Difference between revisions of "Curation Scenarios for new GO Model - GPAD and .ace Representations"
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| − | + | =Different Types of GO Annotations in GPAD File from UniProtKB= | |
*WormBase - manual annotation, no extra information | *WormBase - manual annotation, no extra information | ||
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*Phenotype2GO Pipeline - RNAi Phenotype2GO (Notes: remove secondary targets, remove non-WT background as these are likely to be IGI, rather than IMP annotations?) | *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== | ||
| + | |||
| + | 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/ | ||
Revision as of 19:58, 6 August 2013
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
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/
