Transcript reference-genomes_rchisholm

Rationale
Need a solid base for analysis of
future genomes
Reference genome criteria:
• Sequenced genome
• MOD
• Functional genomics projects
• Adequate research community
• Sufficient Literature base
Reference Genome
Annotation
Provide broad and deep annotations
for reference genomes:
Work with reference genome MODs.
They have agreed:
• To use priorities set by GO
disease relevant genes
genes with human orthologs
• provide data for metrics
Reference Genome Annotation
• GO funded curators will
coordinate the work at the MOD
where they reside. They will also
spend some time involved in
assessing or annotating human
genes when annotating orthologs
in their organism
• Provide outreach and training to
non-reference genomes
Reference Genome Annotation
• Participate in annotation
consistency exercises.
• Review GOA annotations for their
organisms. This requires a bidirectional process with MODs
reviewing GOA annotations and
GOA reviewing human annotations
performed by the GO annotation
team.
Mouse/Human Rat as a Model for
Coordinating Annotations across
Species
Develop metrics to assess both
breadth and depth.
Breadth
•what % of genes are annotated with
experimental data from that organism
•what % of genes are annotated with ISS
annotations (not otherwise annotated)
•what % of genes are annotated with IEAs
goal is to maximize total coverage and
experimental supported annotation
Develop Metrics to Assess
Breadth and Depth of
Annotation
–Depth
• % of papers used for curation
• average # of papers per curated
gene
• can we capture the # of relevant
papers since we know it is a
subset of all papers. How?
Ontology Based Tree metrics
How to coordinate this
annotation effort
• Need process to set priorities
• Need to develop list of “disease
genes” and process to monitor
progress.
• Need to refocus and integrate roles of
GO funded annotators
• Need to establish coordination of GO
Annotation Team. Fortnightly phone
conferences.