A.csr                   ~~data-name / kind ...
LLGOMFcp                concept probabilities for GO MF terms applied
                        to human LocusLink entries
OOC-class               Class "OOC" object-ontology complex
accessMat               matrix utilities for ontoTools.
buildGOgraph            build graphNEL corresponding to bioc GO
                        environment
compoundGraph-class     Class "compoundGraph" list representation of
                        multiple graph::graph objects
depthStruct             tools for manipulating depth concepts for
                        rooted DAGs
gomfAmat                sparse matrix representing accessibilities of
                        terms in GO MF graph; graph also documented
                        here
litOnto                 litOnto: graph illustrating the ontology
                        concept; litObj: matrix illustrating the
                        object-ontology mapping
namedSparse-class       Class "namedSparse" adds margin names to
                        sparse matrices
ontology-class          Class "ontology" wraps a rooted DAG with some
                        ontology metadata
ooMapLL2GOMFdemo        object-term mapping for human locuslink
                        entries and GO MF
otkvEnv2namedSparse     obtain sparse matrix representation of
                        key-value structures
rootedDAG-class         Class "rootedDAG"
semsim                  Compute semantic similarity measure for terms
                        in an object-ontology complex
toDot-methods           Methods for Function toDot in Package
                        'ontoTools' -- should be replaced by Rgraphviz
                        facilities soon
