Expression pattern remodel

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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

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

.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


open questions

  • does ?float have to be always populated? If so, how?
  • how do we deal with male/hermaphrodite
e.g. 'expressed in the tail in males' we have occurrence of 2 anatomy terms


additional changes

Not_detected_in ?Anatomy_term Not_detected_during ?Life_stage

combine the 2?

add ubiquitous tag?


Back to Expression Pattern


the ?Descriptor proposal

Changes that should affect expr_pattern model

?Expression_pattern Expression_of ?Gene ..
...
Detected_in ?Descriptor XREF Expr_pattern
Not_Detected_in ?Descriptor XREF Expr_pattern
..

Algorithm ?Text //for quantitative expression



?Gene	GO_term ?GO_term XREF Gene GO_code ?GO_code ?Descriptor
           		Expr_pattern ?Expr_pattern XREF Gene
**************************************************************************************************************************************************************************************************************************************************************
 
?Expression_pattern Expression_of ?Gene ..
...
Detected_in ?Descriptor XREF Expr_pattern
Not_Detected_in ?Descriptor XREF Expr_pattern

**************************************************************************************************************************************************************************************************************************************************************
                       
?Descriptor	Annotation_relation UNIQUE Relation ?Relation                                   //Used to capture the explicit relation between the gene/gene product and the ontology term.
		Annotation_made_with	Interactor_overlapping_gene ?Gene          //Annotation_made_with captures entries in the With/From column used for IGI, IPI, IMP, ISS, and IC GO annotations.
                                                                        Interactor_overlapping_protein ?Protein
                                     	                        IC_GO_term ?GO_term
                                                                        Motif ?Motif
                                                                        RNAi ?RNAi
                                                                        Variation ?Variation
                                                                       	Phenotype ?Phenotype
                                                                      	Database ?Database ?Database_field ?Text
                   	Annotation_extension	Life_stage_Relation ?Relation ?Life_stage XREF Descriptor #Qualifier          //Annotation_extension captures the information describing the specific contextual details of a single experiment.
                                                                       	Gene_Relation ?Relation ?Gene
                                                                       	Protein_Relation ?Relation ?Protein
                                                                      	Molecule_Relation ?Relation ?Molecule
                                                                        Anatomy_Relation ?Relation ?Anatomy_term XREF Descriptor #Qualifier
                                                                        GO_term_Relation ?Relation ?GO_term XREF Descriptor #Qualifier
                                                                        Quantitative_expression UNIQUE Float 
              	Annotation_isoform          	Protein ?Protein          //This tag is used when the annotation refers to a specific gene product isoform, e.g. one isoform localizes to the plasma membrane, while another localizes to the cytoplasm.
                                                                     	Transcript ?Transcript
                   	Interacting_taxon 		NCBITaxonomyID UNIQUE Int          //This tag captures Taxon IDs when the GO term used refers to a multi-organism process, e.g. defense response to Gram negative bacterium.
	            Reference 			?Paper XREF GO_annotation #Evidence          //This tag captures the Reference used for an annotation when that reference is a published paper.
                  	GO_reference 		?Database ?Database_field ?Text #Evidence          //This tag captures the reference used for an annotation when that reference is one of the GO references (e.g., GO_REF:0000015) 
                   	Annotation_properties 	Text          //This tag will use a controlled vocabulary for meta-data about the annotation.  GO may populate this in the future - we could wait to add it, if needed.


//GOC wiki page for description of GPAD file format (the format in which we get annotations from Protein2GO):  http://wiki.geneontology.org/index.php/Final_GPAD_and_GPI_file_format.
//What will the XREFs in ?Life_stage, etc. look like?  Would the Descriptor tag in Life_stage, etc., then hold a mix of Descriptors from Expr_pattern and GO curation (all ontologies)?
**************************************************************************************************************************************************************************************************************************************************************
//This is just a brainstorm about what we might want to include in a ?Relation class.  If a relation was part of the RO, then we could also include the parent-child relationships, if we wanted, but I haven't included them in this draft yet.

?Relation
Public_name ?Text
Definition Text
Relation_ontology_id UNIQUE ?Text
Synonym ?Text


Possible relations to include (will likely be expanded): involved_in
                                      			                          enables
                                      			                          contributes_to
                                      			                          part_of
                                                                                                  colocalizes_with
                                                                                                  exists_during
                                                                                                  happens_during
                                                                                                  has_regulation_target
                                                                                                  has_input
                                                                                                  has_direct_input
			                                                              in_the_presence_of
                                                                                                  in_the_absence_of
                                                                                                  dependent_on

and the equivalent nots, e.g., not_involved_in