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6bdda696b3ea703c47e87fea61017ec655f91d92nd

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6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd%% Note: If title has linebreaks, you must use a short title without

6bdda696b3ea703c47e87fea61017ec655f91d92nd%% linebreaks, otherwise you'll get funny LaTeX errors.

6bdda696b3ea703c47e87fea61017ec655f91d92nd\title{OntoHub Perspectives}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd%% Note about linebreaks applies here as well.

6bdda696b3ea703c47e87fea61017ec655f91d92nd\author{The Ontohub team}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\date{12.12.12}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\logo{\includegraphics[height=0.8cm]{DFKI-Logo.jpg}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\hspace{5.5cm}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\includegraphics[height=0.8cm]{sfb_tr8_logo.pdf}}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{document}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\maketitle

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{Time plan}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{tabular}{|l|p{9cm}|}\hline

6bdda696b3ea703c47e87fea61017ec655f91d92nd10h & Intro / Motivation / Know-How\\\hline

6bdda696b3ea703c47e87fea61017ec655f91d92nd10.30h & Ontohub and its background (OntoIOp ISO standard, OOR community, Hets community)\\\hline

6bdda696b3ea703c47e87fea61017ec655f91d92nd11h & Ontohub.org web portal demo\\\hline

6bdda696b3ea703c47e87fea61017ec655f91d92nd11.30h & Ontohub architecture and data model\\\hline

6bdda696b3ea703c47e87fea61017ec655f91d92nd13h & Lunch\\\hline

6bdda696b3ea703c47e87fea61017ec655f91d92nd14h & Aims\\\hline

6bdda696b3ea703c47e87fea61017ec655f91d92nd14.30h & Motivation / Know-How / Work areas\\\hline

6bdda696b3ea703c47e87fea61017ec655f91d92nd15h & Organisation (regular meetings, programming sessions, github, issue tracker)\\\hline

6bdda696b3ea703c47e87fea61017ec655f91d92nd15.30h & Setup of development environment\\\hline

6bdda696b3ea703c47e87fea61017ec655f91d92ndca. 16h & End\\\hline

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{tabular}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{External advice}

6bdda696b3ea703c47e87fea61017ec655f91d92ndMichael Gruninger, Toronto

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\includegraphics[width=0.5\textwidth]{MGpic.jpg}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{Ontologies}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Ontology = shared (formal) conceptualisation (of a domain)

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Example: Pizza ontology

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

ac7985784d08a3655291f24f711812b4d8b1cbcffuankg\item using Web Ontology Language OWL

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item tool for editing OWL ontologies: Prot�g� \url{http://protege.stanford.edu/}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{itemize}

ac7985784d08a3655291f24f711812b4d8b1cbcffuankg\end{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{Applications of Ontologies}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Medicine (Snomed)

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Biology, Biochemistry (molecules \ldots)

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Semantic Web

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Semantic Mediawiki

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

ac7985784d08a3655291f24f711812b4d8b1cbcffuankg\item better categories for Wikipedia

0662ed52e814f8f08ef0e09956413a792584eddffuankg\end{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item schema.org (Google, Yahoo, Microsoft)

ac7985784d08a3655291f24f711812b4d8b1cbcffuankg\begin{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item structured content for HTML pages

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{Open Ontology Repository (OOR)}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item ambitious goals:

0662ed52e814f8f08ef0e09956413a792584eddffuankg\begin{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item establishing a hosted registry-repository;

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item enabling and facilitating open, federated, collaborative ontology repositories, and

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{itemize}

0662ed52e814f8f08ef0e09956413a792584eddffuankg\item lots of OOR presentations at conferences

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item regular Skype conferences

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item implementation: only through Bioportal, only for OWL

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item \url{http://www.oor.net}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{BioPortal}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\vspace{-1cm}

0662ed52e814f8f08ef0e09956413a792584eddffuankg\includegraphics[width=1\textwidth]{Screenshot_Bioportal.png}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

ac7985784d08a3655291f24f711812b4d8b1cbcffuankg\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{Ontology Integration and Interoperability (OntoIOp)}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item ISO Standard 17347 (currently: working draft)

ac7985784d08a3655291f24f711812b4d8b1cbcffuankg\item Distributed Ontology Language (DOL)

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item OWL (Web Ontology Language)

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item RDF (Resource Description Framework)

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item EER (Enhanced Entity-Relationship Diagrams)

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Common Logic

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item UML (Unified Modeling Language)

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item \ldots

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Community of 10-15 experts

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item bi-weekly Skype conferences

