Difference between revisions of "Sample paper and data for exploring updates"
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− | '''Paper:''' | + | __TOC__ |
+ | |||
+ | == 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. | 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 | + | 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. | 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 | + | Gene Ontology Annotations - New |
− | Expression Patterns | + | Expression Patterns - New |
− | Gene Regulation | + | Gene Regulation - New |
− | Genetic Interactions | + | Genetic Interactions - New |
− | Physical Interactions - Y2H | + | Physical Interactions - Y2H - New |
Variations - New and Existing, Sequence | Variations - New and Existing, Sequence | ||
Line 38: | Line 79: | ||
Variation Phenotypes | Variation Phenotypes | ||
− | Antibodies | + | 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 | ||
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
- data from our collaborators
- Strain (tuli)
- data from our collaborators
- CGC strain update
- data from our collaborators
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