Merge branch 'master' of https://github.com/opentox/lazar-poster

26 files changed, 187 insertions, 40 deletions

diff --git a/markdown_blocks/integration_links.md b/markdown_blocks/integration_links.md
index 7de44f7..96139e7 100644
--- a/markdown_blocks/integration_links.md
+++ b/markdown_blocks/integration_links.md
@@ -1,15 +1,15 @@
-* eNM Data Warehouse <https://data.enanomapper.net>
+* eNM data warehouse <https://data.enanomapper.net>
 
-* eNM Ontologies <https://github.com/enanomapper/ontologies>
+* eNM ontologies <https://github.com/enanomapper/ontologies>
 
 * nano-lazar GUI <http://nano-lazar.in-silico.ch>
 
-* eNM Ontology Viewer <https://query.enanomapper.net/enm-viewer>
+* eNM ontology viewer <https://query.enanomapper.net/enm-viewer>
 
-* nano-lazar REST interface <https://enm.enanomapper.org>
+* nano-lazar REST interface <https://enm.enanomapper.net>
 
 * eNM SPARQL interface <https://sparql.enanomapper.net>
 
 * BioPortal <http://bioportal.bioontology.org> 
 
-* UniProt <http://www.uniprot.org/uniprot>
\ No newline at end of file
+* UniProt <http://www.uniprot.org/uniprot>
diff --git a/markdown_blocks/integration_summary.md b/markdown_blocks/integration_summary.md
index c62f645..871516a 100644
--- a/markdown_blocks/integration_summary.md
+++ b/markdown_blocks/integration_summary.md
@@ -1,6 +1,6 @@
 During the eNanoMapper project in silico toxicologies (IST) public services
 were adapted to the specification of the eNanoMapper API and new nanoparticle
-specific developments were implemented.  This poster will depict the
+specific developments were implemented.  This poster depict the
 interaction of IST services with eNanoMapper resources of other partners which
 covers use cases like data download/mirroring, augmentation of GUIs with
 ontology queries and nanoparticle descriptor calculation.
diff --git a/markdown_blocks/rest_aa.md b/markdown_blocks/rest_aa.md
index 2022c54..3dca640 100644
--- a/markdown_blocks/rest_aa.md
+++ b/markdown_blocks/rest_aa.md
@@ -1,5 +1,6 @@
 Data confidentiality, authentication and authorization (AA) is a common requirement for many resources. 
 Within the OpenTox\cite{hardy2010collaborative} project, in-silico toxicology gmbh has implemented a single-sign-on method with an OpenLDAP backend for user management
-and OpenAM for authentication and authorization. The revised technic is also used in eNanoMapper services to provide access control.  
-Conforming to the OpenTox web service architecture principles\cite{hardy2010collaborative}, eNanoMapper services will be decoupled from AAI. 
-This provides the opportunity to deploy a service without A&A, if/when possible. 
\ No newline at end of file
+and OpenAM for authentication and authorization. 
+This system was updated and revised for eNanoMapper and provides access control for the current services. 
+Conforming to the OpenTox web service architecture principles\cite{hardy2010collaborative}, eNanoMapper services can be decoupled from AA. 
+This provides the opportunity to deploy a service without A&A, if required (e.g. for local installations). 
\ No newline at end of file
diff --git a/markdown_blocks/rest_examples.md b/markdown_blocks/rest_examples.md
index 3b3789d..7bd49d6 100644
--- a/markdown_blocks/rest_examples.md
+++ b/markdown_blocks/rest_examples.md
@@ -1,14 +1,14 @@
-get an URI list for all models:
+Get an URI list for all models:
 ```Bash
   curl -X GET --header 'Accept: text/uri-list' -H 'accept:text/uri-list' 'https://enm.in-silico.ch/model' 
 ```
 
