Difference between revisions of "Annotation Conf. Call, February 10, 2015"

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==Jenkins reports==
==Jenkins reports==
http://build.berkeleybop.org/view/GAF/


==RNA Central==
==RNA Central==
Please send your RNA identifiers to RNA central (who, how coming!)
Please send the identifiers for RNA gene products that is being used internally by your MOD for GO annotation. This will provide the initial mappings so that we can then switch over to using the RNACentral IDs. Contact RNA Central using this form - http://rnacentral.org/contact


==Demo of CalTech annotation tool==
==Demo of CalTech annotation tool==
We will use CalTech's annotation tool for our curation consistency exercises. This tool allows us to highlight a sentence and enter specific GO terms/evidence etc. Kimberly will give a demo of how it works. If you want an account in this tool, please put your name down here on this wiki page so Kimberly can send one email to her programmer requesting for accounts.
We will use CalTech's annotation tool for our curation consistency exercises. This tool allows us to highlight a sentence and enter specific GO terms/evidence etc. Kimberly will give a demo of how it works. If you want an account in this tool, please put your name down here on this wiki page so Kimberly can send one email to her programmer requesting accounts.
* Petra
* Val
* Bob
* Aleks (EBI)
* Penelope (EBI)
* Dmitry (MGI)
* David H (MGI)
* Stacia (SGD)
* Tanya (TAIR)
* Donghui (TAIR)
* Leonore (TAIR)
* Doug (ZFIN)
* Sabrina (ZFIN)
* Edith (SGD)
* Midori (PomBase)
* Becky (UCL)
 
==Annotation Consistency Exercise - February 24, 2015==
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
**http://www.wormatlas.org/ver1/handbook/reproductivesystem/reproductivesystem1.htm
*Egl phenotype
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0000006
*Pvl phenotype
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0000697
*Burst phenotype
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0000038
*Alae morphology phenotype
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0001412
 
Note that the paper starts with gross anatomical defects and then progresses to a more detailed characterization of the phenotype.  This is fairly typical.
 
--Kimberly
 
 
 


[[Category:Annotation Working Group]]
[[Category:Annotation Working Group]]

Latest revision as of 13:09, 17 February 2015


Agenda

Jenkins reports

http://build.berkeleybop.org/view/GAF/

RNA Central

Please send the identifiers for RNA gene products that is being used internally by your MOD for GO annotation. This will provide the initial mappings so that we can then switch over to using the RNACentral IDs. Contact RNA Central using this form - http://rnacentral.org/contact

Demo of CalTech annotation tool

We will use CalTech's annotation tool for our curation consistency exercises. This tool allows us to highlight a sentence and enter specific GO terms/evidence etc. Kimberly will give a demo of how it works. If you want an account in this tool, please put your name down here on this wiki page so Kimberly can send one email to her programmer requesting accounts.

  • Petra
  • Val
  • Bob
  • Aleks (EBI)
  • Penelope (EBI)
  • Dmitry (MGI)
  • David H (MGI)
  • Stacia (SGD)
  • Tanya (TAIR)
  • Donghui (TAIR)
  • Leonore (TAIR)
  • Doug (ZFIN)
  • Sabrina (ZFIN)
  • Edith (SGD)
  • Midori (PomBase)
  • Becky (UCL)

Annotation Consistency Exercise - February 24, 2015

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:

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

--Kimberly