[Gmod-schema-cmts] schema/chado/modules/cv/doc cv-advanced-usage.tex,NONE,1.1 cv-doc.tex,NONE,1.1

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 454-5900

Update of /cvsroot/gmod/schema/chado/modules/cv/doc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26098/doc

Added Files:
	cv-advanced-usage.tex cv-doc.tex 
Log Message:
new latex docs for cv module

--- NEW FILE: cv-advanced-usage.tex ---
\section{Chado and advanced ontology features}

This section describes advanced usage of the \cv module for use with
OWL-DL \cite{OWL}, advanced Obo format 1.2 \cite{OboFormat} features
or elements from other ontology formalisms.

If you aren't sure what this means, you probably don't need to read
this section yet.

\subsection{Background}

See the document on \cite{ConvertingOboToOWL}

\subsection{Logical definitions}

In a normal ontology DAG representation in chado, the
cvterm_relationship rows represent relationships between terms, or
more formally, {\em necessary conditions}. A logical definition must
have both {\em necessary and sufficient conditions}. A logical
definition often consists of a {\em generic term} (aka genus) and one
or more {\em discriminating characteristics} (aka differentiae). The
discriminating characteristics are typically relationships 

For example, the logical definition of {\tt larval locomotory
behaviour} would be a {\tt locomotory behaviour} (genus) which {\em
hasStage} {\tt larval stage} (where hasStage could be drawn from an
ontology of relations, and larval stage may come from an insect
developmental stage ontology). These constitute both necessary and
sufficient conditions: the conditions are necessary in that all
instances of larval locomotory behavior are necessarily locomotory
behaviors and are necessarily manifested at the larval stage. We could
represent this using a normal DAG. However, because this is a
definition it also constitutes sufficient conditions, in that any
instance of locomotory behavior which manifests at the larval stage is
by definition a larval locomotory behavior.

In an ontology formalism like OWL-DL or Obo-1.2, genus-differentiae
are represented using set-intersections.

Here is the Obo 1.2 representation:

\begin{verbatim}
[Term]
id: GO:0008345
name: larval locomotory behavior
namespace: biological_process
is_a: GO:0007626                      ! locomotory behavior
is_a: GO:0030537                      ! larval behavior
intersection_of: GO:0007626           ! locomotory behavior
intersection_of: during FBdv:00005336 ! larval stage
\end{verbatim}

Here is the equivalent in OWL (note: RDF-XML syntax is very verbose!):

\begin{verbatim}
  <owl:Class rdf:ID="GO_0008345">
    <rdfs:label xml:lang="en">larval locomotory behavior</rdfs:label>
    <rdfs:subClassOf rdf:resource="#GO_0007626"/>
    <rdfs:subClassOf rdf:resource="#GO_0030537"/>
    <owl:equivalentClass>
      <owl:Class>
        <owl:intersectionOf rdf:parseType="Collection">
          <owl:Class rdf:about="#GO_0007626"/>
          <owl:Restriction>
            <owl:onProperty>
              <owl:ObjectProperty rdf:about="#during"/>
            </owl:onProperty>
            <owl:someValuesFrom rdf:resource="#FBdv_00005336"/>
          </owl:Restriction>
        </owl:intersectionOf>
      </owl:Class>
    </owl:equivalentClass>
  </owl:Class>
\end{verbatim}

When converting to chado we employ a more economical representation:

\begin{verbatim}
\end{verbatim}

If you wish to convert Obo-specified logical definitions to chadoxml
you will need go-perl v0.05 or higher (if you have a lower version,
the intersection\_of tags will simply be ignored). 

\subsubsection{How logical definitions are stored in Chado}

This involves no schema changes to the cv module. Each intersection\_of
goes in as a DAG arc of type internal:intersection\_of. The object_id
in the arc is either a term (for the genus) or an anonymous term
representing a restriction (the differentium). the restriction has a
relationship of some type to another term.

