The Ferryman

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

ToxBank Infrastructure - paper available in Open Access

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 …

OpenTox USA 2013 program and goals

The OpenTox USA 2013 speaker program with abstracts is now available at:
http://www.opentox.org/meet/opentoxusa2013/opentoxusa2013speakerprogram

We will be joined by presenters from many leading US research programs including ToxCast, Tox21, US EPA, NIEHS, NTP, NIH, US FDA, Risk21, Hamner and John Hopkins.

The meeting is organised in collaboration with ToxBank and will include participation from SEURAT-1 European research programs including HeMiBio, COSMOS, NOTOX, and ToxBank.

The meeting should provide a valuable opportunity to progress transatlantic goals on interoperability and collaboration supporting SEURAT-1 - Tox21 interactions based on concrete activities related to data resource interoperability, open standards, software development, modelling and integrated analysis.

We will also specifically address key îssues of extrapolation, kinetics modelling and risk assessment application providing roadblocks to be removed from the path to regulatory acceptance.

Abstracts for the poster session presentations should be submitted using:
https://www.easychair.org/conferences/?conf=opentoxusa2013

On behalf of the OpenTox USA 2013 Organising Committee, we look forward to seeing you in Raleigh-Durham.

best regards
Barry Hardy (Douglas Connect)
Scott Auerbach (NIEHS)
Rusty Thomas (US EPA)
Asish Mohapatra (Health Canada)


OpenTox USA 2013

Organised in collaboration with ToxBank.

Hamner Conference Center, North Carolina Biotechnology Center

29 - 30 October 2013

Topics: data management, in silico modelling and application development, integrated data analysis, biokinetics, cheminformatics, bioinformatics, weight of evidence, risk assessment.

Conference Overview:
http://www.opentox.org/meet/opentoxusa2013

Registration:
https://www.surveymonkey.com/s/OpenToxUSA2013

The views presented in this message are those of the authors and do not necessarily reflect those of any US or European organisation.  No official endorsement is intended nor should be inferred.

Related articles

OpenTox Euro 2013 Speaker Program

ToxBank wiki open

Hands-on predictive toxicology workshops

ToxBank Infrastructure - paper available in Open Access

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

Evidence-based Toxicology Collaboration

The Evidence-based Toxicology Collaboration (EBTC) was formed to translate the principles and approaches of Evidence-based Medicine/Health Care to toxicology (http://www.ebtox.com/).

Open approaches to standards, data, software and ontology as promoted by the OpenTox Community (http://www.opentox.org/) can make a valuable contribution to the development of EBTC case studies applying systematic reviews in toxicology.

I will join Thomas Hartung and Sebastian Hoffmann at an EBTC session at EuroTox 2013 to discuss the development of systematic reviews in toxicology, which would be facilitated by a toxicology ontology.

I expect we will also communicate further details on this collaborative effort virtually to the community and look forward to hearing from those who have interest in this initiative.

Evidence-based Toxicology Collaboration
EuroTox 2013, Interlaken, Switzerland
13.00-14.00, Monday, September 2
Room: Grimsel 1+2
Chair: Thomas Hartung, USA
Evidence-based approaches, which were pioneered in medicine, provide the means to transparently, objectively, and consistently assess the evidence bearing on questions in medicine or other fields of science. The EBTC comprises stakeholders in academia, industry, and government seeking to strengthen decision-making in safety sciences, and thereby enhance confidence in the process by which scientific evidence is assessed. The EBTC is primarily interested in assessing the performance of the toxicological test methods and addressing questions about the safety of substances to human health and the environment. The EBTC’s efforts are timely, as there is growing interest in applying systematic reviews in toxicology, which would be facilitated by a toxicology ontology, as well as a growing recognition that new test assessment approaches are needed, for example in the context of composing and assessing integrated testing strategies.
13.00 –13.20
Evidence-based Toxicology (EBT) and the EBT Collaboration: Sebastian Hoffmann, Germany
13.20 –13.40
EBT and Integrated Testing Strategy: Thomas Hartung, USA
13.40–14.00
Toxicology Ontology Development supporting Evidence-based Approaches in Predictive Toxicology: Barry Hardy, Switzerland

 

Related articles

Knowledge Management Training, Geneva

How Reliable is the "Evidence Base"?

