Difference between revisions of "Curation Scenarios for new GO Model - GPAD and .ace Representations"
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Revision as of 19:52, 7 August 2013
Contents
- 1 Different Types of GO Annotations in GPAD File from UniProtKB
- 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
- 1.9 WormBase - manual annotation, use of qualifier
- 1.10 WormBase - manual annotation, multiple additional columns (e.g., With/From and Annotation Extension)
- 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: remove secondary targets, remove non-WT background as these are likely to be IGI, rather than IMP annotations?)
- 2 For Reference
Different Types of GO Annotations in GPAD File from UniProtKB
WormBase - manual annotation, no extra information
OLD .ACE FILE:
Gene : "WBGene00001052" GO_term "GO:0007191" "IDA" Paper_evidence "WBPaper00006389" GO_term "GO:0007191" "IDA" Curator_confirmed "WBPerson1843"
CURRENT GO FILE:
UniProtKB Q86ME3 involved_in GO:0007191 PMID:14739932 ECO:0000314 20070522 WormBase go_evidence=IDA|id=2113475183|curator_name=Kimberly Van Auken
NEW .ACE FILE:
Gene : "WBGene00001052" GO_term "GO:0007191" Relation "RO:0002331" Assigned_by "Gene Ontology Consortium" GO_term "GO:0007191" GO_code "ECO:0000314" Paper_evidence "WBPaper00006389" GO_term "GO:0007191" GO_code "ECO:0000314" Curator_confirmed "WBPerson1843" GO_term "GO:0007191" GO_code "ECO:0000314" Date_last_updated "2007-05-22"
WormBase - manual annotation, entry in With/From column
OLD .ACE FILE:
Gene : "WBGene00000912" GO_term "GO:0040024" "IGI" Paper_evidence "WBPaper00004702" GO_term "GO:0040024" "IGI" Curator_confirmed "WBPerson1843"
CURRENT GO FILE:
UniProtKB O16850 involved_in GO:0040024 PMID:11381260 ECO:0000316 WB:WBGene00000898 20060203 WormBase go_evidence=IGI|id=2113469094|curator_name=Kimberly Van Auken
NEW .ACE FILE:
Gene : "WBGene00000912" GO_term "GO:0040024" Relation "RO:0002331" Assigned_by "Gene Ontology Consortium" GO_term "GO:0040024" GO_code "ECO:0000316" Paper_evidence "WBPaper00004702" GO_term "GO:0040024" GO_code "ECO:0000316" Curator_confirmed "WBPerson1843" GO_term "GO:0040024" GO_code "ECO:0000316" Date_last_updated "2006-02-03" GO_term "GO:0040024" Annotation_made_with "WBGene00000898" Paper_evidence "WBPaper00004702" GO_term "GO:0040024" Annotation_made_with "WBGene00000898" Curator_confirmed "WBPerson1843" GO_term "GO:0040024" Annotation_made_with "WBGene00000898" Date_last_updated "2006-02-03"
WormBase - manual annotation, entry in Annotation Extension column
OLD .ACE FILE:
Gene : "WBGene00020999" GO_term "GO:0005783" "IDA" Paper_evidence "WBPaper00038444" GO_term "GO:0005783" "IDA" Curator_confirmed "WBPerson1843"
CURRENT GO FILE:
UniProtKB O16999 part_of GO:0005783 PMID:21611156 ECO:0000314 20120727 WormBase part_of(WBbt:0006804) go_evidence=IDA|id=2113469099|curator_name=Kimberly Van Auken
NEW .ACE FILE:
Gene : "WBGene00020999" GO_term "GO:0005783" Relation "RO:0000050" Assigned_by "Gene Ontology Consortium" GO_term "GO:0005783" GO_code "ECO:0000314" Paper_evidence "WBPaper00038444" GO_term "GO:0005783" GO_code "ECO:0000314" Curator_confirmed "WBPerson1843" GO_term "GO:0005783" GO_code "ECO:0000314" Date_last_updated "2012-07-27" GO_term "GO:0005783" Annotation_extension "RO:0000050" "WBbt:0006804" Paper_evidence "WBPaper00038444" GO_term "GO:0005783" Annotation_extension "RO:0000050" "WBbt:0006804" Curator_confirmed "WBPerson1843" GO_term "GO:0005783" Annotation_extension "RO:0000050" "WBbt:0006804" Date_last_updated "2012-07-27"
WormBase - manual annotation, isoform-specific annotation (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
WormBase - manual annotation, multiple annotations from a single paper
WormBase - manual annotation, use of qualifier
WormBase - manual annotation, multiple additional columns (e.g., With/From and Annotation Extension)
UniProtKB - manual annotation, no extra information
WormBase and UniProtKB - exact same manual annotation
IntAct - manual protein binding annotation (Question: How many of these annotations have a more granular annotation from WB?)
PAINT - annotation from phylogenetic inference
Function-Process Links - annotations inferred by GOC based on inter-ontology relationships
Phenotype2GO Pipeline - Variation Phenotype2GO
Phenotype2GO Pipeline - RNAi Phenotype2GO (Notes: remove secondary targets, remove non-WT background as these are likely to be IGI, rather than IMP annotations?)
For Reference
- 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