Difference between revisions of "WormBase Model:Expr pattern"
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== Model == | == Model == | ||
<pre> | <pre> | ||
− | ?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern | + | ?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern //For genes that were studied |
− | CDS ?CDS XREF Expr_pattern // | + | CDS ?CDS XREF Expr_pattern //this tag is not used any more |
− | Sequence ?Sequence XREF Expr_pattern // | + | Sequence ?Sequence XREF Expr_pattern //this tag is not used any more |
− | Pseudogene ?Pseudogene XREF Expr_pattern // | + | Pseudogene ?Pseudogene XREF Expr_pattern //this tag is not used any more |
− | Clone ?Clone XREF Expr_pattern | + | Clone ?Clone XREF Expr_pattern //this is to record plasmid names for the study, not used any more |
− | Protein ?Protein XREF Expr_pattern | + | Protein ?Protein XREF Expr_pattern //this tag is not used any more |
− | Protein_description Text // stores information for Expr_patterns with unknown antigens | + | Protein_description Text // stores information for Expr_patterns done with immunostaining with unknown antigens |
− | Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping | + | Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping |
− | Expressed_in Cell ?Cell XREF Expr_pattern #Qualifier | + | Expressed_in Cell ?Cell XREF Expr_pattern #Qualifier //this tag is not used any more |
− | Cell_group ?Cell_group XREF Expr_pattern #Qualifier | + | Cell_group ?Cell_group XREF Expr_pattern #Qualifier //this tag is not used any more |
− | Life_stage ?Life_stage XREF Expr_pattern #Qualifier | + | Life_stage ?Life_stage XREF Expr_pattern #Qualifier //expressed in life stages |
− | Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier | + | Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier //expressed in tissue parts or cells |
− | GO_term ?GO_term XREF Expr_pattern #GR_condition | + | GO_term ?GO_term XREF Expr_pattern #GR_condition //for cellular components |
− | Subcellular_localization ?Text | + | Subcellular_localization ?Text //description on subcellular localization |
− | Type Reporter_gene ?Text | + | Type Reporter_gene ?Text //The following tags indicate what kind of experiments were done. |
In_situ Text | In_situ Text | ||
Antibody ?Text | Antibody ?Text | ||
− | Northern Text | + | Northern Text |
− | Western Text | + | Western Text |
− | RT_PCR Text | + | RT_PCR Text |
− | Localizome ?Text | + | Localizome ?Text |
− | Expression_cluster ?Expression_cluster XREF Expr_pattern // | + | Expression_cluster ?Expression_cluster XREF Expr_pattern //For localizome data to summarize genes with similar expression profiles. |
− | Pattern ?Text | + | Pattern ?Text //description of cellular and/or developmental expression pattern |
− | Picture ?Picture XREF Expr_pattern | + | Picture ?Picture XREF Expr_pattern //link to picture files in WormBase. |
− | MovieURL Text // | + | MovieURL Text //link to movie URLs that store movies externally |
− | Movie ?Movie XREF Expr_pattern // | + | Movie ?Movie XREF Expr_pattern //link to movie files in WormBase. |
− | Remark ?Text #Evidence | + | Remark ?Text #Evidence //for any other information not fitting the model but still important. |
− | Experiment Laboratory ?Laboratory | + | Experiment Laboratory ?Laboratory //Labs who performed the experiment. The following subtags are for data submitted by authors but not published. |
− | Author ?Author | + | Author ?Author //Author of the experiment |
− | Date UNIQUE DateType | + | Date UNIQUE DateType //Date the experiment were performed or data submitted. |
− | Strain UNIQUE ?Strain | + | Strain UNIQUE ?Strain //Stains used for the experiment |
− | Reference ?Paper XREF Expr_pattern | + | Reference ?Paper XREF Expr_pattern //Paper that the experiments were published. |
− | Transgene ?Transgene XREF Expr_pattern | + | Transgene ?Transgene XREF Expr_pattern //Transgene reagent used. |
Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence | Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence | ||
− | Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining | + | Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining, antibody reagent. |
− | + | Curated_by UNIQUE Text //To identify whether the curation was done by Hixton or Caltech. Not useful any more since all data are now curated by Caltech. | |
− | Curated_by UNIQUE Text // | ||
− | |||
</pre> | </pre> | ||
Revision as of 22:39, 6 December 2010
Curator Comments/Description
Model
?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern //For genes that were studied CDS ?CDS XREF Expr_pattern //this tag is not used any more Sequence ?Sequence XREF Expr_pattern //this tag is not used any more Pseudogene ?Pseudogene XREF Expr_pattern //this tag is not used any more Clone ?Clone XREF Expr_pattern //this is to record plasmid names for the study, not used any more Protein ?Protein XREF Expr_pattern //this tag is not used any more Protein_description Text // stores information for Expr_patterns done with immunostaining with unknown antigens Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping Expressed_in Cell ?Cell XREF Expr_pattern #Qualifier //this tag is not used any more Cell_group ?Cell_group XREF Expr_pattern #Qualifier //this tag is not used any more Life_stage ?Life_stage XREF Expr_pattern #Qualifier //expressed in life stages Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier //expressed in tissue parts or cells GO_term ?GO_term XREF Expr_pattern #GR_condition //for cellular components Subcellular_localization ?Text //description on subcellular localization Type Reporter_gene ?Text //The following tags indicate what kind of experiments were done. In_situ Text Antibody ?Text Northern Text Western Text RT_PCR Text Localizome ?Text Expression_cluster ?Expression_cluster XREF Expr_pattern //For localizome data to summarize genes with similar expression profiles. Pattern ?Text //description of cellular and/or developmental expression pattern Picture ?Picture XREF Expr_pattern //link to picture files in WormBase. MovieURL Text //link to movie URLs that store movies externally Movie ?Movie XREF Expr_pattern //link to movie files in WormBase. Remark ?Text #Evidence //for any other information not fitting the model but still important. Experiment Laboratory ?Laboratory //Labs who performed the experiment. The following subtags are for data submitted by authors but not published. Author ?Author //Author of the experiment Date UNIQUE DateType //Date the experiment were performed or data submitted. Strain UNIQUE ?Strain //Stains used for the experiment Reference ?Paper XREF Expr_pattern //Paper that the experiments were published. Transgene ?Transgene XREF Expr_pattern //Transgene reagent used. Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining, antibody reagent. Curated_by UNIQUE Text //To identify whether the curation was done by Hixton or Caltech. Not useful any more since all data are now curated by Caltech.
Proposed Changes
unused tags
CDS
Cell_group
GO_term
Expression_cluster
Movie