[Gmod-schema-cmts] schema/chado/modules/cv cv.sql,1.19.2.1,1.19.2.2

[Chris M. <cmu...@us...>]

Update of /cvsroot/gmod/schema/chado/modules/cv
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14652

Modified Files:
      Tag: bdgp-dev
	cv.sql 
Log Message:
2004-11-30  -   added comments (COMMENT ON syntax)
            -   changed unique constraint to include is_obsolete
            -   removed INSERTs - now taken care of by XSL loader
            -   dbxref_id not nullable, and is also a unique key



Index: cv.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/cv/cv.sql,v
retrieving revision 1.19.2.1
retrieving revision 1.19.2.2
diff -C2 -d -r1.19.2.1 -r1.19.2.2
*** cv.sql	12 Mar 2004 16:33:42 -0000	1.19.2.1
--- cv.sql	30 Nov 2004 21:56:32 -0000	1.19.2.2
***************
*** 35,55 ****
         name varchar(255) not null,
         definition text,
!        dbxref_id int,
         foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null,
         is_obsolete int not null default 0,
         is_relationshiptype int not null default 0,
         
!        unique(name, cv_id)
  );
  create index cvterm_idx1 on cvterm (cv_id);
- -- the primary dbxref for this term.  Other dbxrefs may be cvterm_dbxref
- -- The unique key on termname, cv_id ensures that all terms are 
- -- unique within a given cv
  
! -- all relationship types are extensible, and have user-defined semantics.
! -- the exception is the 'is_a' (subtyping or subclassing) relationship,
! -- which MUST be present, and has fixed semantics)
! INSERT INTO cv (name) VALUES ('__axiomatic');
! INSERT INTO cvterm (name, is_relationshiptype, cv_id) SELECT 'is_a', 1, cv_id FROM cv WHERE name = '__internal';
  
  -- ================================================
--- 35,83 ----
         name varchar(255) not null,
         definition text,
!        dbxref_id int not null,
         foreign key (dbxref_id) references dbxref (dbxref_id) on delete set null,
         is_obsolete int not null default 0,
         is_relationshiptype int not null default 0,
         
!        constraint cvterm_c1 unique (dbxref_id),
!        constraint cvterm_c2 unique (name, cv_id, is_obsolete)
  );
  create index cvterm_idx1 on cvterm (cv_id);
  
! COMMENT ON TABLE cvterm IS
!  'A term, class or concept within an ontology or controlled vocabulary.
!   Also used for relationship types. A cvterm can also be thought of
!   as a node in a graph';
! COMMENT ON COLUMN cvterm.cv_id IS
!  'The cv/ontology/namespace to which this cvterm belongs';
! COMMENT ON COLUMN cvterm.name IS
!  'A concise human-readable name describing the meaning of the cvterm';
! COMMENT ON COLUMN cvterm.definition IS
!  'A human-readable text definition';
! COMMENT ON COLUMN cvterm.dbxref_id IS
!  'Primary dbxref - The unique global OBO identifier for this cvterm.
!   Note that a cvterm may  have multiple secondary dbxrefs - see also
!   table: cvterm_dbxref';
! COMMENT ON COLUMN cvterm.is_obsolete IS
!  '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';
! COMMENT ON COLUMN cvterm.is_relationshiptype IS
!  'Boolean 0=false,1=true
!   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/concept or
!   a relationship type';
! COMMENT ON INDEX cvterm_c1 IS 
!  'the OBO identifier is globally unique';
! COMMENT ON INDEX cvterm_c2 IS 
!  'a name can mean different things in different contexts;
!   for example "chromosome" in SO and GO. A name should be unique
!   within an ontology/cv. A name may exist twice in a cv, in both
!   obsolete and non-obsolete forms - these will be for different
!   cvterms with different OBO identifiers; so GO documentation for
!   more details on obsoletion';
! 
! 
  
  -- ================================================
***************
*** 73,76 ****
--- 101,109 ----
  create index cvterm_relationship_idx3 on cvterm_relationship (object_id);
  
+ COMMENT ON TABLE cvterm_relationship IS
+  'A relationship linking two cvterms. A relationship can be thought of
+   as an edge in a graph, or as a natural language statement about
+   two cvterms. The statement is of the form SUBJECT PREDICATE OBJECT;
+   for example "wing part_of body"';
  
  -- ================================================