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authorgebele <gebele@in-silico.ch>2017-01-26 14:12:42 +0100
committergebele <gebele@in-silico.ch>2017-01-26 14:12:42 +0100
commitd298a3a2d895d0f9fe106a3cb3ec4d8d60fdf031 (patch)
treeeb033a1805dd405abd1d794080189a1a12b8e6fe
parentdf97cdcdbf261853bc67e6b2ee99dc48388a3351 (diff)
parent0dd4584507430dded05726e39039b0b1314ac589 (diff)
Merge branch 'master' of https://github.com/opentox/lazar-poster
-rw-r--r--markdown_blocks/integration_lazar-rest.md2
-rw-r--r--markdown_blocks/integration_lazar.md3
-rw-r--r--markdown_blocks/integration_nano-lazar.md3
-rw-r--r--markdown_blocks/integration_ontoviewer.md2
-rw-r--r--markdown_blocks/integration_rdf.md2
-rw-r--r--markdown_blocks/integration_sparql.md2
-rw-r--r--nmsa-ist-integration.pdfbin339044 -> 340660 bytes
-rw-r--r--nmsa-ist-integration.tex42
-rw-r--r--nmsa-ist-rest.pdfbin735435 -> 733668 bytes
-rw-r--r--nmsa-ist-rest.tex6
-rw-r--r--nmsa-ist-services.pdfbin355395 -> 356469 bytes
-rw-r--r--nmsa-ist-services.tex14
-rw-r--r--references.bib13
13 files changed, 67 insertions, 22 deletions
diff --git a/markdown_blocks/integration_lazar-rest.md b/markdown_blocks/integration_lazar-rest.md
new file mode 100644
index 0000000..80c430b
--- /dev/null
+++ b/markdown_blocks/integration_lazar-rest.md
@@ -0,0 +1,2 @@
+ - Interacts with the `lazar` library (e.g. for toxicity predictions, model creation and validation, descriptor calculation)
+ - Will be maintained and developed in the FP7 OpenRiskNet project \ No newline at end of file
diff --git a/markdown_blocks/integration_lazar.md b/markdown_blocks/integration_lazar.md
new file mode 100644
index 0000000..49453ad
--- /dev/null
+++ b/markdown_blocks/integration_lazar.md
@@ -0,0 +1,3 @@
+ - Mirrors eNanoMapper data for read-across models
+ - Creates read-across predictions for the `nano-lazar` webinterface
+ - Responds to requests from the `lazar-rest` interface (e.g. nanoparticle predictions, model creation and validation, descriptor calculation) \ No newline at end of file
diff --git a/markdown_blocks/integration_nano-lazar.md b/markdown_blocks/integration_nano-lazar.md
new file mode 100644
index 0000000..341272b
--- /dev/null
+++ b/markdown_blocks/integration_nano-lazar.md
@@ -0,0 +1,3 @@
+ - Obtains nanoparticle toxicity predictions from the `lazar` library
+ - Uses ontologies (eNanoMapper, BioPortal, UniProt) to explain domain specific terms in the user interface
+ - Uses ontologies and eNanoMapper data as supporting information for read-across predictions \ No newline at end of file
diff --git a/markdown_blocks/integration_ontoviewer.md b/markdown_blocks/integration_ontoviewer.md
new file mode 100644
index 0000000..7ab7f99
--- /dev/null
+++ b/markdown_blocks/integration_ontoviewer.md
@@ -0,0 +1,2 @@
+ - Sends SPARQL queries to the RDF store
+ - Visualises RDF response from the RDF store \ No newline at end of file
diff --git a/markdown_blocks/integration_rdf.md b/markdown_blocks/integration_rdf.md
new file mode 100644
index 0000000..dec5b8d
--- /dev/null
+++ b/markdown_blocks/integration_rdf.md
@@ -0,0 +1,2 @@
+ - Mirrors eNanoMapper data and ontologies
+ - Responds to SPARQL queries from the ontology viewer and the SPARQL interface
diff --git a/markdown_blocks/integration_sparql.md b/markdown_blocks/integration_sparql.md
