Difference between revisions of "WS248 Models.wrm"

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(Created page with "__TOC__ == GO_annotation class == Simplified the model to that originally incorporated into the WS247 schema. This class captures Gene::GO associateions and additional meta...")
 
 
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With all gene references moving from the ?Transgene model to the
 
With all gene references moving from the ?Transgene model to the
 
?Construct model, this tag is no longer needed.
 
?Construct model, this tag is no longer needed.
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== ?Picture :: ?Life_stage ==
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Add Depict tag to the ?Picture class
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Life_stage ?Life_stage XREF Picture
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== ?Construct ==
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Remove Type_of_construct sub tags as a controlled vocabulary is now imposed in the curation tool
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Type_of_construct ?Text

Latest revision as of 16:15, 19 February 2015

GO_annotation class

Simplified the model to that originally incorporated into the WS247 schema. This class captures Gene::GO associateions and additional meta data associated with a curation event


?GO_annotation  Gene ?Gene XREF GO_annotation
                GO_term ?GO_term XREF GO_annotation
                GO_code ?GO_code
                Annotation_relation NOT
                                    colocalizes_with
                                    contributes_to
                                    enables
                                    involved_in
                                    part_of
                Annotation_made_with Interacting_gene ?Gene
                                     Inferred_from_GO_term ?GO_term
                                     Motif ?Motif
                                     RNAi_result ?RNAi
                                     Variation ?Variation
                                     Phenotype ?Phenotype
                                     Database ?Database ?Database_field ?Text
                Annotation_extension Life_stage_relation ?Text UNIQUE ?Life_stage
                                     Gene_relation ?Text UNIQUE ?Gene
                                     Molecule_relation ?Text UNIQUE ?Molecule
                                     Anatomy_relation ?Text UNIQUE ?Anatomy_term
                                     GO_term_relation ?Text UNIQUE ?GO_term
                Annotation_isoform ?Text ?Protein
                Interacting_species ?Species ?Strain
                Reference ?Paper XREF GO_annotation
                GO_reference ?Database ?Database_field ?Text
                Contributed_by ?Analysis
                Date_last_updated UNIQUE DateType 



Analysis Class Modification

?Analysis
    Project ?Analysis XREF Subproject

Removal of the Unique tag to allow for multiple Sub Projects

Gene::Picture class connection

Depict Gene ?Gene XREF Picture

?Interactor_info, and ?Transgene models

?Interaction model changes:

1) Create a "Variation_interactor" tag under "Interactor":

?Interaction
  Interactor
    Variation_interactor  ?Variation  XREF  Interactor  #Interactor_info

The addition of variations as an interactor type will require a post-variation-to-gene-mapping (during build) population of "Interactor_overlapping_gene" tags. I've corresponded with Kevin and Mary Ann about this separately.

2) Remove the "Deviation_from_expectation" and "Neutrality_function" tags

These tags are not being used and I don't think they will be.

?Interactor_info model changes:

1) Remove the "Variation", "Intragenic_effector_variation", and "Intragenic_affected_variation" tags

?Transgene model change:

1) Remove the "Historical_gene" tag

With all gene references moving from the ?Transgene model to the ?Construct model, this tag is no longer needed.

?Picture :: ?Life_stage

Add Depict tag to the ?Picture class

Life_stage ?Life_stage XREF Picture

?Construct

Remove Type_of_construct sub tags as a controlled vocabulary is now imposed in the curation tool

Type_of_construct ?Text