\contentsline {section}{\numberline {1}Introduction}{2}{section.1}
\contentsline {section}{\numberline {2}Basic structures}{2}{section.2}
\contentsline {subsection}{\numberline {2.1}Rooted DAG}{2}{subsection.2.1}
\contentsline {subsection}{\numberline {2.2} {\tt compoundGraph}}{4}{subsection.2.2}
\contentsline {subsection}{\numberline {2.3}{ \tt ontology}}{7}{subsection.2.3}
\contentsline {subsection}{\numberline {2.4} Mapped key-value list}{7}{subsection.2.4}
\contentsline {subsection}{\numberline {2.5} OOC: object-ontology complex }{7}{subsection.2.5}
\contentsline {section}{\numberline {3}Basic methods}{8}{section.3}
\contentsline {subsection}{\numberline {3.1}Matrix conversion of DAG; namedSparse extension}{8}{subsection.3.1}
\contentsline {subsubsection}{\numberline {3.1.1}child2parent}{8}{subsubsection.3.1.1}
\contentsline {subsubsection}{\numberline {3.1.2}Accessibility}{10}{subsubsection.3.1.2}
\contentsline {subsection}{\numberline {3.2}Coverage matrix for an OOC}{11}{subsection.3.2}
\contentsline {subsection}{\numberline {3.3}Depth of terms in an ontology}{11}{subsection.3.3}
\contentsline {section}{\numberline {4}Applications to large data objects}{11}{section.4}
\contentsline {subsection}{\numberline {4.1}Key-value list for LocusLink to GO}{11}{subsection.4.1}
\contentsline {subsection}{\numberline {4.2}GO graph and ontology for molecular function}{12}{subsection.4.2}
\contentsline {subsection}{\numberline {4.3}Mapping from LocusLink to GO}{12}{subsection.4.3}
\contentsline {section}{\numberline {5}Applications}{12}{section.5}
\contentsline {subsection}{\numberline {5.1}Lord's {\it Bioinformatics} 2003 paper}{12}{subsection.5.1}
\contentsline {subsubsection}{\numberline {5.1.1}Setup of the data}{13}{subsubsection.5.1.1}
\contentsline {subsubsection}{\numberline {5.1.2}Concept probabilities}{14}{subsubsection.5.1.2}
\contentsline {subsubsection}{\numberline {5.1.3}Identifying the most informative subsumer}{15}{subsubsection.5.1.3}
\contentsline {subsection}{\numberline {5.2}Iyer's time-course experiment}{16}{subsection.5.2}
\contentsline {subsubsection}{\numberline {5.2.1}Setup}{16}{subsubsection.5.2.1}
\contentsline {subsubsection}{\numberline {5.2.2}Filtering the IyerAnnotated tags}{17}{subsubsection.5.2.2}
\contentsline {subsubsection}{\numberline {5.2.3}Computing pairwise semantic similarity}{18}{subsubsection.5.2.3}