-retrieve an JSON representation of a model:
-```Bash
+Retrieve an JSON representation of a model:
+```bash
   curl -X GET -H 'Accept: application/json' -H 'accept: application/json' 'https://enm.in-silico.ch/model/<MODELID>'
 ```
 
-predict a nano-particle:
+Predict a nano-particle:
 ```Bash
-  curl -X POST -H 'Content-Type: application/x-www-form-urlencoded' -H 'Accept:text/html' -d 'identifier= \ https://enm.in-silico.ch/nanoparticle/<NANOPARTICLEID>' 'https://enm.in-silico.ch/model/<MODELID>'
+  curl -X POST -H 'Content-Type: application/x-www-form-urlencoded' -H 'Accept:text/html' -d 'identifier= https://enm.in-silico.ch/nanoparticle/<NANOPARTICLEID>' 'https://enm.in-silico.ch/model/<MODELID>'
 ```
\ No newline at end of file
diff --git a/markdown_blocks/rest_integration.md b/markdown_blocks/rest_integration.md
new file mode 100644
index 0000000..d63f909
--- /dev/null
+++ b/markdown_blocks/rest_integration.md
@@ -0,0 +1,9 @@
+lazar-rest provides a REST webservice for the nano-lazar framework. 
+The lazar framework integrates internal libraries, eNanoMapper
+resources (Data Warehouse and Ontologies) and external resources like UniProt and
+BioPortal. lazar-rest services make the lazar framework accessible
+for other webservices and web applications and for users who prefer the
+command line over graphical user interfaces.
+
+
+![nano-lazar service integration](./images/rest_integration.pdf "nano-lazar service integration"){width=1400px}
\ No newline at end of file
diff --git a/markdown_blocks/rest_interaction.md b/markdown_blocks/rest_interaction.md
deleted file mode 100644
index 2effd83..0000000
--- a/markdown_blocks/rest_interaction.md
+++ /dev/null
@@ -1,3 +0,0 @@
-The lazar-rest webservice text ...
-
-![nano-lazar Swagger UI](./images/rest_interaction.png "nano-lazar Swagger UI") 
\ No newline at end of file
diff --git a/markdown_blocks/rest_lazar-rest.md b/markdown_blocks/rest_lazar-rest.md
index 3c887ca..1058e38 100644
--- a/markdown_blocks/rest_lazar-rest.md
+++ b/markdown_blocks/rest_lazar-rest.md
@@ -1,3 +1,3 @@
-lazar-rest is a gem library written in Ruby. It provides a REST API webservice to lazar and nano-lazar. 
-The API is documented in the Swagger RESTful API documentation specification version 2.0. 
-This specification is conform to the Open API Iniciative specification.  
\ No newline at end of file
+lazar-rest is a Ruby library, that provides a REST interface for nano-lazar. 
+The API is compatible with eNanoMapper specifications and documented with the Swagger API framework (version 2.0), 
+which conforms with the Open API Initiative specification. 
\ No newline at end of file
diff --git a/markdown_blocks/rest_lazar_description.md b/markdown_blocks/rest_lazar_description.md
index 2096877..1272146 100644
--- a/markdown_blocks/rest_lazar_description.md
+++ b/markdown_blocks/rest_lazar_description.md
@@ -1,4 +1,3 @@
 *lazar* (lazy structure–activity relationships)\cite{Maunz2013} is a modular framework for read across predictions of chemical toxicities. 
-Within the European Union’s FP7 eNanoMapper project lazar was extended with capabilities to handle nanomaterial data, 
-interfaces to other eNanoMapper services (databases and ontologies) and a stable and user-friendly graphical interface 
-for nanoparticle read-across predictions. lazar provides a ruby gem library to this developments.
\ No newline at end of file
+Within the European Union’s FP7 eNanoMapper project lazar was extended with capabilities to handle nanomaterial data and interfaces 
+to other eNanoMapper services (databases and ontologies). lazar libraries are publicly distributed as Ruby gems.
\ No newline at end of file
diff --git a/markdown_blocks/rest_links.md b/markdown_blocks/rest_links.md
index 682e16e..356f473 100644
--- a/markdown_blocks/rest_links.md
+++ b/markdown_blocks/rest_links.md
@@ -1,21 +1,27 @@
-* Nano-lazar Restful API GUI. Swagger UI based documentation for API visualization and interaction.
+* Nano-lazar REST API GUI. Swagger UI based documentation for API visualization and interaction.
