Difference between revisions of "WS247 Models.wrm"

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== Analysis class - Gary ==
 
== 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
 
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
 +
 +
'''Done'''
  
 
== #Address hash - Cecilia ==
 
== #Address hash - Cecilia ==
Line 10: Line 12:
  
 
  #Address
 
  #Address
  Institution UNIQUE Text  
+
  Institution UNIQUE Text
 +
 
 +
'''Done'''
  
 
== GO_annotation class - Kimberly ==
 
== GO_annotation class - Kimberly ==
Line 16: Line 20:
 
Introduction of this new class to capture Gene::GO associateions and additional meta data associated with a curation event.
 
Introduction of this new class to capture Gene::GO associateions and additional meta data associated with a curation event.
  
== Feature - M.A.==
+
'''Done'''
 +
 
 +
== Feature unused tag removal - M.A.==
  
 
Can we remove Annotation and Defined_by_author
 
Can we remove Annotation and Defined_by_author
 +
 +
'''Done'''
  
 
== Tag additions for connecting ?Picture to ?WBProcess (Topic) ==
 
== Tag additions for connecting ?Picture to ?WBProcess (Topic) ==
Line 35: Line 43:
  
 
  ?WBProcess
 
  ?WBProcess
   Picture  ?Picture  XREF  WBProcess  #Evidence  
+
   Picture  ?Picture  XREF  WBProcess  #Evidence
 +
 
 +
 
 +
'''Done'''
  
 
== Unique -> UNIQUE housekeeping change ==
 
== Unique -> UNIQUE housekeeping change ==
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  Corresponding_transgene Unique ?Transgene XREF Corresponding_variation
 
  Corresponding_transgene Unique ?Transgene XREF Corresponding_variation
  
== Expr_patter - Daniela ==
+
also
 +
 
 +
Add UNIQUE to the second text value as it should be a single pair of values and not 1 to many which could be stored (and a couple were there in error)
 +
 
 +
?Variation
 +
    Type_of_mutation Substitution UNIQUE Text Text #Evidence // wild type and mutant sequence
 +
    Type_of_mutation Substitution UNIQUE Text UNIQUE Text #Evidence // wild type and mutant sequence
 +
 
 +
 
 +
'''Done'''
 +
 
 +
== Expr_patter Microarray_results connection - Daniela ==
  
 
I would like to add
 
I would like to add
Line 56: Line 78:
 
this will allow to map graphs for expression for remanei, briggsae and japonica to 'gene' through already existing probe-to-genome mappings
 
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 ==
+
'''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
 
I would also like to add a Species tag in the Expr_pattern class
Line 62: Line 86:
 
  Species UNIQUE ?Species
 
  Species UNIQUE ?Species
  
==  Wen has two model proposals for WS247: ==
+
'''Done'''
  
1. Can we move Microarray_results tag from under "Experimental_info" to under "Molecular_info"?
+
== ?Expression_cluster Wen ==
  
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.
+
Under ?Expression_cluster model
 
 
 
 
2. Under ?Expression_cluster model
 
  
 
Please change:
 
Please change:
 
  
 
  Regulation  Regulated_by_gene ?Gene                  // Wen WS228
 
  Regulation  Regulated_by_gene ?Gene                  // Wen WS228
 
               Regulated_by_treatment Text                // Wen WS228
 
               Regulated_by_treatment Text                // Wen WS228
 
               Regulated_by_molecule ?Molecule        // Wen WS228
 
               Regulated_by_molecule ?Molecule        // Wen WS228
 
  
 
into
 
into
 
  
 
  Regulation  Regulated_by_gene ?Gene  XREF Regulate_expr_cluster
 
  Regulation  Regulated_by_gene ?Gene  XREF Regulate_expr_cluster
Line 86: Line 104:
 
               Regulated_by_molecule ?Molecule XREF Regulate_expr_cluster
 
               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.
  
Corresponding XREF already exist in ?Gene and ?Molecule class, the XREFs in Expression_cluster were probably forgotten when I proposed them for WS228.
+
'''Done'''
  
 
== ?Position_Matrix - Xiaodong ==
 
== ?Position_Matrix - Xiaodong ==
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I would like to remove UNIQUE for Transcription_factor tag. In some PFM/PWM cases, motifs can be bound by multiple TFs.
 
I would like to remove UNIQUE for Transcription_factor tag. In some PFM/PWM cases, motifs can be bound by multiple TFs.
  
 +
'''Done'''
 +
 +
== 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.
  
== For Discussion - Nomenclature_history  tag - Kimberly ==
+
The type of association (e.g. proximity, etc.) would be specified by an appropriate Analysis object in the #Evidence
  
*Addition of a Nomenclature_history tag as part of the Structured_description grouping tag.
+
Additional tag in ?Transcription_factor to hold further information on the type of that factor.
  
*This tag would provide some additional textual information about gene names and changes in order to clarify better some of the naming issues.
+
?Gene
 +
Associated_transcription_factor ?Transcription_factor XREF Associated_with_gene #Evidence
  
*Entries could be very simple:
+
?Transcription_factor
 +
Associated_with_gene ?Gene XREF Associated_transcription_factor #Evidence
 +
Type Text #Evidence
  
**umps-1 was originally identified in screens for radiation-sensitive mutant animals and thus originally named rad-6.
+
'''Done'''
  
*Or more detailed:
+
== Transgene - tag removal ==
  
**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.
+
Remove Historical_gene from ?Transgene
  
@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.
+
'''Done'''

Latest revision as of 16:47, 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

Done

#Address hash - Cecilia

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

#Address
Institution UNIQUE Text

Done

GO_annotation class - Kimberly

Introduction of this new class to capture Gene::GO associateions and additional meta data associated with a curation event.

Done

Feature unused tag removal - M.A.

Can we remove Annotation and Defined_by_author

Done

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


Done

Unique -> UNIQUE housekeeping change

Corresponding_transgene Unique ?Transgene XREF Corresponding_variation

also

Add UNIQUE to the second text value as it should be a single pair of values and not 1 to many which could be stored (and a couple were there in error)

?Variation
   Type_of_mutation Substitution UNIQUE Text Text #Evidence // wild type and mutant sequence
   Type_of_mutation Substitution UNIQUE Text UNIQUE Text #Evidence // wild type and mutant sequence


Done

Expr_patter Microarray_results connection - 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

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

Done

?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.

Done

?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.

Done

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.

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

Done

Transgene - tag removal

Remove Historical_gene from ?Transgene

Done