The Ferryman

ToxBank wiki open

I am happy to inform that we have now made the first version of the ToxBank wiki (wiki.toxbank.net) open.

The first version of this wiki contains information on reference compounds which will be used to probe mechanisms of toxicity as carried out by experiments and modelling under the SEURAT-1 predictive toxicolgy research program. The long term strategic target of this program is "Safety Evaluation Ultimately Replacing Animal Testing". We make this resource public to provide useful information in support of other research projects with similar goals and to foster cross-fertilisation, alignment and collaboration.

I will be happy to receive your feedback and suggestions on this new resource.

Barry Hardy

barry.hardy -!(at)- douglasconnect.com

https://www.facebook.com/barry.hardy3

Predictive Toxicology Ontology Perspectives and Roadmap

Re: #OpenTox, ontology, new predictive toxicology systems

The following papers are now available from the new issue of Altex:

Toxicology ontology perspectives
This article provides an overview of some of the leading developments in
incorporating ontology into new knowledge-based systems in predictive toxicology.

http://www.altex.ch/en/index.html?id=16&aid=3

A toxicology ontology roadmap
In this article we lay out the main justifications and needs for ontology
development to enable the building of interoperable predictive toxicology systems
and services for industry to design and test safer products.

http://www.altex.ch/en/index.html?id=16&aid=2

OpenTox Toxicology Ontology Development

This article is just out online describing initial #OpenTox ontology work:

#OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337268/

#OpenTox - #Bioclipse Cloud article

The final version of our first #OpenTox - #Bioclipse paper on getting our tox cloud working with the Bioclipse workbench for interactive design for safety purposes is now available in open access. See http://www.biomedcentral.com/1756-0500/4/487

Updated progress of Scientists Against Malaria initiative

I presented a progress update on our Scientists Against Malaria drug discovery initiative at the BIO-IT Europe conference in October. You can download the presentation as a pdf:

Collaborative Virtual Organisation and Infrastructure for Anti-Malarial Drug Design

Bioclipse and OpenTox partner up to create a unique workbench semantic web combination

#OpenTox and #Bioclipse have partnered up on a new open platform we hope you will try out!

We describe the combination of the Bioclipse workbench and distributed OpenTox web services to create a unique safety assessment exploration and design environment for chemists, biologists and toxicologists in the following new paper:

Computational toxicology using the OpenTox application programming interface and Bioclipse

BMC Research Notes 2011, 4:487

http://www.biomedcentral.com/1756-0500/4/487

I believe future developments of this platform are looking promising. Welcome your feedback!

Barry

New OpenTox Exercises

Try out some new #OpenTox predictive toxicology exercises!

Based on our recent OpenTox 2011 workshop activities, we have set
up several demonstration applications and exercises at the following
address:
http://www.opentox.org/meet/opentox2011/exercises

I hope you can try an exercise there of interest to you!

You can provide feedback via the evaluation form at:
https://www.surveymonkey.com/s/652XY7C

Please feel free to contact me your questions and suggestions!

OpenTox 1.0 - what we have reached on its third birthday

 


On the eve of its 3rd birthday, I told the story so far of our development of OpenTox in Slovenia last week.

The lecture (slides and video) recorded at the Josef Stefan institute in Ljubljana on "OpenTox - the creation of a semantic web for toxicology" is available at:
http://videolectures.net/solomon_hardy_semantic/

I look forward to that future "Sixth Sense" journey interoperating with OpenTox to revisit the Tamboti Trees in South Africa and the Mopane Trees in Namibia, and to test the delivery of safety advice from the distributed semantic knowledge of OpenTox 3.0 use cases in the field :)!

Innovation Questions for the field of Predictive Toxicology

What are key innovation questions for the field of predictive toxicology? I propose we discuss the following questions at our Knowledge Cafe at the #OpenTox 2011 meeting in Munich. We can use the discussions as a basis to formulate an innovation white paper to provide direction to innovators who can accelerate developments in the field with strategy and technology development.

A. Mechanistic Strategies - What are the key innovations needed to accelerate progress?

B. Predictive Metabolism - What is needed for a complete and reliable prediction of metabolites?

C. Computational Chemistry - Emerging challenges and opportunities in receptor-mediated predictive toxicology

D. Systems Biology - How can we bridge the divide between modelling molecular pathways and quantitative prediction at the organelle level?

E. Integrated Analysis - Experimental designs for optimising biomarker discovery

F. Kinetics - Extrapolating in vitro data to model human hazard and exposure

G. Weight of Evidence - Developing holistic approaches to compound profiling and prioritisation-based decision making

H. Read Across and Categories - What are the key components for a more rigorous approach to a best practice?

I. Regulatory Needs - How do we accelerate the acceptance of emerging scientific methods in regulatory applications?

J. High Content Assays - What information can they provide today and what are the key gaps requiring new innovation?



OpenTox Services and Applications

I have posted a presentation summarising recent developments in #OpenTox services and applications, as reported at the AXLR8 meeting in Berlin at:

http://www.opentox.org/data/documents/development/presentations/opentoxpresAXLR82011/view

Developments include:

- OpenTox data infrastructure based on Ambit containing quality labelled data for over 185, 000 chemicals

- Development of OpenTox ontology including ToxML conversion

- Deployment of Authorisation & Authentication (A&A) services

- Extension of ToxPredict to 23 endpoints (as of May 2011) with A&A deployed

- Extension of ToxCreate to include confidences and ToxPredict integration with A&A deployed

- Development of Validation & Reporting services (including QMRF and QPRF)

- QPRF reporting with Q-edit

- Read Across (alpha prototype)

- CheS-Mapper for chemical dataset visualisation

- Descriptor calculations with ToxDesc, IBMC Desc and MaxTox

- Bioclipse-OpenTox interoperation

- Deployment in Scientists Against Malaria drug discovery collaboration

- Development and testing of Taverna workflows across OpenTox resources