From bc25b877900750e7c5a355791604a892c2ef0467 Mon Sep 17 00:00:00 2001 From: rautenberg Date: Thu, 26 Jan 2017 12:11:43 +0100 Subject: add G. Kilic et al. to references --- nmsa-ist-rest.pdf | Bin 735435 -> 735435 bytes references.bib | 13 +++++++++++++ 2 files changed, 13 insertions(+) diff --git a/nmsa-ist-rest.pdf b/nmsa-ist-rest.pdf index a2ee10a..ebbdedd 100644 Binary files a/nmsa-ist-rest.pdf and b/nmsa-ist-rest.pdf differ 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}, -- cgit v1.2.3 From bb7d9009a9be8a8f2244944885ed9fec5086e26c Mon Sep 17 00:00:00 2001 From: rautenberg Date: Thu, 26 Jan 2017 12:59:44 +0100 Subject: split integation Text to blocks --- markdown_blocks/integration_lazar-rest.md | 2 ++ markdown_blocks/integration_lazar.md | 3 +++ markdown_blocks/integration_nano-lazar.md | 3 +++ markdown_blocks/integration_ontoviewer.md | 2 ++ markdown_blocks/integration_rdf.md | 2 ++ markdown_blocks/integration_sparql.md | 2 ++ nmsa-ist-integration.tex | 42 ++++++++++++++++++++++--------- nmsa-ist-rest.tex | 6 ++--- nmsa-ist-services.tex | 12 ++++----- 9 files changed, 53 insertions(+), 21 deletions(-) create mode 100644 markdown_blocks/integration_lazar-rest.md create mode 100644 markdown_blocks/integration_lazar.md create mode 100644 markdown_blocks/integration_nano-lazar.md create mode 100644 markdown_blocks/integration_ontoviewer.md create mode 100644 markdown_blocks/integration_rdf.md create mode 100644 markdown_blocks/integration_sparql.md 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.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.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.tex b/nmsa-ist-services.tex index 9ab14ef..9d42ba8 100644 --- a/nmsa-ist-services.tex +++ b/nmsa-ist-services.tex @@ -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} -- cgit v1.2.3 From 958bdf798d49cf1699bafe93a77f1e8ac9dae7cd Mon Sep 17 00:00:00 2001 From: rautenberg Date: Thu, 26 Jan 2017 13:00:42 +0100 Subject: update PDFs --- nmsa-ist-integration.pdf | Bin 339044 -> 340660 bytes nmsa-ist-rest.pdf | Bin 735435 -> 733668 bytes nmsa-ist-services.pdf | Bin 355395 -> 356422 bytes 3 files changed, 0 insertions(+), 0 deletions(-) diff --git a/nmsa-ist-integration.pdf b/nmsa-ist-integration.pdf index f6b77a4..c6ae41d 100644 Binary files a/nmsa-ist-integration.pdf and b/nmsa-ist-integration.pdf differ diff --git a/nmsa-ist-rest.pdf b/nmsa-ist-rest.pdf index ebbdedd..c1d660e 100644 Binary files a/nmsa-ist-rest.pdf and b/nmsa-ist-rest.pdf differ diff --git a/nmsa-ist-services.pdf b/nmsa-ist-services.pdf index 5803260..0ecf19c 100644 Binary files a/nmsa-ist-services.pdf and b/nmsa-ist-services.pdf differ -- cgit v1.2.3 From 0dd4584507430dded05726e39039b0b1314ac589 Mon Sep 17 00:00:00 2001 From: rautenberg Date: Thu, 26 Jan 2017 13:05:34 +0100 Subject: add full address to footer --- nmsa-ist-services.pdf | Bin 356422 -> 356469 bytes nmsa-ist-services.tex | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/nmsa-ist-services.pdf b/nmsa-ist-services.pdf index 0ecf19c..06cafc5 100644 Binary files a/nmsa-ist-services.pdf and b/nmsa-ist-services.pdf differ diff --git a/nmsa-ist-services.tex b/nmsa-ist-services.tex index 9d42ba8..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} -- cgit v1.2.3