Chado Schema Documentation HOWTO
The Chado schema documentation on this wiki is a mixture of generated content and material directly entered by GMOD users into this wiki. The generated part of the documentation consists of the table definitions that are included on the Chado module pages and on the Chado Tables page, listing all the tables in Chado.
Contents
Module and Table Documentation
All of the table descriptions on Chado module pages and the Chado Tables page are generated every time their is a new release of Chado. The column and table details, including comments, come from the PostgreSQL data dictionary.
Showing a Table Description
To show the information about any table, use the Chado Table Template for that table:
{{ChadoTable_tablename}}
For example,
{{ChadoTable_cvterm}}
will show the table description for cvterm:
<protect>
Table: | cvterm |
Module: | CV |
A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.
FK | Name | Type | Description |
---|---|---|---|
cvterm_id | serial | PRIMARY KEY | |
cv | cv_id | integer | UNIQUE#1 NOT NULL |
name | character varying(1024) | UNIQUE#1 NOT NULL | |
definition | text | A human-readable text
definition. | |
dbxref | dbxref_id | integer | UNIQUE NOT NULL |
is_obsolete | integer | UNIQUE#1 NOT NULL | |
is_relationshiptype | integer | NOT NULL Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there. |
Tables referencing cvterm via foreign key constraints:
- acquisition_relationship
- acquisitionprop
- analysisfeatureprop
- analysisprop
- arraydesign
- arraydesignprop
- assayprop
- biomaterial_relationship
- biomaterial_treatment
- biomaterialprop
- cell_line_cvterm
- cell_line_cvtermprop
- cell_line_relationship
- cell_lineprop
- contact
- contact_relationship
- control
- cvterm_dbxref
- cvterm_relationship
- cvtermpath
- cvtermprop
- cvtermsynonym
- dbxrefprop
- element
- element_relationship
- elementresult_relationship
- environment_cvterm
- expression_cvterm
- expression_cvtermprop
- expressionprop
- feature
- feature_cvterm
- feature_cvtermprop
- feature_expressionprop
- feature_genotype
- feature_pubprop
- feature_relationship
- feature_relationshipprop
- featuremap
- featureprop
- library
- library_cvterm
- libraryprop
- nd_experiment
- nd_experiment_stock
- nd_experiment_stockprop
- nd_experimentprop
- nd_geolocationprop
- nd_protocol_reagent
- nd_protocolprop
- nd_reagent
- nd_reagent_relationship
- nd_reagentprop
- organismprop
- phendesc
- phenotype
- phenotype_comparison_cvterm
- phenotype_cvterm
- phenstatement
- phylonode
- phylonode_relationship
- phylonodeprop
- phylotree
- project_relationship
- projectprop
- protocol
- protocolparam
- pub
- pub_relationship
- pubprop
- quantification_relationship
- quantificationprop
- stock
- stock_cvterm
- stock_dbxrefprop
- stock_relationship
- stock_relationship_cvterm
- stockcollection
- stockcollectionprop
- stockprop
- studydesignprop
- studyfactor
- studyprop
- studyprop_feature
- synonym
- treatment
</protect>
Linking to Module Documentation
To link to a module on a wiki page use:
{{ChadoModuleLink|Module Name|text to show}}
For example:
{{ChadoModuleLink|Publication|pub module}}
Which is shown as:
Linking to Table Documentation
To link to a specific table's description on a wiki page, use:
{{ChadoTableLink|table_name}}
For example:
{{ChadoTableLink|feature}}
will result in:
Note that this links to the table description on the Chado Tables page, not to the description on the table's module page.
A Chado Table Template itself is a perplexing nest of smaller and smaller templates. This means it's hard to figure out how the wiki decides how it decides what to show. However, all this complexity doesn't really matter as it is all auto-generated.
The up side of this complexity is it is easy to change the appearance of all Chado tables in the wiki. All you do is modify the appropriate template.