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.