_evidence "WBVar00088337" | GO_term "GO:0008406" "IMP" Variation_evidence "WBVar00088337" | ||
− | + | ||
− | |||
− | |||
CURRENT GO FILE: | CURRENT GO FILE: | ||
n/a | n/a | ||
− | NEW .ACE FILE: | + | 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?)== | |
− | |||
− | ==Phenotype2GO Pipeline - RNAi Phenotype2GO (Notes: | ||
OLD .ACE FILE (NOT SURE ABOUT THIS): | OLD .ACE FILE (NOT SURE ABOUT THIS): | ||
Line 429: | Line 465: | ||
GO_term "GO:0000003" "IMP" Inferred_automatically "sterile progeny (WBPhenotype:0001037|WBRNAi00027490)" | GO_term "GO:0000003" "IMP" Inferred_automatically "sterile progeny (WBPhenotype:0001037|WBRNAi00027490)" | ||
− | |||
CURRENT GO FILE: | 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 | 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: | + | 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 - | + | ==IEA Annotations - UniProtKB Keyword Mapping== |
OLD .ACE FILE: | OLD .ACE FILE: | ||
− | + | na | |
− | |||
− | |||
CURRENT GO FILE: | CURRENT GO FILE: | ||
− | UniProtKB | + | UniProtKB A5JYS3 part_of GO:0016020 GO_REF:0000038 ECO:0000323 UniProtKB-KW:KW-0472 20141129 UniProt go_evidence=IEA |
NEW .ACE FILE: | NEW .ACE FILE: | ||
Gene : "WBGene00006543" | 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" | |
− | part_of GO_term "GO:0005634" | + | 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= | =For Reference= |
Latest revision as of 22:44, 17 December 2014
Contents
- 1 Different Types of GO Annotations
- 1.1 WormBase - manual annotation, no extra information
- 1.2 WormBase - manual annotation, IPI when entry in With/From column is a WBGene
- 1.3 WormBase - manual annotation, IPI when entry in With/From column is a UniProtKB protein ID
- 1.4 WormBase - manual annotation, IPI when entry in With/From column is multiple WBGene IDs
- 1.5 WormBase - manual annotation, IPI when entry in With/From column is a WBGene ID and a rat UniProtKB ID not in WB
- 1.6 WormBase - manual annotation, cross-species complementation assay
- 1.7 WormBase - manual annotation, entry in Annotation Extension column
- 1.8 WormBase - manual annotation, isoform-specific annotation (Need to map specific protein isoforms in UniProt to WP:CE ids)
- 1.9 WormBase - manual annotation, use of ND evidence code which requires use of a GO_REF for evidence
- 1.10 WormBase - manual annotation, including interacting taxon
- 1.11 WormBase - manual annotation, same GO term and evidence code but different papers
- 1.12 WormBase - manual annotation, multiple annotations from a single paper (also includes an entry in the With/From column)
- 1.13 WormBase - manual annotation, use of qualifier
- 1.14 WormBase - manual annotation, multiple additional columns (e.g., With/From and Annotation Extension)
- 1.15 UniProtKB - manual annotation, no extra information
- 1.16 WormBase and UniProtKB - exact same manual annotation
- 1.17 IntAct - manual protein binding annotation (Question: How many of these annotations have a more granular annotation from WB? Also, specific isoform issue.)
- 1.18 PAINT - annotation from phylogenetic inference (The supporting evidence in the With/From column is an identifier for a Panther Tree Node (PTN)
- 1.19 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)
- 1.20 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.)
- 1.21 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?)
- 1.22 IEA Annotations - UniProtKB Keyword Mapping
- 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:
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
- 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