2007 Reference Genome Action Items (Achived)

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Reference Genome Annotation Project - Rex

Recapped goals

- broad/deep annotation

- progress metrics

- results display interface


Metrics:

- breadth: percentage genes annotated in a genome, and

- depth: percentage of annotations with high quality evidence, and percentage of papers associated with a gene that have been curated


Target selection process recap:

The group created a target list based on OMIM morbid map collection, and attempted 20-22 target genes per month, which was probably too many. Progress results are reported in Google spreadsheets.


Annotation process:

a) Identify orthologs in assigned organism, via Inparanoid, Compara (Treefam), OrthoMCL and Homologene, b) determine number of relevant papers, c) curate for GO annotations, include annotations in file, d) report papers used. It is possible to assert annotations are complete, even if not all papers have been used. At a certain date, the annotator can assert “completeness”. Orthologs and relevant papers are identified by method(s) judged best by curators. If there are no papers, an ISS annotation is still possible which refers to the orthologs in which experimental work has been carried out.


Issues

- rate of progress

- display of metrics

- display of results


Rex enjoins us to make information about this project more readily available to users, as the Reference Genomes are a public resource, especially by providing a user interface that makes the project meta-data immediately available.

Discussed the possibility of some interface to see if a gene has been annotated across all reference genomes. AmiGO is discussed for this purpose. Discussion suggests that extensions to existing tools like AmiGO AND some brand new tools might be necessary.


Action Item (Hub): Make proposals for various displays of reference genome data