WS247 Models.wrm

Analysis class - Gary

Add Independent_variable for storing the condition of interest so that it is easy to find out what are the experimental variables that are being varied in an experiment

#Address hash - Cecilia

Remove UNIQUE so that multiple affiliations can be stored along with a single address??

#Address
Institution UNIQUE Text 

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

?Expression_cluster Wen

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.

?Position_Matrix - Xiaodong

I would like to propose a model change for ?Position_matrix:

?Position_Matrix  Description  ?Text #Evidence
   Brief_id  UNIQUE ?Text // Addition Xiaodong
                  Type  UNIQUE Frequency
                               Weight
                  Background_model Text UNIQUE Float
                  Site_values      Text UNIQUE Float REPEAT
                  Threshold        Float
                  Consensus    Text #Evidence
   Associated_feature ?Feature XREF Associated_with_Position_Matrix #Evidence
                  Sites_used UNIQUE Int
   Derived_from_matrix ?Position_Matrix
   Bound_by_gene_product ?Gene XREF Product_binds_matrix #Evidence
   Transcription_factor  UNIQUE ?Transcription_factor XREF Position_matrix #Evidence //gw3
                  Remark ?Text  #Evidence

I would like to remove UNIQUE for Transcription_factor tag. In some PFM/PWM cases, motifs can be bound by multiple TFs.

For Discussion - Nomenclature_history tag - Kimberly

• 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.

@Pdavis I guess this is formalising what has been stored as a remark in the ?Gene objects. M.A. is probably the best person to advise on this and will also be able to contribute/promote lots of remarks into this field if we go ahead with it.