Expression pattern remodel
From WormBaseWiki
This is a proposal for changing the current ?Expr_pattern model in order to capture
- quantitative expression
- life_stage, cellular_compartment expression specificity
we will also take the opportunity to clean up some unused tags
- CDS: no objects
- Sequence: 8 objects I could consolidate with other classes -e.g. clone
- Pseudogene: no objects
- Protein: 1 object, found by Paul D should figure out where it comes from
- Cell: no objects
- Cell_group: no objects
Contents
Current model (WS242)
?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern #Evidence
CDS ?CDS XREF Expr_pattern // for coding genes
Sequence ?Sequence XREF Expr_pattern // for clones???
Pseudogene ?Pseudogene XREF Expr_pattern // [030801 krb]
Clone ?Clone XREF Expr_pattern
Protein ?Protein XREF Expr_pattern
Protein_description Text // stores information for Expr_patterns with unknown antigens [031105 krb]
Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2]
Expressed_in Cell ?Cell XREF Expr_pattern #Qualifier
Cell_group ?Cell_group XREF Expr_pattern #Qualifier
Life_stage ?Life_stage XREF Expr_pattern #Qualifier
Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
GO_term ?GO_term XREF Expr_pattern #GR_condition
Subcellular_localization ?Text
Type Reporter_gene ?Text
In_situ Text
Antibody ?Text
Northern Text // Wen [krb 030425]
Western Text // Wen
RT_PCR Text // Wen
Localizome ?Text //added by Wen
Microarray ?Microarray_experiment
Tiling_array ?Analysis
EPIC ?Text
Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome
Pattern ?Text
Picture ?Picture XREF Expr_pattern
MovieURL Text //Added by wen for link to movie URLs.
Movie ?Movie XREF Expr_pattern //Added by Wen to curate Expr_pattern video
Remark ?Text #Evidence
DB_info ?Database ?Database_field Text
Experiment Laboratory ?Laboratory
Author ?Author
Date UNIQUE DateType
Strain UNIQUE ?Strain
Reference ?Paper XREF Expr_pattern
Transgene ?Transgene XREF Expr_pattern
Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence
Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining
// added [031120 krb]
Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb]
Historical_gene ?Gene #Evidence
//Qualifer hash will be used for Expr_pattern curation to specify the reliability of data.
#Qualifier Certain Text
Uncertain Text //For faint or variable expression
Partial Text //For expression of unidentified cell in a cell group
Proposed model (WS244?)
This is an ntermediate version until all legacy objects will be remodeled accordingly. In this version of the model the 2 scenarios will coexist:
?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern #Evidence
Clone ?Clone XREF Expr_pattern
Protein_description Text // stores information for Expr_patterns with unknown antigens [031105 krb]
Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2]
Detected_in ?Anatomy_term ?Life_stage ?GO_term ?float #Qualifier //added for quantitative/qualitative expression
Algorithm ?Text //for quantitative expression
Expressed_in Life_stage ?Life_stage XREF Expr_pattern #Qualifier
Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
GO_term ?GO_term XREF Expr_pattern #GR_condition
Subcellular_localization ?Text
Type Reporter_gene ?Text
In_situ Text
Antibody ?Text
Northern Text // Wen [krb 030425]
Western Text // Wen
RT_PCR Text // Wen
Localizome ?Text //added by Wen
Microarray ?Microarray_experiment
Tiling_array ?Analysis
EPIC ?Text
Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome
Pattern ?Text
Picture ?Picture XREF Expr_pattern
MovieURL Text //Added by wen for link to movie URLs.
Movie ?Movie XREF Expr_pattern //Added by Wen to curate Expr_pattern video
Remark ?Text #Evidence
DB_info ?Database ?Database_field Text
Experiment Laboratory ?Laboratory
Author ?Author
Date UNIQUE DateType
Strain UNIQUE ?Strain
Reference ?Paper XREF Expr_pattern
Transgene ?Transgene XREF Expr_pattern
Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence
Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining
// added [031120 krb]
Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb]
Historical_gene ?Gene #Evidence
#Qualifier Certain Text
Uncertain Text //For faint or variable expression
Partial Text //For expression of unidentified cell in a cell group
Present //for quantitative expression
Absent //for quantitative expression
simplified summary of the changes for WS244
removed
CDS ?CDS XREF Expr_pattern // for coding genes
Sequence ?Sequence XREF Expr_pattern // for clones???
Pseudogene ?Pseudogene XREF Expr_pattern // [030801 krb]
Protein ?Protein XREF Expr_pattern
Cell ?Cell XREF Expr_pattern #Qualifier
Cell_group ?Cell_group XREF Expr_pattern #Qualifier
added
Detected_in ?Anatomy_term ?Life_stage ?GO_term ?float #Qualifier //added for quantitative/qualitative expression
Algorithm ?Text //for quantitative expression
#Qualifier ...
Present //for quantitative expression
Absent //for quantitative expression
model of the future (WS2XX??)
This will be the final version once all legacy objects will be remodeled accordingly.
?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern #Evidence
Clone ?Clone XREF Expr_pattern
Protein_description Text // stores information for Expr_patterns with unknown antigens [031105 krb]
Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2]
Detected_in ?Anatomy_term ?Life_stage ?GO_term ?float #Qualifier //added for quantitative/qualitative expression
Algorithm ?Text //for quantitative expression
Subcellular_localization ?Text
Type Reporter_gene ?Text
In_situ Text
Antibody ?Text
Northern Text // Wen [krb 030425]
Western Text // Wen
RT_PCR Text // Wen
Localizome ?Text //added by Wen
Microarray ?Microarray_experiment
Tiling_array ?Analysis
EPIC ?Text
Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome
Pattern ?Text
Picture ?Picture XREF Expr_pattern
MovieURL Text //Added by wen for link to movie URLs.
Movie ?Movie XREF Expr_pattern //Added by Wen to curate Expr_pattern video
Remark ?Text #Evidence
DB_info ?Database ?Database_field Text
Experiment Laboratory ?Laboratory
Author ?Author
Date UNIQUE DateType
Strain UNIQUE ?Strain
Reference ?Paper XREF Expr_pattern
Transgene ?Transgene XREF Expr_pattern
Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence
Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining
// added [031120 krb]
Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb]
Historical_gene ?Gene #Evidence
#Qualifier Certain Text
Uncertain Text //For faint or variable expression
Partial Text //For expression of unidentified cell in a cell group
Present //for quantitative expression
Absent //for quantitative expression
simplified summary of the changes for WS2XXX
removed
Expressed_in Life_stage ?Life_stage XREF Expr_pattern #Qualifier
Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
GO_term ?GO_term XREF Expr_pattern #GR_condition
.ace examples
cell cycle specificity
One way to go and add cell cycle specificity could be to add the ?CCO (cell cycle ontology, http://www.ebi.ac.uk/ontology-lookup/)
The Cell cycle ontology has XREFs to ?GO biological_process. A mapping could provide GO cc curators the info needed to fill in the Annotation_extension
Detected_in ?Anatomy_term ?Life_stage ?GO_term ?CCO ?float #Qualifier
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Expression Pattern
