WS247 Models.wrm

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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)


  Depict  WBProcess  ?WBProcess  XREF  Picture

and change:

  Picture  ?Picture  #Evidence


  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

Expression_cluster ?Expression_cluster XREF Expr_pattern
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


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
                  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

  • 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.
  • Paul D. 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.