\BOOKMARK [1][-]{section.1}{Introduction}{}
\BOOKMARK [1][-]{section.2}{Basic structures}{}
\BOOKMARK [2][-]{subsection.2.1}{Rooted DAG}{section.2}
\BOOKMARK [2][-]{subsection.2.2}{ compoundGraph}{section.2}
\BOOKMARK [2][-]{subsection.2.3}{ ontology}{section.2}
\BOOKMARK [2][-]{subsection.2.4}{ Mapped key-value list}{section.2}
\BOOKMARK [2][-]{subsection.2.5}{ OOC: object-ontology complex }{section.2}
\BOOKMARK [1][-]{section.3}{Basic methods}{}
\BOOKMARK [2][-]{subsection.3.1}{Matrix conversion of DAG; namedSparse extension}{section.3}
\BOOKMARK [3][-]{subsubsection.3.1.1}{child2parent}{subsection.3.1}
\BOOKMARK [3][-]{subsubsection.3.1.2}{Accessibility}{subsection.3.1}
\BOOKMARK [2][-]{subsection.3.2}{Coverage matrix for an OOC}{section.3}
\BOOKMARK [2][-]{subsection.3.3}{Depth of terms in an ontology}{section.3}
\BOOKMARK [1][-]{section.4}{Applications to large data objects}{}
\BOOKMARK [2][-]{subsection.4.1}{Key-value list for LocusLink to GO}{section.4}
\BOOKMARK [2][-]{subsection.4.2}{GO graph and ontology for molecular function}{section.4}
\BOOKMARK [2][-]{subsection.4.3}{Mapping from LocusLink to GO}{section.4}
\BOOKMARK [1][-]{section.5}{Applications}{}
\BOOKMARK [2][-]{subsection.5.1}{Lord's Bioinformatics 2003 paper}{section.5}
\BOOKMARK [3][-]{subsubsection.5.1.1}{Setup of the data}{subsection.5.1}
\BOOKMARK [3][-]{subsubsection.5.1.2}{Concept probabilities}{subsection.5.1}
\BOOKMARK [3][-]{subsubsection.5.1.3}{Identifying the most informative subsumer}{subsection.5.1}
\BOOKMARK [2][-]{subsection.5.2}{Iyer's time-course experiment}{section.5}
\BOOKMARK [3][-]{subsubsection.5.2.1}{Setup}{subsection.5.2}
\BOOKMARK [3][-]{subsubsection.5.2.2}{Filtering the IyerAnnotated tags}{subsection.5.2}
\BOOKMARK [3][-]{subsubsection.5.2.3}{Computing pairwise semantic similarity}{subsection.5.2}
