Curation Scenarios for new GO Model - GPAD and .ace Representations

Different Types of GO Annotations in GPAD File from UniProtKB

• WormBase - manual annotation, no extra information

• 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/