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:
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.
- 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 predictivetoxicology 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.
A. Data Management and Analysis, chaired by Nina Jeliazkova (Ideaconsult
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
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
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
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)
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.
Evidence-based Toxicology (EBT) and the EBT Collaboration: Sebastian
EBT and Integrated Testing Strategy: Thomas Hartung, USA
Toxicology Ontology Development supporting Evidence-based Approaches in
Predictive Toxicology: Barry Hardy, Switzerland
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
- 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)
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 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.