Hands-on predictive toxicology workshops

OpenTox Euro 2013 program

OpenTox USA 2013 program

ToxBank Infrastructure - paper available in Open Access

"Burn Your Textbooks"

Hands-on predictive toxicology workshops

We are organising a variety of hands-on interactive workshops for OpenTox Euro 2013 which will provide attendees the opportunity to work on predictive toxicology analysis and modelling problems with a variety of methods and software applications. Sessions will include:

- Predicting Chemical Liabilities with Bioclipse and OpenTox, Ola Spjuth (Uppsala University) and Egon Willighagen (Maastricht University)
- Developing a Weight of Evidence for a Library, Barry Hardy (Douglas Connect)
- Using ToxML for Data Exchange, Philip Judson and Mohammed Ali (Lhasa Ltd)
- Use lazar and OpenTox for (Q)SAR model development and validation, Micha Rautenberg and David Vorgrimmler (in silico toxicology)
- Predicting interactions with drug metabolizing enzymes, Patrik Rydberg (University of Copenhagen)
- Visualise and Explore Chemical Feature Space of a Dataset, Martin Gütlein (Univ. Freiburg) and Andreas Karwath (Johannes Gutenberg University of Mainz)
- Integrated Enrichment and Analysis of Omics datasets mapped to Pathways,  Johannes Eichner (University of Tuebingen)
- Using Scaffold Hunter for the Visual Analysis of Chemical Datasets, Nils Kriege and Till Schäfer (TU Dortmund)
- Identifying and Selecting ChEMBL datasets for toxicology modelling, Anne Hersey (EMBL-EBI)

More information will be posted at:

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

OpenTox USA 2013 program

The OpenTox USA 2013 community meeting on innovative developments and
applications in predictive toxicology will take place in RTP, North Carolina 29 - 30 October. The meeting is being organised as a collaboration between OpenTox and ToxBank.

The preliminary program is available at:
http://www.opentox.org/meet/opentoxusa2013

The meeting provides an opportunity for researchers to learn about best
practices and new applications in data management, modelling and analysis applied for predictive toxicology and risk assessment purposes.

Abstracts for the poster session are being accepted through 30 September.

On behalf of the OpenTox USA 2013 Organising Committee,
we look forward to seeing you in Raleigh-Durham.

Barry Hardy (Douglas Connect)
Scott Auerbach (NIEHS)
Rusty Thomas (Hamner Institutes)
Asish Mohapatra (Health Canada)


OpenTox USA 2013

Hamner Conference Center, North Carolina Biotechnology Center

29 - 30 October

Topics: data management, in silico modelling and application development, integrated data analysis, biokinetics, cheminformatics, bioinformatics, weight of evidence, risk assessment.

Abstract Submission:
https://www.easychair.org/conferences/?conf=opentoxusa2013

Registration:
https://www.surveymonkey.com/s/OpenToxUSA2013

Knowledge Management Training, Geneva

We will run our international Knowledge Management Training week in Geneva, Switzerland 18-22 November 2013.

Topics:
Knowledge Management (KM) Concepts, KM Practices, Business Case, Strategy, Program Planning, KM Frameworks, KM & Organisational Culture & Development, Change Management for KM Programs, Leadership and Competencies for KM Knowledge Assessment, Metrics, Enterprise Knowledge Management, Process-oriented Knowledge Management, Knowledge Mapping, Benchmarking, Expertise Location, Search, Personal Knowledge Management, Web 2.0, Communities, Collaboration


More Information:
http://douglasconnect.com/km/km-training

http://douglasconnect.com/events/Geneva2013

Program Brochure (pdf):
http://www.douglasconnect.com/sites/default/files/Geneva_flyer.pdf

OpenTox Euro 2013 program

The OpenTox Euro 2013 community meeting on innovative developments and
applications in predictive toxicology will take place in Mainz 30 Sept -
2 October. The meeting is being organised as a collaboration between OpenTox and ToxBank.

The preliminary program is available at:
http://www.opentox.org/meet/opentoxeu2013

The meeting provides an opportunity for researchers to learn about best
practices and new applications in data management, modelling and analysis.

Hands-on interactive workshops will provide attendees the opportunity to
work on analysis and modelling problems with a variety of software
applications.

Abstracts for the poster session are being accepted through 31 August.

On behalf of the OpenTox Euro 2013 Organising Committee,
we look forward to seeing you in Mainz

Barry Hardy (Douglas Connect) and Stefan Kramer (Johannes Gutenberg University of Mainz)


OpenTox Euro 2013

Johannes Gutenberg University of Mainz, Mainz, Germany

30 September - 2 October

Session Topics: Integrated Data Analysis, Open Data, Open Source, Open
Standards, Systems Biology and Toxicology, Visualisation and Analysis,
Innovative Developments

Organising Committee: Barry Hardy (Douglas Connect), Andreas Karwath,
Stefan Kramer (Johannes Gutenberg University of Mainz), Nina Jeliazkova
(Ideaconsult), Egon Willighagen (Maastricht University), and Juergen
Borlak (Hannover Medical School)

Abstract Submission:
https://www.easychair.org/conferences/?conf=opentoxeuro2013

Registration:
https://www.surveymonkey.com/s/OpenToxEU2013