Curation Scenarios for new GO Model - GPAD and .ace Representations
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- 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
- 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
WormBase - manual annotation, entry in Annotation Extension column
WormBase - manual annotation, isoform-specific annotation
WormBase - manual annotation, use of ND evidence code and GO_REF
WormBase - manual annotation, including interacting taxon
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/
