slib.graph.io.loader.bio.obo

Class GraphLoader_OBO_1_2

java.lang.Object

slib.graph.io.loader.bio.obo.GraphLoader_OBO_1_2

All Implemented Interfaces:

GraphLoader

public class GraphLoader_OBO_1_2
extends Object
implements GraphLoader

OBO specification
Compatibility with other format-version than 1.2 is not supported.
The mapping consider

• [Term] as RDF/OWL class mapping to build vertices
• [Typedef] as relationships definitions between nodes
• "is_a" as the only predefined relationType
• [instance] are not loaded

Meta informations:

• format-version : Only required argument of the specification expect 1.2 throw non warning exception () if 1.2 version is not detected
• default-namespace: the graph URI

[Term]
Each Term are loaded as a specific vertex in the graph.
A Term is then mapped as a of equals to V_TYPE_CLASS.
Note that obsolete Terms/Typedefs are excluded during graph construction (see below is_obsolete).

Flag considered :

• id: Loaded as the URI of the current [Term/Class/Vertex] specification
• is a: Loaded as an of IS_A with currently defined Vertex as source and specified as target Vertex
• relationships: Loaded as an of specified with source as current Vertex and target specified by the precise The EdgeType have to be defined by a [TypeDef] specification to be taken into account.
• is_obsolete: Specifying the validity of the current Term specification
• intersection_of/XREF...: These information are not loaded.

[Typedef] as
Every Typedef definition is loaded as an .
This definition is used to specify the type authorized for specification

• id: the URI of the
• is_transitive: Specifying if the relationship have to be considered as transitive
• inverse_of Used to defined the URI of the to consider as the inverse of the current specified EdgeType e.g if an edge type X is defined as the inverse of Y, a relationship of type X defined between A and B will lead to the creation of:
  • an edge of type X betwween v(A) -> v(B)
  • an edge of type Y betwween v(B) -> v(A)
• is_symmetric Used to defined an EdgeType as the inverse of itself e.g if an edge type X is transitive, a relationship defined as an edge of type X betwween v(A) -> v(B) is defined will imply the creation of an edge of type X as v(B) -> v(A)
• is_obsolete: Specifying the validity of the current Typedef specification
• transitive_over/XREF...: These information are not loaded.

TODO : load instances

Author:

Sébastien Harispe

Constructor Summary

Constructors

Constructor and Description
GraphLoader_OBO_1_2()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	isAllow_all_gafVersion()
void	populate(GDataConf conf, G g) Populate an existing graph considering the given configuration
void	setAllow_all_gafVersion(boolean allow_all_gafVersion)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GraphLoader_OBO_1_2

public GraphLoader_OBO_1_2()

Method Detail

populate

public void populate(GDataConf conf,
            G g)
              throws SLIB_Exception

Description copied from interface: GraphLoader

Populate an existing graph considering the given configuration

Specified by:

populate in interface GraphLoader

Parameters:

conf - a GraphConf object specifying the configuration the loader must takes into account

Throws:

SLIB_Exception

isAllow_all_gafVersion

public boolean isAllow_all_gafVersion()

Returns:

true if all GAF version are supported.

setAllow_all_gafVersion

public void setAllow_all_gafVersion(boolean allow_all_gafVersion)

Parameters:

allow_all_gafVersion -