   \
   <https://enm.in-silico.ch>
 
 * Nano-lazar Swagger API definition file
   <https://enm.in-silico.ch/api/api.json> 
 
-* Nano-lazar Restful API services source code repository
+* Nano-lazar REST API services source code repository
   <https://github.com/opentox/lazar-rest>
   
-* Nano-lazar Restful API services Rubydocs gem library documentation
+* Nano-lazar REST API services gem library
+  <https://rubygems.org/gems/lazar-rest>
+
+* Nano-lazar REST API services Rubydocs gem library documentation
   <http://www.rubydoc.info/gems/lazar-rest>
 
-* Nano-lazar Restful API issue tracker
+* Nano-lazar REST API issue tracker
   <https://github.com/opentox/lazar-rest/issues>
 
 * Lazar (source code)
   <https://github.com/opentox/lazar>
 
-* Nano-lazar GUI (graphical user interface)
-  <https://github.com/eNanoMapper/nano-lazar>
+* Swagger framework for APIs 
+  <http://swagger.io/>
+
+* Open API Initiative
+  <https://www.openapis.org/>
\ No newline at end of file
diff --git a/markdown_blocks/rest_qmrf.md b/markdown_blocks/rest_qmrf.md
new file mode 100644
index 0000000..6a3997b
--- /dev/null
+++ b/markdown_blocks/rest_qmrf.md
@@ -0,0 +1,6 @@
+lazar-rest supports (Q)SAR Model Reporting Format (QMRF). The integrated QSAR-report library\cite{rautenberg_micha_2016_179038} 
+generates QMRF reports in XML format with basic model information (e.g.
+validation results according to OECD guidelines). The QMRF report
+library is independent of other IST libraries (e.g. lazar,
+nano-lazar-gui, lazar-rest) and can be used by other applications that
+need QMRF reporting.
\ No newline at end of file
diff --git a/markdown_blocks/rest_rest.md b/markdown_blocks/rest_rest.md
new file mode 100644
index 0000000..d8d670e
--- /dev/null
+++ b/markdown_blocks/rest_rest.md
@@ -0,0 +1,4 @@
+Representational State Transfer or RESTful API is an architectural style to design webservices. 
+REST uses HTTP protocol requests GET, POST, PUT, DELETE for the communication between distributed webservices.
+nano-lazar as a part of the eNanoMapper analysis and modelling infrastructure is built upon the OpenTox web services framework following 
+the principles of the Representational State Transfer (REST) design model.
\ No newline at end of file
diff --git a/markdown_blocks/rest_screenshot.md b/markdown_blocks/rest_screenshot.md
new file mode 100644
index 0000000..4d6140c
--- /dev/null
+++ b/markdown_blocks/rest_screenshot.md
@@ -0,0 +1 @@
+![Swagger UI for the nano-lazar REST API](./images/rest_swagger_2.png "Swagger UI for the nano-lazar REST API"){width=1540px}
\ No newline at end of file
diff --git a/markdown_blocks/rest_screenshot_1.md b/markdown_blocks/rest_screenshot_1.md
deleted file mode 100644
index 51116f2..0000000
--- a/markdown_blocks/rest_screenshot_1.md
+++ /dev/null
@@ -1,8 +0,0 @@
-![nano-lazar Swagger UI](./images/rest_swagger_ui.png "nano-lazar Swagger UI"){width=1540px}
-\
-\tiny Figure 1: nano-lazar Swagger UI - service overview
-\ 
-![nano-lazar to GET a model](./images/rest_model_get.png "nano-lazar get a model"){width=1540px}
-\
-\tiny Figure 2: nano-lazar GET model data
-\ 
diff --git a/markdown_blocks/rest_summary.md b/markdown_blocks/rest_summary.md
index 7785192..3b77d93 100644
--- a/markdown_blocks/rest_summary.md
+++ b/markdown_blocks/rest_summary.md
@@ -1,5 +1,5 @@
 During the eNanoMapper project *in silico* toxicologies (IST) webservices were
 adapted in order to provide REST interfaces that adhere to eNanoMapper
 standards and specifications and supplemented with interactive SWAGGER
-documentation. This poster will give an overview of ISTs eNanoMapper API
+documentation. This poster gives an overview of ISTs eNanoMapper API
 compatible REST services\cite{rautenberg_micha_2016_187328} and demonstrate its usage with practical examples.
diff --git a/markdown_blocks/rest_swagger_ui.md b/markdown_blocks/rest_swagger_ui.md
new file mode 100644
index 0000000..2e8e5eb
--- /dev/null
+++ b/markdown_blocks/rest_swagger_ui.md
@@ -0,0 +1 @@
