Difference between revisions of "WS247 Models.wrm"

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== Expr_patter Microarray_results connection - Daniela ==
== Expr_patter Microarray_results connection - Daniela ==

Revision as of 16:41, 5 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 unused tag removal - 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 Microarray_results connection - 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

Done, fixed typo in the class name ?Expr_Pattern/pattern

Expr_pattern Species tag - 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.


Associations between Genes and Transcription_factor objects - Gary

Tag additions to hold information on associations between Genes and Transcription_factor objects. Often these associations are based on very weak evidence that would not be suitable for justifying the use of Interaction objects to link them. The primary example I have would be using proximity of a transcription factor binding site to a gene. We have an explicit request from a user (Oliver Hobart) to be able to give the name of a transcription factor and be able to pull out all genes that are near to the binding sites based on ChIP-Seq evidence. This would be facilitated by holding information on this proximity in the Transcription_factor object.

The type of association (e.g. proximity, etc.) would be specified by an appropriate Analysis object in the #Evidence

Additional tag in ?Transcription_factor to hold further information on the type of that factor.

Associated_transcription_factor ?Transcription_factor XREF Associated_with_gene #Evidence
Associated_with_gene ?Gene XREF Associated_transcription_factor #Evidence
Type Text #Evidence