Difference between revisions of "WS247 Models.wrm"

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  Species UNIQUE ?Species
  Species UNIQUE ?Species
== Wen has two model proposals for WS247: ==
== ?Expression_cluster Wen ==
1. Can we move Microarray_results tag from under "Experimental_info" to under "Molecular_info"?
Under ?Expression_cluster model
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:
Please change:
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               Regulated_by_treatment Text                // Wen WS228
               Regulated_by_treatment Text                // Wen WS228
               Regulated_by_molecule ?Molecule        // Wen WS228
               Regulated_by_molecule ?Molecule        // Wen WS228
  Regulation  Regulated_by_gene ?Gene  XREF Regulate_expr_cluster
  Regulation  Regulated_by_gene ?Gene  XREF Regulate_expr_cluster

Revision as of 16:16, 4 December 2014

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??

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)


  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

?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


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 - 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.