+Swagger UI is used as an interactive documentation and visualization platform for the lazar-rest API.
\ No newline at end of file
diff --git a/markdown_blocks/services_aa.md b/markdown_blocks/services_aa.md
new file mode 100644
index 0000000..b28afa5
--- /dev/null
+++ b/markdown_blocks/services_aa.md
@@ -0,0 +1,4 @@
+Infrastructure for eNanoMapper authentication and authorization.
+
+* Single sign-on authorization & authentication service
+  <https://openam.in-silico.ch/openam/>
diff --git a/markdown_blocks/services_docker.md b/markdown_blocks/services_docker.md
new file mode 100644
index 0000000..f06a0ac
--- /dev/null
+++ b/markdown_blocks/services_docker.md
@@ -0,0 +1,4 @@
+Docker, is an open platform container management tool that allows easily to manage, build, ship, and run distributed applications.
+
+* Public available dockerized IST services on Docker Hub
+  <https://hub.docker.com/u/insilicotox/>
diff --git a/markdown_blocks/services_infrastructure.md b/markdown_blocks/services_infrastructure.md
new file mode 100644
index 0000000..ddcc090
--- /dev/null
+++ b/markdown_blocks/services_infrastructure.md
@@ -0,0 +1,22 @@
+eNanoMapper infrastructure services implemented and maintained by IST.
+
+* Bugzilla issue tracker for eNanoMapper
+  <https://bugzilla.enanomapper.net/>
+
+* Mailman mailing list for partner, developers and associate-partners
+  <http://lists.enanomapper.net/>
+
+* Registration form and user management
+  <https://purl.enanomapper.net/register/>
+
+* Online visualization of eNanoMapper specification documents 
+  <http://specs.enanomapper.net>
+
+* Maintenance for scripts to query the eNM ontology at purl.enanomapper.net
+  (e.g. <https://purl.enanomapper.net/php/ENM_0000018>)
+
+* LDAP user database server and replication server
+  <ldap.opentox.org>
+  
+* Blog entries with technical details about eNanoMapper implementations
+  <http://opentox.github.io/archive>
diff --git a/markdown_blocks/services_lazar-rest.md b/markdown_blocks/services_lazar-rest.md
new file mode 100644
index 0000000..9a1b028
--- /dev/null
+++ b/markdown_blocks/services_lazar-rest.md
@@ -0,0 +1,20 @@
+`lazar-rest` provides an eNanoMapper compatible REST API for the `nano-lazar` read-across framework
+
+* `lazar-rest` Swagger UI documentation for API visualization and interaction. \cite{rautenberg_micha_2016_187328}
+  <https://enm.in-silico.ch>
+
+* `lazar-rest` Swagger API definition file
+  <https://enm.in-silico.ch/api/api.json> 
+
+* `lazar-rest` source code
+  <https://github.com/opentox/lazar-rest>
+
+* `lazar-rest` Ruby gem library
+  <https://rubygems.org/gems/lazar-rest>
+
+* `lazar-rest` issue tracker
+  <https://github.com/opentox/lazar-rest/issues>
+
+* `lazar-rest` API documentation
+  <http://www.rubydoc.info/gems/lazar-rest>
+
diff --git a/markdown_blocks/services_lazar.md b/markdown_blocks/services_lazar.md
new file mode 100644
index 0000000..e63888d
--- /dev/null
+++ b/markdown_blocks/services_lazar.md
@@ -0,0 +1,19 @@
+`lazar` is a framework for read-across predictions. Within eNanoMapper `lazar` was extended with interfaces for the eNanoMapper infrastructure and capabilities to predict nanomaterial toxicities.
+
+* `lazar` source code \cite{helma_christoph_2016_215483}
+  <https://github.com/opentox/lazar>
+
+* `lazar` Ruby gem library
+  <https://rubygems.org/gems/lazar>
+
+* `lazar` issue tracker
+  <https://github.com/opentox/lazar/issues>
+
+- `lazar` methodology and validation
+  <https://github.com/enanomapper/nano-lazar-paper/blob/master/nano-lazar.pdf>
+
+* `lazar` tutorial
+  <https://github.com/opentox/lazar/blob/master/README.md>
+
+* `lazar` API documentation
+  <http://www.rubydoc.info/gems/lazar>
diff --git a/markdown_blocks/services_nano-lazar-paper.md b/markdown_blocks/services_nano-lazar-paper.md
new file mode 100644
index 0000000..c61390f
--- /dev/null
+++ b/markdown_blocks/services_nano-lazar-paper.md
@@ -0,0 +1,13 @@
+Detailed description of `nano-lazar` methods and validation results. Results can be reproduced by external researchers with the accompanying docker image.
