WS248 Models.wrm

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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
                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

    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":

    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


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

Type_of_construct ?Text