Annotation Conf. Call, February 24, 2015

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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've included some links to entries on the anatomy terms and phenotypes described in the paper, in case they're helpful:

Note that the paper starts with gross anatomical defects and then progresses to a more detailed characterization of the phenotype. This is fairly typical.

Summary of Molecular Markers Affected in bcl-7 Mutant Animals

Gene/Marker Name Molecular Identity Anatomical Expression Pattern Result
scm::gfp not known nuclei of seam cells, all larval stages reduced number except for early L1 larval stage
cdh-3::gfp cadherin cytoplasm of seam cells reduced number
col-19::gfp collagen hypodermal syncytium (hyp7) and seam cells in adult stage decreased in hyp7 (not significant), decreased in seam cells (significant)
des-2::gfp nicotinic acetylcholine receptor PVD neurons no extra neurons
dat-1::gfp dopamine transporter PDE neurons no extra neurons
egl-27::mCherry MTA1 homolog, NODE complex strong in intestine, weak in epidermis in L4 larval stage increased expression ubiquitously, but especially in in seam cells and hyp7; increased expression - qRT-PCR
ceh-6 POU-homeodomain transcription factor, NODE complex not reported in this paper, but head and tail region, excretory cell, neurons, vulva - dynamic expression pattern increased expression - qRT-PCR