Annotation Conf. Call, February 24, 2015: Difference between revisions
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Revision as of 13:32, 18 February 2015
Agenda
Annotation Consistency Exercise
Here is a link to the paper that I've chosen for the first annotation consistency exercise/discussion:
http://www.ncbi.nlm.nih.gov/pubmed/25569233
It describes studies on C. elegans bcl-7 (http://www.wormbase.org/species/c_elegans/gene/WBGene00016192) and human BCL7B (http://www.uniprot.org/uniprot/Q9BQE9).
The main thing I'd like to focus on for the annotation exercise is what Biological Process annotations curators make, noting that, at the moment, the all-encompassing Biological Process terms might not yet exist for what is described in the paper. In particular, I'd like to discuss annotating to a process vs. regulation of a process, and the use of annotation extensions to provide more context for the BP terms.
I don't want people to get too hung up on the C. elegans biology, but I've included some links to entries on the anatomy terms and phenotypes described in the paper, in case they're helpful:
- Seam cells
- During larval development, seam cells divide to generate new seam cells renew as well as a number of differentiated cell types (hypodermal/epidermal cell, neuron, glia). They stop renewing once the animals reach adulthood and do not appear to reside in a stem cell-like 'niche'.
- http://www.wormatlas.org/hermaphrodite/seam%20cells/mainframe.htm
- http://www.wormatlas.org/hermaphrodite/seam%20cells/Images/Seamfig3leg.htm
- Somatic gonad development
- Egl phenotype
- Pvl phenotype
- Burst phenotype
- Alae morphology phenotype
Note that the paper starts with gross anatomical defects and then progresses to a more detailed characterization of the phenotype. This is fairly typical.