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From: Chris Mungall <cmungall@us...>  20060420 23:00:32

Update of /cvsroot/gmod/schema/chado/modules/cv/doc In directory sc8prcvs1.sourceforge.net:/tmp/cvsserv13830/doc Modified Files: cvdoc.tex Log Message: Index: cvdoc.tex =================================================================== RCS file: /cvsroot/gmod/schema/chado/modules/cv/doc/cvdoc.tex,v retrieving revision 1.1 retrieving revision 1.2 diff C2 d r1.1 r1.2 *** cvdoc.tex 19 Apr 2006 17:45:09 0000 1.1  cvdoc.tex 20 Apr 2006 23:00:24 0000 1.2 *************** *** 39,43 **** are allowed to form cycles. ! \section{Transitive Closure}  39,157  are allowed to form cycles. ! \subsection{Transitive Closure} ! ! \subsubsection{Rules} ! ! The cvtermpath is for calculating the reflexive transitive closure of ! a relationship, and any derived relationships ! ! Normal (direct) relationships are stored in the cvterm_relationship ! table. A entry in this table represents a cvterm_relationship S over ! some relation R. ! ! \begin{verbatim} ! S = Subj R Obj ! \end{verbatim} ! ! For example: ! ! {\tt S = "cardioblast" develops_from "mesodermal cell"} ! ! The relation \isa represents a special kind of relation  ! subsumption, or inheritance. ! ! If X \isa Y, then it follows that all of Y's cvterm\_relationship ! statements are inherited by X ! ! \begin{verbatim} ! [Rule 1] ! If X is_a Y ! and Y R Z ! then X R(inh) Z ! \begin{verbatim} ! ! For example ! ! \begin{verbatim} ! "cilium axoneme" is_a "axoneme" ! "axoneme" part_of "cell projection" ! THEREFORE: ! "cilium axoneme" part_of(inh) "cell projection" ! \end{verbatim} ! ! Here we use T(inh) to represent an inherited relationship. ! ! \subsubsection{Populating cvterm\_path} ! ! The cvtermpath table stores the reflexive transitive closure of a ! relationship, taking into account subsumption/inheritance. The number ! of intermediate relationships is represented in the 'distance' column ! of the table. ! ! Here we use T(path) to represent the 'path' or closure of a ! relationship. Every T(path) is stored in cvtermpath. We use the same ! cvterm for T, the fact that it is a path is implicit. ! ! We use these rules: ! ! Reflexive relationships: ! ! for all relations T, ! X T(path) X ! ! In this case the distance=0 ! ! Direct relationships: ! ! these are also included in the cvtermpath table, distance=1 ! ! If X T Y ! Then X T(path) Y ! ! Transitive relationships: ! ! these have distance > 1; these also make use of inheritance rule, ! [Rule1], which gives us T(inh) ! ! If X T(inh) Y ! and Y T(path) Z ! Then X T(path) Z ! ! Note that this rule is recursive. ! ! These rules should be used for populating cvtermpath. Attempting to ! calculate a more general closure where all relations are ! treated equally or ignored will produce combinatorial explosions over ! certain ontologies (eg flybase anatomy ontology) ! ! What does this mean in practice? ! ! For a typical database, which may only have relations is_a, ! part_of and develops_from, we will end up with 3 sets of paths. ! ! The "is_a" closure, is_a(path) will include paths over ! cvterm_relationships that look like this: ! ! a is_a b is_a c is_a d is_a e ! ! The "part_of" closure, part_of(path) will include paths over ! cvterm_relationships that look like this: ! ! a is_a b part_of c part_of d is_a e part_of f ! ! The "develops_from" closure, develops_from(path) will include paths over ! cvterm_relationships that look like this: ! ! a develops_from b develops_from c is_a d is_a e develops_from f ! ! It may be tempting to mix different nonis_a relationships in the same ! path, but this should NEVER be done  there will be an unacceptable ! combinatorial explosion in many cases. Besides, there is no use for ! such a cvtermpath; it is meaningless. ! ! Note that for amigolike query behaviour, it is necessary only to query ! cvtermpath ignoring cvtermpath.type_id (these are obtained by querying ! cvterm_relationship) ! 
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