new file mode 100644
index 0000000..158c0cd
--- /dev/null
+++ b/markdown_blocks/integration_sparql.md
@@ -0,0 +1,2 @@
+ - Sends SPARQL queries to the RDF store
+ - Receives SPARQL query results in different formats \ No newline at end of file
diff --git a/nmsa-ist-integration.pdf b/nmsa-ist-integration.pdf
index f6b77a4..c6ae41d 100644
--- a/nmsa-ist-integration.pdf
+++ b/nmsa-ist-integration.pdf
Binary files differ
diff --git a/nmsa-ist-integration.tex b/nmsa-ist-integration.tex
index 2f473ff..2c35387 100644
--- a/nmsa-ist-integration.tex
+++ b/nmsa-ist-integration.tex
@@ -1,6 +1,6 @@
\documentclass[final]{beamer}
\usetheme{IST}
-\usepackage[orientation=portrait,size=a0,scale=1.3,debug]{beamerposter} % poster size
+\usepackage[orientation=portrait,size=a0,scale=1.24,debug]{beamerposter} % poster size
\usepackage[absolute,overlay]{textpos}
\usepackage[utf8]{inputenc}
@@ -21,38 +21,56 @@
\input{./markdown_blocks/integration_summary}
\end{block}
- \begin{exampleblock}{Links}
- \input{./markdown_blocks/integration_links}
- \end{exampleblock}
-
+ \begin{block}{{\tt lazar} \cite{helma_2017}\cite{helma_christoph_2016_215483}}
+ \input{./markdown_blocks/integration_lazar}
+ \end{block}
- \begin{block}{References}
- \small\bibliography{references}
+ \begin{block}{{\tt nano-lazar} GUI \cite{gebele_denis_2017_250818}}
+ \input{./markdown_blocks/integration_nano-lazar}
\end{block}
\end{textblock}
\begin{textblock}{40.5}(42.6,10)
- \begin{block}{Integration details}
- \input{./markdown_blocks/integration_text}
+ \begin{block}{{\tt nano-lazar} REST interface \cite{rautenberg_micha_2016_187328}}
+ \input{./markdown_blocks/integration_lazar-rest}
+ \end{block}
+
+ \begin{block}{eNM {\tt ontology viewer} \cite{gebele_denis_2017_259384}}
+ \input{./markdown_blocks/integration_ontoviewer}
+ \end{block}
+
+ \begin{block}{RDF store}
+ \input{./markdown_blocks/integration_rdf}
+ \end{block}
+
+ \begin{block}{eNM SPARQL interface}
+ \input{./markdown_blocks/integration_sparql}
\end{block}
+
\end{textblock}
- \begin{textblock}{82.1}(1,50)
+ \begin{textblock}{82.1}(1,36)
\input{./markdown_blocks/integration_diagram}
\end{textblock}
- \begin{textblock}{40.5}(1,82)
+ \begin{textblock}{40.5}(1,97)
+ \begin{exampleblock}{Links}
+ \input{./markdown_blocks/integration_links}
+ \end{exampleblock}
\end{textblock}
- \begin{textblock}{40.5}(42.6,82)
+ \begin{textblock}{40.5}(42.6,97)
+ \begin{block}{References}
+ \small\bibliography{references}
+ \end{block}
\end{textblock}
diff --git a/nmsa-ist-rest.pdf b/nmsa-ist-rest.pdf
index a2ee10a..c1d660e 100644
--- a/nmsa-ist-rest.pdf
+++ b/nmsa-ist-rest.pdf
Binary files differ
diff --git a/nmsa-ist-rest.tex b/nmsa-ist-rest.tex
index 4f840f1..b8fc2df 100644
--- a/nmsa-ist-rest.tex
+++ b/nmsa-ist-rest.tex
@@ -22,7 +22,7 @@
\input{./markdown_blocks/rest_summary}
\end{block}
- \begin{block}{\tt{lazar}}
+ \begin{block}{{\tt lazar}}
\justifying
\input{./markdown_blocks/rest_lazar_description}
\end{block}
@@ -32,12 +32,12 @@
\input{./markdown_blocks/rest_rest}
\end{block}
- \begin{block}{\tt{lazar-rest} services}
+ \begin{block}{{\tt lazar-rest} services}
\justifying
\input{./markdown_blocks/rest_lazar-rest}
\end{block}
- \begin{block}{\tt{lazar-rest} Swagger interface}
