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User:Clements/Chado Module CV
Contents
Table: cv
<protect>
Table: | cv |
Module: | CV |
A controlled vocabulary or ontology. A cv is composed of cvterms (AKA terms, classes, types, universals - relations and properties are also stored in cvterm) and the relationships between them.
FK | Name | Type | Description |
---|---|---|---|
cv_id | serial | PRIMARY KEY | |
name | character varying(255) | UNIQUE NOT NULL | |
definition | text | A text description of the criteria for
membership of this ontology. |
Tables referencing cv via foreign key constraints:
</protect>
cv Aditional Comments
Add your comments here and they will be integrated into the Template:ChadoSchemaDocHowLink as part of the next Chado release.
Table: 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>
cvterm Aditional Comments
Add your comments here and they will be integrated into the schema documentation as part of the next Chado release.
Table: cvterm_relationship
<protect>
Table: | cvterm_relationship |
Module: | CV |
A relationship linking two cvterms. Each cvterm_relationship constitutes an edge in the graph defined by the collection of cvterms and cvterm_relationships. The meaning of the cvterm_relationship depends on the definition of the cvterm R refered to by type_id. However, in general the definitions are such that the statement "all SUBJs REL some OBJ" is true. The cvterm_relationship statement is about the subject, not the object. For example "insect wing part_of thorax".
FK | Name | Type | Description |
---|---|---|---|
cvterm_relationship_id | serial | PRIMARY KEY | |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
cvterm | subject_id | integer | UNIQUE#1 NOT NULL |
cvterm | object_id | integer | UNIQUE#1 NOT NULL |
Tables referencing cvterm_relationship via foreign key constraints:
- None.</protect>
cvterm_relationship Aditional Comments
Add your comments here and they will be integrated into the Template:ChadoSchemaDocHowLink as part of the next Chado release.
Table: cvtermpath
<protect>
Table: | cvtermpath |
Module: | CV |
The reflexive transitive closure of the cvterm_relationship relation.
FK | Name | Type | Description |
---|---|---|---|
cvtermpath_id | serial | PRIMARY KEY | |
cvterm | type_id | integer | UNIQUE#1 The relationship type that this is a closure over. If null, then this is a closure over ALL relationship types. If non-null, then this references a relationship cvterm - note that the closure will apply to both this relationship AND the OBO_REL:is_a (subclass) relationship. |
cvterm | subject_id | integer | UNIQUE#1 NOT NULL |
cvterm | object_id | integer | UNIQUE#1 NOT NULL |
cv | cv_id | integer | NOT NULL Closures will mostly be within one cv. If the closure of a relationship traverses a cv, then this refers to the cv of the object_id cvterm. |
pathdistance | integer | UNIQUE#1 The number of steps required to get from the subject cvterm to the object cvterm, counting from zero (reflexive relationship). |
Tables referencing cvtermpath via foreign key constraints:
- None.</protect>
cvtermpath Aditional Comments
Add your comments here and they will be integrated into the Template:ChadoSchemaDocHowLink as part of the next Chado release.
Table: cvtermsynonym
<protect>
Table: | cvtermsynonym |
Module: | CV |
A cvterm actually represents a distinct class or concept. A concept can be refered to by different phrases or names. In addition to the primary name (cvterm.name) there can be a number of alternative aliases or synonyms. For example, "T cell" as a synonym for "T lymphocyte".
FK | Name | Type | Description |
---|---|---|---|
cvtermsynonym_id | serial | PRIMARY KEY | |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL |
synonym | character varying(1024) | UNIQUE#1 NOT NULL | |
cvterm | type_id | integer | A synonym can be exact,
narrower, or broader than. |
Tables referencing cvtermsynonym via foreign key constraints:
- None.</protect>
cvtermsynonym Aditional Comments
Add your comments here and they will be integrated into the Template:ChadoSchemaDocHowLink as part of the next Chado release.
Table: cvterm_dbxref
<protect>
Table: | cvterm_dbxref |
Module: | CV |
In addition to the primary identifier (cvterm.dbxref_id) a cvterm can have zero or more secondary identifiers/dbxrefs, which may refer to records in external databases. The exact semantics of cvterm_dbxref are not fixed. For example: the dbxref could be a pubmed ID that is pertinent to the cvterm, or it could be an equivalent or similar term in another ontology. For example, GO cvterms are typically linked to InterPro IDs, even though the nature of the relationship between them is largely one of statistical association. The dbxref may be have data records attached in the same database instance, or it could be a "hanging" dbxref pointing to some external database. NOTE: If the desired objective is to link two cvterms together, and the nature of the relation is known and holds for all instances of the subject cvterm then consider instead using cvterm_relationship together with a well-defined relation.
FK | Name | Type | Description |
---|---|---|---|
cvterm_dbxref_id | serial | PRIMARY KEY | |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL |
dbxref | dbxref_id | integer | UNIQUE#1 NOT NULL |
is_for_definition | integer | NOT NULL A cvterm.definition should be supported by one or more references. If this column is true, the dbxref is not for a term in an external database - it is a dbxref for provenance information for the definition. |
Tables referencing cvterm_dbxref via foreign key constraints:
- None.</protect>
cvterm_dbxref Aditional Comments
Add your comments here and they will be integrated into the Template:ChadoSchemaDocHowLink as part of the next Chado release.
Table: cvtermprop
<protect>
Table: | cvtermprop |
Module: | CV |
Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.
FK | Name | Type | Description |
---|---|---|---|
cvtermprop_id | serial | PRIMARY KEY | |
cvterm | cvterm_id | integer | UNIQUE#1 NOT NULL |
cvterm | type_id | integer | UNIQUE#1 NOT NULL |
value | text | UNIQUE#1 NOT NULL | |
rank | integer | UNIQUE#1 NOT NULL |
Tables referencing cvtermprop via foreign key constraints:
- None.</protect>
cvtermprop Aditional Comments
Add your comments here and they will be integrated into the Template:ChadoSchemaDocHowLink as part of the next Chado release.