User:Clements/Chado Module CV

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Table: cv

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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.

cv columns
FK Name Type Description
cv_id serial PRIMARY KEY
name character varying(255) UNIQUE

NOT NULL
The name of the ontology. This corresponds to the obo-format -namespace-. cv names uniquely identify the cv. In OBO file format, the cv.name is known as the namespace.

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

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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.

cvterm columns
FK Name Type Description
cvterm_id serial PRIMARY KEY
cv cv_id integer UNIQUE#1

NOT NULL
The cv or ontology or namespace to which this cvterm belongs.

name character varying(1024) UNIQUE#1

NOT NULL
A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.

definition text A human-readable text

definition.

dbxref dbxref_id integer UNIQUE

NOT NULL
Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref.

is_obsolete integer UNIQUE#1

NOT NULL
Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.

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:

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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

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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".

cvterm_relationship columns
FK Name Type Description
cvterm_relationship_id serial PRIMARY KEY
cvterm type_id integer UNIQUE#1

NOT NULL
The nature of the relationship between subject and object. Note that relations are also housed in the cvterm table, typically from the OBO relationship ontology, although other relationship types are allowed.

cvterm subject_id integer UNIQUE#1

NOT NULL
The subject of the subj-predicate-obj sentence. The cvterm_relationship is about the subject. In a graph, this typically corresponds to the child node.

cvterm object_id integer UNIQUE#1

NOT NULL
The object of the subj-predicate-obj sentence. The cvterm_relationship refers to the object. In a graph, this typically corresponds to the parent node.

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

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Table: cvtermpath
Module: CV

The reflexive transitive closure of the cvterm_relationship relation.

cvtermpath columns
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

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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".

cvtermsynonym columns
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

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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.

cvterm_dbxref columns
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

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Table: cvtermprop
Module: CV

Additional extensible properties can be attached to a cvterm using this table. Corresponds to -AnnotationProperty- in W3C OWL format.

cvtermprop columns
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
The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.

value text UNIQUE#1

NOT NULL
DEFAULT ''::text
The value of the property, represented as text. Numeric values are converted to their text representation.

rank integer UNIQUE#1

NOT NULL
Property-Value ordering. Any cvterm can have multiple values for any particular property type - these are ordered in a list using rank, counting from zero. For properties that are single-valued rather than multi-valued, the default 0 value should be used.

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.