+ \begin{block}{{\tt lazar-rest} Swagger interface}
\vskip.2ex
\input{./markdown_blocks/rest_swagger_ui}
\vskip.2ex
diff --git a/nmsa-ist-services.pdf b/nmsa-ist-services.pdf
index 5803260..06cafc5 100644
--- a/nmsa-ist-services.pdf
+++ b/nmsa-ist-services.pdf
Binary files differ
diff --git a/nmsa-ist-services.tex b/nmsa-ist-services.tex
index 9ab14ef..82550e3 100644
--- a/nmsa-ist-services.tex
+++ b/nmsa-ist-services.tex
@@ -10,7 +10,7 @@
\title{In silico toxicology services for nanoparticle risk assessment}
\author{C. Helma, D. Gebele, M. Rautenberg}
\institute{\emph{in silico} toxicology gmbh, Basel, Switzerland}
-\footer{Contact: \texttt{support@in-silico.ch}. Information: \texttt{www.in-silico.ch}}
+\footer{Contact: \texttt{support@in-silico.ch}. Information: \texttt{www.in-silico.ch} \\ \emph{in silico} toxicology gmbh - Rastatterstrasse 41 - CH-4057 Basel, Switzerland }
\begin{document}
@@ -21,19 +21,19 @@
\input{./markdown_blocks/services_summary}
\end{block}
- \begin{block}{\tt{lazar}}
+ \begin{block}{{\tt lazar}}
\input{./markdown_blocks/services_lazar}
\end{block}
- \begin{block}{\tt{nano-lazar}}
+ \begin{block}{{\tt nano-lazar}}
\input{./markdown_blocks/services_nano-lazar}
\end{block}
- \begin{block}{\tt{nano-lazar}-paper}
+ \begin{block}{{\tt nano-lazar-paper}}
\input{./markdown_blocks/services_nano-lazar-paper}
\end{block}
- \begin{block}{\tt{lazar-rest}}
+ \begin{block}{{\tt lazar-rest}}
\input{./markdown_blocks/services_lazar-rest}
\end{block}
@@ -45,11 +45,11 @@
\begin{textblock}{40.5}(42.6,8.6)
- \begin{block}{eNM ontoviewer}
+ \begin{block}{eNM {\tt ontology viewer}}
\input{./markdown_blocks/services_ontoviewer}
\end{block}
- \begin{block}{\tt{qsar-report}}
+ \begin{block}{{\tt qsar-report}}
\input{./markdown_blocks/services_qsar-report}
\end{block}
diff --git a/references.bib b/references.bib
index 9b5cee8..a9de0e7 100644
--- a/references.bib
+++ b/references.bib
@@ -58,6 +58,19 @@
doi = {10.5281/zenodo.179038},
url = {https://doi.org/10.5281/zenodo.179038}
}
+@article{Kilic2016S118,
+ title = "eNanoMapper – A database and ontology framework for design and safety assessment of nanomaterials ",
+ journal = "Toxicology Letters ",
+ volume = "258, Supplement",
+ number = "",
+ pages = "S118 - S119",
+ year = "2016",
+ note = "Abstracts of the 52nd Congress of the European Societies of Toxicology (EUROTOX) Fibes Congress Center Seville, Spain, 04th-07th September 2016 ",
+ issn = "0378-4274",
+ doi = "http://dx.doi.org/10.1016/j.toxlet.2016.06.1481",
+ url = "//www.sciencedirect.com/science/article/pii/S0378427416316307",
+ author = "G. Kilic and B. Fadeel and L. Farcal and H. Sarimveis and P. Doganis and G. Drakakis and G. Tsiliki and C. Chomenidis and C. Helma and M. Rautenberg and D. Gebele and N. Jeliazkova and N. Kochev and G. Owen and J. Chang and E.L. Willighagen and F. Ehrhart and L. Rieswijk and V. Hongisto and P. Nymark and P. Kohonen and R. Grafström and B. Hardy"
+}
@article{batke2016innovative,
title={Innovative Strategies to Develop Chemical Categories Using a Combination of Structural and Toxicological Properties},
author={Batke, Monika and G{\"u}tlein, Martin and Partosch, Falko and Gundert-Remy, Ursula and Helma, Christoph and Kramer, Stefan and Maunz, Andreas and Seeland, Madeleine and Bitsch, Annette},