Transcript PATO exercise at TAIR

Phenotype Annotation at TAIR
Tanya Berardini
Current Status
• Phenotypes are associated to organisms
(germplasms) and linked to references
• Curation is mainly done in unstructured full
text
• Pilot study of structured annotation
completed
• PaTO not yet implemented
papillae:abnormal
style:abnormal
septum development:incomplete
leaf:serrate
Same challenges as other
databases
• Large corpus of literature
• Set number of curators with many diverse
responsibilities
• Different ways of paper prioritization
Capturing phenotypes from the
literature
• Single paper, describing single aspect of
phenotype
• Single paper, describing multiple aspects of the
organism’s phenotype
• Multiple papers describing different aspects of the
organism’s phenotype
• Multiple papers, describing the same phenotype
Storing complex annotations in the
database
• Right now, GO as a model for assocations:
– 1 association = 1 gene product + 1 CV term
• How do we deal with multiple ontologies in
one association?
– 1 association = 1 germplasm + 1 anatomy term
+ 1 PATO term (+ others)