Search results for "dist:GOBO Graph"
GOBO::Graph
A collection of inter-related GOBO::Node objects. With a simple ontology these are typically GOBO::TermNode objects, although other graphs e.g. instance graphs are possible. This module deliberately omits any kind of graph traversal functionality. Th...
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 UTC
GOBO
OBJECT MODEL Basic overview * L<GOBO::Node> ** L<GOBO::ClassNode> *** L<GOBO::TermNode> *** L<GOBO::ClassExpression> ** L<GOBO::RelationNode> ** L<GOBO::InstanceNode> * L<GOBO::Statement> ** L<GOBO::LinkStatement> INPUT/OUTPUT Parsers * L<GOBO::Parse...
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 UTC
GOBO::Node
A unit in a graph. The Node class hierarchy: * L<GOBO::ClassNode> ** L<GOBO::TermNode> ** L<GOBO::ClassExpression> * L<GOBO::RelationNode> * L<GOBO::InstanceNode> With a simple ontology graph, the core units are TermNodes. POD ERRORS Hey! The above d...
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 UTC
GOBO::Gene
An GOBO::Node that corresponds to a specific SO:gene In GO, genes are the subject of GOBO::Annotation statements TBD This should really be in bioperl. Modeled as nodes as they can be elements in a graph. cf Chado...
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 UTC
GOBO::ClassNode
Formally, a class is a collection of instances. However, in many cases these are not instantiated in perl. ClassNodes can either be explicitly named (GOBO::TermNode) or they can be logical boolean expressions (GOBO::ClassExpression) +--- InstanceNode...
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 UTC
GOBO::Annotation
An GOBO::LinkStatement that has GOBO::Evidence attached Annotations need not be stored in the main ontology GOBO::Graph, but this is possible Use in GO In GO, annotations are also thought of as associations between genes and GOBO::TermNode objects. T...
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 UTC
GOBO::LinkStatement
A type of GOBO::Statement that connects two GOBO::Node objects via a GOBO::RelationNode object. Can also be thought of as an "edge" in an GOBO::Graph LiteralStatements inherit the roles GOBO::Attributed and GOBO::Identified (via GOBO::Statement). Thi...
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 UTC
GOBO::Phylo::PhyloTree
An GOBO::Graph in which each node has at most 1 parents, and each node is a GOBO::Phylo::PhyloNode...
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 UTC
GOBO::InferenceEngine
An GOBO::Graph is a collection of GOBO::Statements. These statements can be either 'asserted' or 'inferred'. Inferred statements are created by an Inference Engine. An InferenceEngine object provides two accessors, 'graph' for the source graph and 'i...
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 UTC
GOBO::Parsers::Parser
Base class for all parsers. Parsers take formats (e.g. GOBO::Parsers::OBOParser) and generate objects, typically some combination of GOBO::Node and GOBO::Statement objects...
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 UTC
GOBO::LiteralStatement
LiteralStatements are one of two basic types of GOBO::Statement. Whereas an GOBO::LinkStatement will connect a node to another node, a literal statement connects a node to a "literal", or Value which can be a a string, number of other kind of moose V...
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 UTC
GOBO::Parsers::OBOParser
An GOBO::Parsers::Parser that parses OBO Files. The goal is to be obof1.3 compliant: http://www.geneontology.org/GO.format.obo-1_3.shtml however, obof1.2 and obof1.0 are also supported Term stanzas These are converted to GOBO::TermNode objects Typede...
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 UTC
GOBO::Indexes::NodeIndex
Stores a collection of GOBO::Node objects, optimized for fast access. In general you should not need to use this directly - use GOBO::Graph instead, which includes different indexes for links, annotations etc TODO Currently there are 2 indexes, by no...
CMUNGALL/GOBO-0.03 - 17 Aug 2009 18:03:10 UTC