Function	Description
accessMat	matrix utilities for ontoTools.
A.csr	~~data-name / kind ...
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
GDI_NCIThesaurus	Structures for working with formal nomenclatures
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
LLGOMFcp	resources saved for computation of concept probabilities for GO MF terms applied to human LocusLink entries
namedSparse-class	Class "namedSparse" adds margin names to sparse matrices
ontology-class	Class "ontology" wraps a rooted DAG with some ontology metadata
OOC-class	Class "OOC" object-ontology complex
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
SGDIvocab	Vocabulary for genomic data integration
STMA	Vocabulary from statistics theory and methods abstracts
taggedHierNomenclature-class	Class "taggedHierNomenclature" ~~~
toDot	Methods for Function toDot in Package 'ontoTools' -- should be replaced by Rgraphviz facilities soon