The Ferryman

ToxBank uses ISA-Tab to describe a diverse range of biological datasets

ToxBank uses ISA-Tab to describe a diverse range of biological datasets to ensure higher quality analysis #ToxBank #opentox #2014SOT #ToxExpo Visit Douglas Connect booth 1770

 

 

ToxBank supports 75 organisations within SEURAT-1 cluster

ToxBank supports a wide diversity of experimental and modelling activities carried out by 75 organisations within the SEURAT-1 research cluster, which is developing replacement alternatives for safety assessment.

SEURAT-1 is a public-private partnership funded by Cosmetics Europe and the EC.

 

 

#ToxBank Launch at SOT 2014 #opentox #2014SOT #ToxExpo

 

 

Complex (Big Data) Omics Analysis supported by ToxBank

ToxBank provides a unique combination of people and scalable infrastructure enabling Complex (Big Data) Omics Analysis. Come and discuss with us at #sot2014 #opentox #toxbank #toxexpo Demos at Douglas Connect Stand 1770 #opentox

 

ToxBank Launch at SOT 2014

We are launching ToxBank at the SOT 2014 conference in Phoenix, Arizona this week.

ToxBank provides a 21st century data and analysis infrastructure for predictive toxicology.

ToxBank builds on the unique advantages of the OpenTox framework.

Come by the Douglas Connect stand 1770 to try out and discuss.

If you are not at the event please contact us to arrange a virtual meeting.

http://www.toxbank.net/

First ToxBank Tutorial released

We have released the first ToxBank tutorial on Searching the Data Warehouse:

http://www.youtube.com/watch?v=mE54EnY8uB4

More to follow in coming days!

Building a data and analysis architecture based on Open Standards

At the OpenTox Euro 2013 meeting in Mainz I presented on our developments with ToxBank in a data and analysis architecture based on Open Standards.

The background of developing Open Standards, Open Specifications and related Open Source Components with OpenTox provides a valuable foundation on which we are developing ToxBank as a reference extensible architecture for predictive toxicology.

I suggested OpenTox is developing itself as an Open Knowledge Community supporting accelerating innovation through knowledge sharing, application development, semantic interoperability and ontology for combining data and models, and learning from the application of developed tools to problem solving.

We are interacting with many partners on the SEURAT-1 program providing a rich context for requirements gathering, design and implementation, working closely with the evolving needs and development goals of the program.

We have been working on putting in place best practices on the description of data, and importantly the protocols used to generate and process that data.

I suggested it is also a priority that this practice includes the contributions of computational science and integrated analysis, and I encouraged both the OpenTox community and the ToxBank development to progress this important goal.

The above approaches provide a foundation on which we can integrate many advances in integrated analysis, systems biology, in vitro assay development, omics, and bioengineeering to support an event driven Weight of Evidence approach and semantic reasoning across ontology-linked heterogenous evidence.

You can download a copy of the slides here as a pdf:

Download ToxBank OpenTox Euro 131001 1.2

or view them on slideshare:

http://www.slideshare.net/barryhardy3/tox-bank-opentox-euro-131001-12

 

Related articles

OpenTox Euro 2013 program

OpenTox Euro 2013 Speaker Program

OpenTox USA 2013 program and goals

Open Data, Open Source, and Open Standards for Toxicology, chaired by Egon Willighagen (Maastricht University)

Discussion of Open Source, Standards, and Data running at OpenTox Euro 2013 -and what you can build with them :)!

