Sample paper and data for exploring updates

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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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