Difference between revisions of "Sample paper and data for exploring updates"

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'''Paper:'''
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__TOC__
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== Examples ==
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'''Example 1: Paper describes cloning of a new gene, epg-8:'''
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Title: The coiled-coil domain protein EPG-8 plays an essential role in the autophagy pathway in C. elegans.
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Authors: Yang P; Zhang H
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Journal: Autophagy
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Year: 2011-02-01
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Doc ID: WBPaper00037833
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Data in the paper/objects to curate:
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Two paper-person conncections
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Paper-gene connections
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Gene name - New
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Variations - New, Existing
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Variation Phenotype - New
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Concise description - New
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Gene Ontology Annotations - New
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Expression Pattern - New
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Gene Regulation - New
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'''Example 2: Paper describes molecular cloning of an existing locus, lin-56:'''
  
 
Title: The LIN-15A and LIN-56 Transcriptional Regulators Interact to Negatively Regulate EGF/Ras Signaling in Caenorhabditis elegans Vulval Cell-fate Determination.
 
Title: The LIN-15A and LIN-56 Transcriptional Regulators Interact to Negatively Regulate EGF/Ras Signaling in Caenorhabditis elegans Vulval Cell-fate Determination.
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Data in the new paper and objects affected:
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Data in the new paper/objects to curate:
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Six paper-person connections - New
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Gene-Sequence Connection - Merge two WBGenes? WBGene00003038 (lin-56) and WBGene00014059 (ZK673.3)
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If a merger and obsoletion, move objects to appropriate gene page?
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Five paper-gene connections
 +
 
 +
Concise descriptions - Update both lin-56 and ZK673.3?  Dependent upon merger status.  ZK673.3 would be an update, lin-56 would be new.
 +
 
 +
Gene Ontology Annotations - New
 +
 
 +
Expression Patterns - New
 +
 
 +
Gene Regulation - New
 +
 
 +
Genetic Interactions - New
 +
 
 +
Physical Interactions - Y2H - New
  
Six Person Objects (as authors) - Update person page?
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Variations - New and Existing, Sequence
  
Four Gene Objects (paper-gene connections) - Update gene page?
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Rearrangements - Existing
  
Gene-Sequence Connection - Merge two WBGenes: WBGene00003038 (lin-56) and WBGene00014059 (ZK673.3)
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Variation Phenotypes
  
Concise descriptions - Update ZK673.3
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Antibodies - New
  
Gene Ontology Annotations
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== Issues to watch out for ==
  
Expression Patterns
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* Anything that will diverge the database from the gff files.
  
Gene Regulation
 
  
Genetic Interactions
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==Data Types to Update==
  
Physical Interactions - Y2H
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*Gene
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** Gene names (CGC_name, Public_name, Other_name) (tuli)
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ATTENTION: merging and splitting genes is non-trivial (tuli)
  
Variations - New, Existing
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*Person
  
RNAi Phenotype
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*Paper
  
Variation Phenotype
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* Variation (tuli)
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** data which has been submitted via submission form etc.
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ATTENTION: mapping is non-trivial
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** data from our collaborators
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*** KO consortium
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*** Japanese KO
  
Antibodies
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* Strain (tuli)
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** data from our collaborators
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*** CGC strain update
  
  

Latest revision as of 10:39, 30 March 2011

Examples

Example 1: Paper describes cloning of a new gene, epg-8:

Title: The coiled-coil domain protein EPG-8 plays an essential role in the autophagy pathway in C. elegans.

Authors: Yang P; Zhang H

Journal: Autophagy

Year: 2011-02-01

Doc ID: WBPaper00037833


Data in the paper/objects to curate:

Two paper-person conncections

Paper-gene connections

Gene name - New

Variations - New, Existing

Variation Phenotype - New

Concise description - New

Gene Ontology Annotations - New

Expression Pattern - New

Gene Regulation - New


Example 2: Paper describes molecular cloning of an existing locus, lin-56:

Title: The LIN-15A and LIN-56 Transcriptional Regulators Interact to Negatively Regulate EGF/Ras Signaling in Caenorhabditis elegans Vulval Cell-fate Determination.

Authors: Davison EM; Saffer AM; Huang LS; Demodena J; Sternberg PW; Horvitz HR

Journal: Genetics

Year: 2010-12-31

Doc ID: WBPaper00037906


Data in the new paper/objects to curate:

Six paper-person connections - New

Gene-Sequence Connection - Merge two WBGenes? WBGene00003038 (lin-56) and WBGene00014059 (ZK673.3)

If a merger and obsoletion, move objects to appropriate gene page?

Five paper-gene connections

Concise descriptions - Update both lin-56 and ZK673.3? Dependent upon merger status. ZK673.3 would be an update, lin-56 would be new.

Gene Ontology Annotations - New

Expression Patterns - New

Gene Regulation - New

Genetic Interactions - New

Physical Interactions - Y2H - New

Variations - New and Existing, Sequence

Rearrangements - Existing

Variation Phenotypes

Antibodies - New

Issues to watch out for

  • Anything that will diverge the database from the gff files.


Data Types to Update

  • Gene
    • Gene names (CGC_name, Public_name, Other_name) (tuli)

ATTENTION: merging and splitting genes is non-trivial (tuli)

  • Person
  • Paper
  • Variation (tuli)
    • data which has been submitted via submission form etc.

ATTENTION: mapping is non-trivial

    • data from our collaborators
      • KO consortium
      • Japanese KO
  • Strain (tuli)
    • data from our collaborators
      • CGC strain update






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