Difference between revisions of "Curation Scenarios for new GO Model - GPAD and .ace Representations"
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==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://wiki.geneontology.org/index.php/Final_GPAD_and_GPI_file_format | + | *http://www.geneontology.org/cgi-bin/references.cgi |
− | http://wiki.geneontology.org/index.php/Evidence_Code_Ontology_%28ECO%29 | + | *http://obo-relations.googlecode.com/svn/trunk/src/ontology/ro.obo |
− | http://www.geneontology.org/cgi-bin/references.cgi | + | *http://evidenceontology.googlecode.com/svn/trunk/eco.obo |
− | http://obo-relations.googlecode.com/svn/trunk/src/ontology/ro.obo | + | *ftp://ftp.ebi.ac.uk/pub/contrib/goa/ |
− | http://evidenceontology.googlecode.com/svn/trunk/eco.obo | ||
− | ftp://ftp.ebi.ac.uk/pub/contrib/goa/ |
Revision as of 19:59, 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
- 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/