For example, for "larval locomotory behavior" we would normally just have:

\begin{verbatim}
LLB is_a LocomotoryBehavior
LLB is_a LarvalBehavior
\begin{verbatim}

If we load a logical definition for this term (see
go-dev/go-perl/t/data/llm/obo), like this:

\begin{verbatim}
[Term]
id: GO:0008345
name: larval locomotory behavior
namespace: biological_process
is_a: GO:0007626                      ! locomotory behavior
is_a: GO:0030537                      ! larval behavior
intersection_of: GO:0007626           ! locomotory behavior
intersection_of: during FBdv:00005336 ! larval stage
\end{verbatim}

Then the intersection\_ofs get stored using the basic DAG tables as:

\begin{table}[htb]
\center
{ \small
\begin{tabular}{l l l}
Subject & Relation & Object \\ \hline
LLB & intersection\_of & LocomotoryBehavior
LLB & intersection\_of & anon:xxx
anon:xxx & during & FBv:00005336

\label{tab:intersections-in-Chado}
\end{tabular}
}
\caption{Logical definition stored ib cvterm\_relationship table}
\label{tab:tab-esc-str}
\end{table}

\subsubsection{Logical Definition Views}

Two views: cvterm\_genus and cvterm\_differentium views are in
chado/modules/cv/views 

\subsubsection{Example use case: Phenotypes}

The idea here is that queries for composed term "syndactyly" should
automatically return the same results as a boolean query for
"fusion"+inheres_in="finger" regardless of whether the annotation is
to the composed term or is a composed annotation (provided we put the
logical definition of syndactyly in the database)

\subsubsection{Example use case: feature types}

The Sequence Ontology has some logical definitions - you will need to
load the file {\tt so-xp.obo}

\subsubsection{Example use case: GO}

See
http://www.fruitfly.org/~cjm/obol

\subsubsection{Example use case: Drawing DAGs}

Currently the DAGs of many OBO ontologies are highly tangled; see:
http://www.fruitfly.org/~cjm/obol/doc/go-complexity.html

If all terms have logical definitions, then there is only one 'true'
(genus) \isa parent. This enables us to disentangle the DAGs and draw
distinct hierarchies. For example, the GO term {\em cysteine
biosynthesis} could be drawn as two distinct hierarchies - one process
and one chemical

--- NEW FILE: cv-doc.tex ---
\chapter{The cv Module: Ontologies}

\section{Introduction}

We have seen how the sequence module makes extensive use of terms
taken from various ontologies such as SO and the OBO Relations
Ontology, using the type\_id foreign key column. In addition, features
can be annotated using ontologies such as GO using the feature\_cvterm
linking table. These terms are modelled using the cv module, the core
of which is the cvterm table.

An ontology, terminology or cv (controlled vocabulary) , is a
collection of terms (here equivalent to what are more typically called
classes, types, categories or kinds in the ontology literature[REF])
in a particular domain of interest. Examples include "gene" (from SO),
"transcription factor activity" (from GO molecular function) and
"lymphocyte" (from OBO-Cell).  The chado cv module is based on the GO
Database schema, described here[14].  Terms are stored in the cvterm
table, and relationships between terms are stored in the
cvterm\_relationship table. This table follows an analogous structure
to the feature\_relationship table, in that it has columns subject\_id,
object\_id and type\_id. Here, all three of these foreign keys refer to
rows in the cvterm table.

A detailed treatment of relationship types in biological ontologies
can be found here[13]. Of particular interest to Chado is the is\_a
relation, which specifies a sub- typing relationship between two terms
or classes. Recall that tables in the sequence module frequently (such
as the feature table) defined a type\_id foreign key column to indicate
the specific type or class of entity for each row in that table. The
combination of the type\_id column and the is\_a relationship gives
Chado a data sub- classing system, beyond what is possible with
traditional SQL database semantics.

This is discussed further in a later section The collection of
cvterms and cvterm\_relationships can be considered to constitute
vertices and edges in a graph. This graph is typically acyclic (a
DAG), though it is not guaranteed to be as certain relationship types
are allowed to form cycles.

\section{Transitive Closure}