Reference Genome progress report for 2010 (Archived)

Publications/communications

• Conference calls are held every month to discuss annotation target prioritization, annotation issues, development of the PAINT software, requirements for uploading PAINT generated GAF files, and other issues relevant to the reference genome group.

Annotation camp

The 3rd Gene Ontology’s Annotation Camp was held from June 16-18 2010 at the Centre Medical Universitaire (CMU) Geneva, Switzerland. The Gene Ontology project (GO) provides a set of controlled vocabularies for use in annotation of gene products (http://geneontology.org/). Members from several model organism databases were represented, for a total of 63 attendees, including 40 from the SIB and 23 external delegates. This annotation camp aimed to update and refine the skills of GO biocurators, including the Swiss-Prot curation team. The major themes of the meeting covered processes difficult to represent in the Gene Ontology such as regulation, responses to stimulus, and protein complexes. The goal is to improve annotation consistency for GO users to have high quality data to support their work.

Curation Targets

As of November 2009, the selection of the curation targets is done from a 'systems' perspective, for example with respect to a biological pathway. The rationale is that if targets encompass a single biological phenomenon the annotation will be more accurate and more complete since the curators will be able to familiarize themselves with the subject.

We have started this effort with lung branching morphogenesis. This project was difficult because available experimental data does not allow to clearly infer how specific proteins individually influence the development of the lung (which is the level at which GO annotations are captured)

In the it next phase we have started to annotate the Wnt_signaling_Pathway. We have annotated 9 families of proteins implicated in this pathway, both at the primary level and using PAINT to propagate annotations across all the proteins from the 48 species currently in Panther.

Electronic annotation jamborees

• Electronic_jamboree_feb22-2010: SLIT2 and NIPBL