And we should consider Open Specifications and Open Projects (as introduced by Egon at start)

AMBIT Web services: chemical data and models via OpenTox API, Nina Jeliazkova (IdeaConsult Ltd)

Chemical decision support in toxicology and pharmacology, Ola Spjuth (Uppsala University)

Phenotype Database, Jildau Bouwman (TNO)

Assessing compound carcinogenicity in vitro using connectivity mapping, Florian Claiment (Maastricht University)

The ChEMBL Database: Open data for use in Toxicity Prediction, Anne Hersey (EMBL-EBI)

More info at:

http://www.opentox.org/meet/opentoxeu2013/opentoxeu2013program

Related articles

OpenTox Euro 2013 Speaker Program

Hands-on predictive toxicology workshops

OpenTox Euro 2013 program

Predictive Toxicology Ontology Perspectives and Roadmap

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OpenTox Euro 2013 workshops running

1. #oteu13#OpenTox Euro 2013 Workshop - Identifying and Selecting ChEMBL datasets for toxicology modelling http://www.opentox.org/meet/opentoxeu2013/chembl …
2. #oteu13#OpenTox Euro 2013 Workshop - Using Scaffold Hunter for the Visual Analysis of Chemical Datasets http://www.opentox.org/meet/opentoxeu2013/scaffoldhunter …

3. #oteu13#OpenTox Euro 2013 Workshop - Integrated Enrichment and Analysis of Omics datasets mapped to Pathways http://www.opentox.org/meet/opentoxeu2013/omics …

4. #oteu13#OpenTox Euro 2013 Workshop - Predicting interactions with drug metabolizing enzymes http://www.opentox.org/meet/opentoxeu2013/metabolism …

5. #oteu13#OpenTox Euro 2013 Workshop - Use lazar-GUI for predictions with QSAR models based on lazar-OpenTox framework http://www.opentox.org/meet/opentoxeu2013/lazar …

6. #oteu13#OpenTox Euro 2013 Workshop - Adverse Outcome Pathway (AOP) building with the AOP Knowledge Base http://www.opentox.org/meet/opentoxeu2013/aop/aop …

7. #oteu13#OpenTox Euro 2013 Workshop - ToxML Workshop: Using the ToxML Wiki Site http://www.opentox.org/meet/opentoxeu2013/toxml …

8. #oteu13#OpenTox Euro 2013 Workshop - Predicting Chemical Liabilities with Bioclipse and OpenTox http://www.opentox.org/meet/opentoxeu2013/chemicalliabilities …

9. #oteu13 #OpenTox Euro 2013 Workshop - Visualise and Explore Chemical Feature Space of a Dataset http://www.opentox.org/meet/opentoxeu2013/chesmapper …

Predictive Toxicology Discussion Questions

- How can we advance better data management practices?
- How do we progress access to data?
- How can we improve quality evaluation of data?
- What are achievable next steps to increase public data resource interoperability?
- What are requirements for integrating confidential and public data?
- What are opportunities for collaboration between different Open Standards?
- What are key requirements for semantic interoperability?
- Can we identify concrete actions to advance interoperability in and between projects?
- How do we advance greater adoption of open standards for public resources?
- How do we advance greater adoption of open standards by commercial providers?
- What are the key visualisation requirements in predictive toxicology use cases?
- What gaps need to be filled?
- How can open standards be used to advance visualisation and analysis applications?
- How interactive should visualization be for the end-user?
- What platforms should visualization be available on (web based, stand-alone)?
- How can we better integrate data resources with visualisation and analysis applications?
- How can we better integrate algorithm resources with visualisation applications?
- What are key capabilities we have today in systems biology that can be used for predictive toxicology?
- What are the challenges? What gaps need to be filled?
- How can we use systems biology to make better sense of omics data?
- How can we use systems biology in hypothesis generation and experimental planning?
- How can open standards be used to advance systems toxicology applications?
- What are key information resources we have today in metabolism that can be used for predictive toxicology?
- What are key modelling resources that can be used for predictive toxicology?
- What are the challenges? What gaps need to be filled?
- How can we advance the use of metabolic networks in predictive toxicology?
- How can open standards be used to advance applications incorporating metabolism?
- What kind of data integration do we need for predictive toxicology use cases?
- What is the role of ontology in supporting integrated anaylsis?
- How do we best integrate heterogenous data?
- How do we advance weight of evidence approaches?
- How can we better incorporate kinetics modelling in our analysis?
- What are key steps to progress research applications and data for industrial use and regulatory acceptance?

