Difference between revisions of "Annotation Conf. Call, February 24, 2015"

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(Created page with " =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....")
 
(Annotation Consistency Exercise)
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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.   
 
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:
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I've included some links to entries on the anatomy terms and phenotypes described in the paper, in case they're helpful:
 
*Seam cells
 
*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'.
 
**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'.
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Note that the paper starts with gross anatomical defects and then progresses to a more detailed characterization of the phenotype.  This is fairly typical.
 
Note that the paper starts with gross anatomical defects and then progresses to a more detailed characterization of the phenotype.  This is fairly typical.
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==Summary of Molecular Markers Affected in bcl-7 Mutant Animals==
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{| border=1 cell-padding=5 cell-spacing=10
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|-
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! Gene/Marker Name
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! Molecular Identity
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! Anatomical Expression Pattern
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! Result
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|-
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|-
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|}
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Revision as of 12:14, 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'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