Difference between revisions of "Phasing out the manual annotations"

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The plan is to look at the groups of annotations by date and/or their text in order to phase them out from the concise descriptions dump that is submitted for upload, and possibly from Postgres as well.
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The plan is to look at groups of annotations by date and/or their text in order to phase them out from the concise descriptions dump that is submitted for upload (we may need to delete from Postgres as well, eventually).
  
Note: These are only the Description Type 'Concise_descritpion', not looking at Provisional descriptions'.
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Note: These are only descriptions of the Description Type 'Concise_description', in the OA, and not 'Provisional_description'.
 
*Those that have a Date last updated date of 2004-06-17 in the OA, 3075 genes  
 
*Those that have a Date last updated date of 2004-06-17 in the OA, 3075 genes  
  
*Those genes that have the following description (also from 2004-06-17)
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*Those genes that have the description below (also from 2004-06-17)
 
   
 
   
  This gene encodes a protein containing an F-box, a motif predicted to mediate protein-protein
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  This gene encodes a protein containing an F-box, a motif predicted to mediate  
interactions either with homologs of yeast Skp-1p or with other proteins.
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protein- protein interactions either with homologs of yeast Skp-1p or with other
 +
proteins.
 
Examples: fbxb genes, fbxa genes, a few sdz genes, number of unnamed (uncloned?) genes, total 295 genes
 
Examples: fbxb genes, fbxa genes, a few sdz genes, number of unnamed (uncloned?) genes, total 295 genes
  
*Those genes with the description:
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*Those genes with the description below (most are from 2004-06-17)
  
  The protein product of this gene is predicted to contain a glutamine/asparagine (Q/N)-rich ('prion')
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  The protein product of this gene is predicted to contain a glutamine/asparagine
  domain, by the algorithm of Michelitsch and Weissman (as of the WS77 release of WormBase, i.e., in
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(Q/N)-rich ('prion')
wormpep77).
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  domain, by the algorithm of Michelitsch and Weissman (as of the WS77 release of
 +
WormBase, i.e., in wormpep77).
 
Examples: pqn genes, some abu genes, some unnamed (uncloned?) genes, total 72 genes
 
Examples: pqn genes, some abu genes, some unnamed (uncloned?) genes, total 72 genes
 +
 +
*Those genes that have the word 'disease' in the description (113 genes), will need to check if these can be represented in human disease model data
 +
hex-1 encodes a beta-N-acetylhexosaminidase that is orthologous to the human gene 
 +
CERVICAL CANCER PROTO-ONCOGENE 7 (HEXB; OMIM:606873), which when mutated leads to 
 +
disease.
 +
 +
*Those genes that have the description with the word 'syndrome' (85 genes), will need to check if these can be represented in human disease model data

Latest revision as of 19:11, 19 February 2016

The plan is to look at groups of annotations by date and/or their text in order to phase them out from the concise descriptions dump that is submitted for upload (we may need to delete from Postgres as well, eventually).

Note: These are only descriptions of the Description Type 'Concise_description', in the OA, and not 'Provisional_description'.

  • Those that have a Date last updated date of 2004-06-17 in the OA, 3075 genes
  • Those genes that have the description below (also from 2004-06-17)
This gene encodes a protein containing an F-box, a motif predicted to mediate 
protein- protein interactions either with homologs of yeast Skp-1p or with other  
proteins.

Examples: fbxb genes, fbxa genes, a few sdz genes, number of unnamed (uncloned?) genes, total 295 genes

  • Those genes with the description below (most are from 2004-06-17)
The protein product of this gene is predicted to contain a glutamine/asparagine  
(Q/N)-rich ('prion')
domain, by the algorithm of Michelitsch and Weissman (as of the WS77 release of  
WormBase, i.e., in wormpep77).

Examples: pqn genes, some abu genes, some unnamed (uncloned?) genes, total 72 genes

  • Those genes that have the word 'disease' in the description (113 genes), will need to check if these can be represented in human disease model data
hex-1 encodes a beta-N-acetylhexosaminidase that is orthologous to the human gene   
CERVICAL CANCER PROTO-ONCOGENE 7 (HEXB; OMIM:606873), which when mutated leads to  
disease.
  • Those genes that have the description with the word 'syndrome' (85 genes), will need to check if these can be represented in human disease model data