+
+* Source code for nano-lazar publication (and oral presentations).
+  <https://github.com/enanomapper/nano-lazar-paper>
+
+* Manuscript submitted to Frontiers in Pharmacology
+  <https://github.com/enanomapper/nano-lazar-paper/blob/master/nano-lazar.pdf>
+
+* Tutorial for repeating `nano-lazar` validation experiments
+  <https://github.com/enanomapper/nano-lazar-paper/blob/master/README.md>
+
+* Docker image for inspection and reproduction of validation experiments
+  <https://hub.docker.com/r/insilicotox/nano-lazar-paper/>
diff --git a/markdown_blocks/services_nano-lazar.md b/markdown_blocks/services_nano-lazar.md
new file mode 100644
index 0000000..3122fda
--- /dev/null
+++ b/markdown_blocks/services_nano-lazar.md
@@ -0,0 +1,16 @@
+The `nano-lazar` GUI provides a public webinterface for `nano-lazar` models
+
+* `nano-lazar` public webinterface \cite{gebele_denis_2017_250818}. 
+  <https://nano-lazar.in-silico.ch>
+
+* `nano-lazar` source code
+  <https://github.com/eNanoMapper/nano-lazar>
+
+* `nano-lazar` Ruby gem library
+  <https://rubygems.org/gems/nano-lazar>
+
+* `nano-lazar` issue tracker
+  <https://github.com/eNanoMapper/nano-lazar/issues>
+
+* `nano-lazar` API documentation
+  <http://www.rubydoc.info/gems/nano-lazar>
diff --git a/markdown_blocks/services_ontoviewer.md b/markdown_blocks/services_ontoviewer.md
new file mode 100644
index 0000000..d50c2d7
--- /dev/null
+++ b/markdown_blocks/services_ontoviewer.md
@@ -0,0 +1,10 @@
+The eNanoMapper ontology viewer visualizes SPARQL query results from eNM ontologies and data.
+
+* eNanoMapper ontology viewer \cite{gebele_denis_2017_259384}
+  <https://query.enanomapper.net/>
+
+* eNanoMapper ontology viewer source code
+  <https://github.com/enanomapper/enm-ontoviewer>
+ 
+* eNanoMapper ontology viewer issue tracker
+  <https://github.com/enanomapper/enm-ontoviewer/issues>
diff --git a/markdown_blocks/services_qsar-report.md b/markdown_blocks/services_qsar-report.md
new file mode 100644
index 0000000..d29a97d
--- /dev/null
+++ b/markdown_blocks/services_qsar-report.md
@@ -0,0 +1,16 @@
+QMRF and QPRF reporting features for `nano-lazar`. This library is accessible from the `nano-lazar` GUI and the `lazar-rest` webservices.
+
+* `qsar-report` source code \cite{rautenberg_micha_2016_179038}
+  <https://github.com/opentox/qsar-report>
+
+* `qsar-report` Ruby gem library
+  <https://rubygems.org/gems/qsar-report/>
+
+* `qsar-report` issue tracker
+  <https://github.com/opentox/qsar-report/issues>
+
+* `qsar-report` tutorial
+  <http://opentox.github.io/usage/2016/10/05/qmrf-and-qprf-reporting-library-gem>
+
+* `qsar-report` API documentation
+  <http://www.rubydoc.info/gems/qsar-report>
diff --git a/markdown_blocks/services_sparql.md b/markdown_blocks/services_sparql.md
new file mode 100644
index 0000000..b2a9562
--- /dev/null
+++ b/markdown_blocks/services_sparql.md
@@ -0,0 +1,7 @@
+SPARQL query interface for eNanoMapper data and ontologies
+
+* SPARQL endpoint
+  <https://sparql.enanomapper.net/>
+
+* Documentation
+  <http://enanomapper.net/deliverables/d3/20160420_eNanoMapper_D3.2_Data_Management_System_with_extended_search_capabilities_FINAL.pdf>
diff --git a/markdown_blocks/services_summary.md b/markdown_blocks/services_summary.md
index 3b7305c..9f13628 100644
--- a/markdown_blocks/services_summary.md
+++ b/markdown_blocks/services_summary.md
@@ -1,6 +1,6 @@
 During the eNanoMapper project *in silico* toxicologies (IST) public server
 infrastructure was adapted to the requirements of the eNanoMapper project and
-augmented with new developments. This poster will give a comprehensive overview
-all IST resources developed within eNanoMapper. Each service will be presented
+augmented with new developments. This poster gives a comprehensive overview of
+all IST resources developed within eNanoMapper. Each service is presented
 with a brief description and links to the public interface, source code,
 documentation and download links for self-contained docker images.