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item \url{http://ontoiop.org}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{OntoIOp Logic Graph}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\includegraphics[width=\textwidth]{ontograph}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{Heterogeneous Tool Set (Hets)}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Logic backend for OntoHub

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item can parse and analyse all involved languages

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item implements logic translations

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item interface to about 15 proof tools

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item anchored in algebraic specification community\\ (WADT, CoFI, IFIP WG 1.3)

cf7ca2f9eaa6523fefcccba4287b91637391fb51fuankg\item \url{http://www.dfki.de/cps/hets}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{OntoHub mission}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item \emphc{generalise} Bioportal and OOR\\

6bdda696b3ea703c47e87fea61017ec655f91d92nd $\Rightarrow$ provide a repository for \emphc{heterogeneous} ontologies

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item provide a \emphc{repository for OntoIOp/DOL}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item provide a \emphc{web-frontend for Hets}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

ac7985784d08a3655291f24f711812b4d8b1cbcffuankg\frametitle{Ontohub architecture}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\vspace{-1cm}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\includegraphics[width=0.8\textwidth]{architecture/ontohub-oor-architecture.png}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{Ontohub data model}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\includegraphics[width=\textwidth]{DBVisualization.png}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{OntoHub short-term and long-term goals}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Documentation / rdoc / top-down overview

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Keep functionality through tests

8ffac2c334103c0336602aaede650cb578611151fuankg\item CRUD functionality not only for ontologies, but also for logics,

8ffac2c334103c0336602aaede650cb578611151fuankg translations, \ldots

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item display graph of ontologies and links (and logic graph)

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Reasoning (provide Hets GUI)

ac7985784d08a3655291f24f711812b4d8b1cbcffuankg\item Git backend (distributed development of ontologies)

ac7985784d08a3655291f24f711812b4d8b1cbcffuankg\item long-term goal: OOR architecture

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{Tests}

ac7985784d08a3655291f24f711812b4d8b1cbcffuankgTest-driven development:\\

ac7985784d08a3655291f24f711812b4d8b1cbcffuankg\emphc{No line of code without test}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Fixtures: provide data for tests

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Unit tests: test single methods of models

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item Functional tests: test controller actions

ac7985784d08a3655291f24f711812b4d8b1cbcffuankg\item Integration tests: test sessions (sequences of actions)

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{CRUD functionality for logics etc.}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item re-use existing functionality for ontologies

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item transfer this to links, logics, logic mappings,

6bdda696b3ea703c47e87fea61017ec655f91d92ndlanguages,

6bdda696b3ea703c47e87fea61017ec655f91d92ndlanguage mappings, and

ac7985784d08a3655291f24f711812b4d8b1cbcffuankgserializations

0662ed52e814f8f08ef0e09956413a792584eddffuankg\item involve further tables like supports

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item display lists of these things: see display of graphs

6bdda696b3ea703c47e87fea61017ec655f91d92nd\item read in logic graph from OntoIOp registry (RDF)

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{itemize}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\frametitle{OntoIOp registry}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\vspace{-1cm}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\includegraphics[width=0.9\textwidth]{DOL-ontograph-layers-TKE.pdf}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\end{frame}

6bdda696b3ea703c47e87fea61017ec655f91d92nd

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{frame}

0662ed52e814f8f08ef0e09956413a792584eddffuankg\frametitle{display of graphs}

6bdda696b3ea703c47e87fea61017ec655f91d92nd\begin{itemize}

\item use graphviz / dot to generate svg from graph

\item html and javascript can be embedded to svg

\item use this to realise menus for nodes and links

\item long-term goal: re-use Bioportal's fancy display

\end{itemize}

\end{frame}

\begin{frame}

\frametitle{OOR architecture}

\includegraphics[width=\textwidth]{revised-OOR-architecture-proposal--ToddSchneider-KenBaclawski_20101119.jpg}

\end{frame}

\begin{frame}

\frametitle{Git backend}

\begin{itemize}

\item New Rails model ``repository'', which simultaneously provides namespace for ontologies

\item underlying git or svn repositories

\item permissions per repository (not per ontology)

\item only contents of master branch is displayed in Ontohub

\item store who has pushed when what

\item server side git hooks

\end{itemize}

\end{frame}

\begin{frame}

\frametitle{Organisation}

\begin{itemize}

\item who does what?

\item meetings

\item shared office in Cartesium

\end{itemize}

\end{frame}

\end{document}

Zielskizzen

Speichern: Wer hat was wann wohin gepusht?

server side hooks

http://git-scm.com/book/en/Customizing-Git-Git-Hooks#Server-Side-Hooks

Suche?

Evtl. NoSQL (MongoDB, CouchDB)

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