WS247 Models.wrm

GO_annotation class - Kimberly

Introduction of this new class to capture Gene::GO associateions and additional meta data associated with a curation event.

Feature - M.A.

Can we remove Annotation and Defined_by_author

Tag additions for connecting ?Picture to ?WBProcess (Topic)

Add:

?Picture
  Depict  WBProcess  ?WBProcess  XREF  Picture

and change:

?WBProcess
  Picture  ?Picture  #Evidence

to:

?WBProcess
  Picture  ?Picture  XREF  WBProcess  #Evidence 

Unique -> UNIQUE housekeeping change

Corresponding_transgene Unique ?Transgene XREF Corresponding_variation

Expr_patter - Daniela

I would like to add

Microarray_results ?Microarray_results XREF Expr_Pattern

to the Expr_pattern class

between
Expression_cluster ?Expression_cluster XREF Expr_pattern
and	      
Pattern ?Text

this will allow to map graphs for expression for remanei, briggsae and japonica to 'gene' through already existing probe-to-genome mappings

Expr_patter 2 - Daniela

I would also like to add a Species tag in the Expr_pattern class

Species UNIQUE ?Species

Wen has two model proposals for WS247:

1. Can we move Microarray_results tag from under "Experimental_info" to under "Molecular_info"?

This tag used to store microarray data, but now it is only used to specify probe names corresponding to this gene. It is better staying under super tag "Molecular_info". This model change should not affect database build or website display.

2. Under ?Expression_cluster model

Please change:

Regulation   Regulated_by_gene ?Gene                   // Wen WS228
             Regulated_by_treatment Text                // Wen WS228
             Regulated_by_molecule ?Molecule        // Wen WS228

into

Regulation   Regulated_by_gene ?Gene  XREF Regulate_expr_cluster
             Regulated_by_treatment Text
             Regulated_by_molecule ?Molecule XREF Regulate_expr_cluster

Corresponding XREF already exist in ?Gene and ?Molecule class, the XREFs in Expression_cluster were probably forgotten when I proposed them for WS228.

For Discussion - Nomenclature_history tag

Addition of a Nomenclature_history tag as part of the Structured_description grouping tag.

This tag would provide some additional textual information about gene names and changes in order to clarify better some of the naming issues.

Entries could be very simple:

umps-1 was originally identified in screens for radiation-sensitive mutant animals and thus originally named rad-6.

Or more detailed:

gene x was originally named 'xxx-1'. This gene name is now retired because of .... and the current name assigned based on sequence similarity to the human ortholog.