opentox-2023-knowledge-graph-for-chemical-safety.tex

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\section{Problem space}
\begin{frame}\frametitle{\secname}
	Before you can answer a particular cheminformatics
	question:
	\begin{description}
		\item[P0] Many different data sources for
			cheminformatics and chemical safety.
		\pause
		\item[P1] Retrieving data sources for local
			analysis.
		\pause
		\item[P2] Differences in how data are represented.
	\end{description}
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\section{Solution: tabular data}
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	\begin{itemize}
		\item multiple data sources
		\item local analysis
	\end{itemize}
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	\begin{center}
		BioBricks
	\end{center}
\end{frame}

\section{Solution: graph data}
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	\begin{itemize}
		\item multiple data sources
		\item local analysis
		\pause
		\item \textbf{interoperable data through common
			vocabularies, identifiers, and ontologies}
	\end{itemize}
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	\begin{center}
		BioBricks-OKG
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\section{BioBricks-OKG}
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	\begin{itemize}
		\item Working as part of NSF Proto-OKN program (Award: NSF SBIR 2333728)
		\pause
		\item Agency partner: NICEATM
		\pause
		\item Built on RDF metadata standard
	\end{itemize}
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\begin{frame}[fragile]{RDF}
  \begin{itemize}
  \item RDF based on triple relationships
  \end{itemize}
  \begin{figure}[tbp]
   \centering
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  \label{fig:rdf}
  \end{figure}
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\section{Technology}
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  \begin{enumerate}
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  \item Build on existing BioBricks infrastructure
  \item Use tabular data as a data source (tabular brick)
  \item Map tabular data to graph data (triple brick)
  \item Load this triple brick into a triplestore
  graph database or use directly
  \end{enumerate}
\end{frame}

\section{Knowledge organization}
\begin{frame}[fragile]{\secname}
        \begin{figure}[tbp]%
        \centering%
        \input{gfx/knowledge-org.tex}%
        %%\caption{\textbf{Knowledge organization}}\label{fig:knowledge-org}%
        \end{figure}
\end{frame}

\section{Early prototype}
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	\begin{itemize}
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		\item datasets: ICE, tox21, CTDbase, MeSH, HGNC, CosIng
		\pause
		\item Looking for
		\begin{itemize}
			\item New datasets
			\item New use cases
			\item Improvements to data modeling
		\end{itemize}
	\end{itemize}
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