Difference between revisions of "Chado Phenotype Module"

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m (New page: ==Introduction== ==Tables== ===phenstatement=== Phenotypes are things like ”larval lethal”. Phenstatements are things like ”dpp[1] is recessive larval lethal”. So essentially...)
 
m (→‎Introduction)
 
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=Introduction=
  
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==Introduction==
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{{NeedsEditing}}
  
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Chris Mungall's 2006 [[Media:02-chado-for-nescent-2006.pdf|Chado for evolutionary science]] presentation discusses the Phenotype module.
  
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==Tables==
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=Tables=
  
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== Table: feature_phenotype ==
  
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===phenstatement===
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{| border="1" cellpadding="3"
 +
|+ feature_phenotype Structure
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|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| feature_phenotype_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
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[[Chado_Tables#Table:_feature| feature]]
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| feature_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
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|- class="tr0"
 +
|
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[[Chado_Tables#Table:_phenotype| phenotype]]
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| phenotype_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
  
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Phenotypes are things like ”larval lethal”. Phenstatements are things like ”dpp[1] is recessive
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----
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larval lethal”. So essentially phenstatement is a linking table expressing the relationship between
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genotype, environment, and phenotype.
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  Table 4.39: phenstatement
 
  
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Column  DatatypeDescription
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== Table: phenotype ==
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phenstatement id integer
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−
genotype idinteger
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−
environment idinteger
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−
phenotype id  integer
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−
type id integer
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pub id  integer
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A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.
  
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===phendesc===
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{| border="1" cellpadding="3"
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|+ phenotype Structure
 +
|-
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! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| phenotype_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
| uniquename
 +
| text
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| '' UNIQUE NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
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| observable_id
 +
| integer
 +
| '' ''<br /><br />The entity: e.g. anatomy_part, biological_process.
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|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| attr_id
 +
| integer
 +
| '' ''<br /><br />Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.
 +
|- class="tr0"
 +
|
 +
| value
 +
| text
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| '' ''<br /><br />Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.
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|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| cvalue_id
 +
| integer
 +
| '' ''<br /><br />Phenotype attribute value (state).
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|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
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| assay_id
 +
| integer
 +
| '' ''<br /><br />Evidence type
 +
|}
  
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a summary of a set of phenotypic statements for any one gcontext made in any one publication
+
Tables referencing this one via Foreign Key Constraints:
  
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* [[Chado_Tables#Table:_feature_phenotype| feature_phenotype]]
  
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Table 4.40: phendesc
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* [[Chado_Tables#Table:_phenotype_comparison| phenotype_comparison]]
  
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ColumnDatatype Description
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* [[Chado_Tables#Table:_phenotype_cvterm| phenotype_cvterm]]
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phendesc id integer
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genotype id integer
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−
environment id integer
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−
description text
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−
pub idinteger
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* [[Chado_Tables#Table:_phenstatement| phenstatement]]
  
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===phenotype_comparison===
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* [[Chado_Tables#Table:_wwwuser_phenotype| wwwuser_phenotype]]
  
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comparison of phenotypes eg, genotype1/environment1/phenotype1 ”non-suppressible” wrt geno-
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----
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type2/environment2/phenotype2
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Table 4.41: phenotype comparison
 
  
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ColumnDatatype Description
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== Table: phenotype_cvterm ==
−
phenotype comparison id integer
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−
genotype1 idinteger
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−
environment1 idinteger
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−
genotype2 idinteger
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−
environment2 idinteger
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−
phenotype1 id  integer
+
−
phenotype2 id  integer
+
−
type id  integer
+
−
pub idinteger
+
  
 +
{| border="1" cellpadding="3"
 +
|+ phenotype_cvterm Structure
 +
|-
 +
! F-Key
 +
! Name
 +
! Type
 +
! Description
 +
|- class="tr0"
 +
|
 +
| phenotype_cvterm_id
 +
| serial
 +
| '' PRIMARY KEY ''
 +
|- class="tr1"
 +
|
 +
[[Chado_Tables#Table:_phenotype| phenotype]]
 +
| phenotype_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|- class="tr0"
 +
|
 +
[[Chado_Tables#Table:_cvterm| cvterm]]
 +
| cvterm_id
 +
| integer
 +
| '' UNIQUE#1 NOT NULL ''
 +
|}
  
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===phenotype===
+
----
  
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a phenotypic statement, or a single atomic phenotypic observation a controlled sentence describing
 
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observable effect of non-wt function – e.g. Obs=eye, attribute=color, cvalue=red
 
−
 
−
 
−
Table 4.42: phenotype
 
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Column  Datatype Description
 
−
phenotype id  integer
 
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uniquename text
 
−
observable id integer  The entity: e.g. anatomy part, biological process
 
−
attr id integer  Phenotypic attribute (quality, property, attribute,
 
−
character) - drawn from PATO
 
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valuetext  value of attribute - unconstrained free text. Used
 
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only if cvalue id is not appropriate
 
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cvalue id  integer  Phenotype attribute value (state)
 
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assay idinteger  evidence type
 
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−
 
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===phenotype_cvterm===
 
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NULL
 
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  Table 4.43: phenotype cvterm
 
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  Column  Datatype Description
 
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  phenotype cvterm id integer
 
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  phenotype id  integer
 
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  cvterm id  integer
 
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−
 
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===feature_phenotype===
 
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NULL
 
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Table 4.44: feature phenotype
 
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  ColumnDatatype Description
 
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  feature phenotype id integer
 
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  feature id  integer
 
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  phenotype idinteger
 
  
 
[[Category:Chado]]
 
[[Category:Chado]]
−
[[Category:To Do]]
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[[Category:Phenotypes]]

Latest revision as of 21:11, 6 February 2008

Introduction

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Chris Mungall's 2006 Chado for evolutionary science presentation discusses the Phenotype module.

Tables

Table: feature_phenotype

feature_phenotype Structure
F-Key Name Type Description
feature_phenotype_id serial PRIMARY KEY

feature

feature_id integer UNIQUE#1 NOT NULL

phenotype

phenotype_id integer UNIQUE#1 NOT NULL


Table: phenotype

A phenotypic statement, or a single atomic phenotypic observation, is a controlled sentence describing observable effects of non-wild type function. E.g. Obs=eye, attribute=color, cvalue=red.

phenotype Structure
F-Key Name Type Description
phenotype_id serial PRIMARY KEY
uniquename text UNIQUE NOT NULL

cvterm

observable_id integer

The entity: e.g. anatomy_part, biological_process.

cvterm

attr_id integer

Phenotypic attribute (quality, property, attribute, character) - drawn from PATO.
value text

Value of attribute - unconstrained free text. Used only if cvalue_id is not appropriate.

cvterm

cvalue_id integer

Phenotype attribute value (state).

cvterm

assay_id integer

Evidence type

Tables referencing this one via Foreign Key Constraints:


Table: phenotype_cvterm

phenotype_cvterm Structure
F-Key Name Type Description
phenotype_cvterm_id serial PRIMARY KEY

phenotype

phenotype_id integer UNIQUE#1 NOT NULL

cvterm

cvterm_id integer UNIQUE#1 NOT NULL
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