 

We will discuss these questions at the OpenTox Euro 2013 Knowledge Café.

http://www.opentox.org/meet/opentoxeu2013/opentoxeuro2013knowledgecafe/

Related articles

OpenTox Euro 2013 Speaker Program

ToxBank Infrastructure - paper available in Open Access

OpenTox USA 2013 program

Data Gaps in Toxicity Testing of Chemicals allowed in Food in the United States, Study #FDA

OpenTox Euro 2013 Speaker Program

The OpenTox Euro 2013 speaker program with abstracts is now available at:
http://www.opentox.org/meet/opentoxeu2013/opentoxeu2013program

and includes the following presentations:

A. Data Management and Analysis, chaired by Nina Jeliazkova (Ideaconsult Ltd)

XMetDB - Xenobiotics Metabolism Database, Patrik Rydberg (University of Copenhagen)
PathVisio 3: new features for pathway analysis and visualization, Martina Kutmon (Maastricht University)
ToxML: Community Based Development of a Common Data Exchange Standard for Toxicology, Mohammed Ali (Lhasa Ltd)
The ISA infrastructure: from experimental planning to data publication, Alejandra Gonzalez-Beltran (University of Oxford)
The Open Pharmacological Triple Store Concepts, Egon Willighagen (Maastricht University)

B. Open Data, Open Source, and Open Standards for Toxicology, chaired by Egon Willighagen (Maastricht University)

AMBIT Web services: chemical data and models via OpenTox API, Nina Jeliazkova (IdeaConsult Ltd)
Chemical decision support in toxicology and pharmacology, Ola Spjuth (Uppsala University)
Phenotype Database, Jildau Bouwman (TNO)
Assessing compound carcinogenicity in vitro using connectivity mapping, Florian Claiment (Maastricht University)
The ChEMBL Database: Open data for use in Toxicity Prediction, Anne Hersey (EMBL-EBI)

C. Visualization & Visual Analytics, chaired by Andreas Karwath (Johannes Gutenberg University of Mainz)

The Chemical Space Project, Jean-Louis Reymond (University of Berne)
Visual Analytics for the Comparison of Chemical and Biologic Data, Tatiana von Landesberger (Technische Universität Darmstadt)
Visual Analysis of Chemical Space with Scaffold Hunter, Nils Kriege (TU Dortmund)
CheS-Mapper, Martin Gütlein (University of Freiburg)

D. Systems Biology & Predictive Toxicology, chaired by Jürgen Borlak (Hannover Medical School)

Integrated Analysis of Toxicology Data supported by ToxBank, Barry Hardy (Douglas Connect)
HeMiBio - Generation of hepatic microfluidic bioreactors with a regenerative cell source of parenchymal and non-parenchymal liver cells for high throughput long-term hepatotoxicity testing, Stefan Heinz (Medicyte)
Application of toxicogenomics and TG-GATEs database for drug safety screening, Takeki Uehara (Shionogi Pharmaceutical Research Center)
The Systems Biology Simulation Core Library: A numerical method for the quantitative simulation of biochemical reaction networks , Alexander Dörr (University of Tuebingen)

E. Innovative Developments in Predictive Toxicology, chaired by Barry Hardy (Douglas Connect) and Stefan Kramer (Johannes Gutenberg University of Mainz)

This session will feature presentations on a variety of innovative developments in current predictive toxicology applications and projects.

Approaches to analyze and datamine the eTOX database, Jörg Wichard (Bayer)
InCroMAP – a tool for the integrated analysis and pathway-centered visualization of cross-omics datasets,  Johannes Eichner (University of Tuebingen)
Integration of molecular detail from OMICS-technologies for prediction of toxicity, André Schrattenholz (ProteoSys AG)
DNA Repair and Damage Response Following Exposure of Cells to Alkylating Carcinogens, Bernd Kaina (University Medical Center, Mainz)

 

Related articles

Predictive Toxicology Ontology Perspectives and Roadmap

Hands-on predictive toxicology workshops

Evidence-based Toxicology Collaboration

OpenTox USA 2013 program