The theme of the ACS meeting activities in Boston the next few days is one close to our values and current attention with Douglas Connect and our communities and partners: Innovation from Discovery to Application.
I will present on a few of our initiatives on this innovation path at the meeting in Boston and will upload the presentations on the net (including here).
Look forward to interacting in Boston or virtually!
Monday 17 August
8-10.30, room 103
Session on Workflow Tools & Data Pipelining in Drug Discovery
chaired by Tim Dudgeon and Erin Davis
Workflows supporting drug discovery against malaria
Barry Hardy, Thomas Exner and Alessandro Contini
The goal of Scientists Against Malaria (SAM) is the discovery of novel anti-malarial compounds. SAM supports virtual drug discovery organizational structures collaborating on target selection and modeling, protein expression and assay development, computational drug design, and screening. A combination of interoperable information systems, ontologies and web services were designed and deployed to manage the data, documents, computational and assay results, activity and toxicology predictions, as well as dashboards to track project progress and to support decision making. Workflows were developed for consensus virtual screening of candidate malarial kinase inhibitors including docking, pharmacophore-based screening and free energy-based molecular simulations. The models were applied to the discovery of active ligands against a novel target with previously unknown structure or ligands. The workflows were extended to include OpenTox model web services to prioritize drug candidates according to their predicted toxicities, supporting a weight of evidence categorization of candidate molecules according to their activity and toxicity profiles.
DOWNLOAD SAM Drug Discovery Presentation Download 150817 SAM ACS
13-18.00, room 103
Session on The Growing Impact of Openness in Chemistry: A Symposium in Honor of JC Bradley
chaired by Andrew Lang and Antony Williams
OpenTox - an open community and framework supporting predictive toxicology and safety assessment
One important goal of OpenTox is to support the development of an Open Standards-based predictive toxicology framework that provides a unified access to toxicological data and models. OpenTox supports the development of tools for the integration of data, for the generation and validation of in silico models for toxic effects, libraries for the
development and integration of modelling algorithms, and scientifically sound validation and reporting routines.
The OpenTox Application Programming Interface (API) is an important open standards development for software development purposes. It provides a specification against which development of global interoperable toxicology resources by the broader community can be carried out. The use of OpenTox API-compliant web services to communicate instructions between linked resources with URI addresses supports the use of a wide variety of commands to carry out operations such as data integration, algorithm use, model building and validation. The OpenTox Framework currently includes, with its APIs, services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, reporting, investigations, studies, assays, and authentication and authorisation, which may be combined into multiple applications satisfying a variety of different user needs. As OpenTox creates a semantic web for toxicology, it should be an ideal framework for incorporating toxicology data, ontology and modelling developments, thus supporting both a mechanistic framework for toxicology and best practices in statistical analysis and computational modelling.
In this presentation I will review the recent OpenTox-based development of applications including the ToxBank data infrastructure supporting integrated analysis across biochemical, functional and omics datasets supporting the safety assessment goals of the SEURAT-1 program which aims to develop alternatives to animal testing.
Finally, I will provide an overview of the working group activities of the newly formed OpenTox Association which aim to progress the development of open source, data, standards and tools in this area.
DOWNLOAD OpenTox Presentation: Download 150817 OpenTox ACS
Tuesday 18 August
13.30-17.00, waterfront 1A/1B
Session on Current Topics in Chemical Safety Information
chaired by Leah McEwen and Ralph Stuart
eNanoMapper - A Database and Ontology Framework for Nanomaterials Design and Safety Assessment
Barry Hardy, Egon L. Willighagen, Janna Hastings, Markus Hegi, Lucian Farcal, Nina Jeliazkova, Haralambos Sarimveis
The eNanoMapper EU FP7 project is developing a data management and analysis infrastructure together with ontologies supporting the safety assessment activities of the European nanomaterials research and development community. The project addresses the requirements of safety assessment of nanomaterials by providing databases, analysis tools and ontologies for risk assessment and linking them with existing resources in this area.
The work involves close cooperation with the EC NanoSafety Cluster members and other international organisations such as the EC JRC, and the EU-US NanoEHS cooperation initiative. Their requirements guide the development of tools for experimental design, model building, systems biology, and meta analysis across multiple datasets.
An ontology for nanosafety research is being developed to provide the following features: annotation of nanostructures and relevant biological properties, annotation of experimental model systems (e.g. cell lines), conditions, and protocols, complex search and reasoning capabilities, and the integration of data from existing nanotoxicology sources.
Systematic physicochemical, geometrical, structural, and biological studies of nanomaterials are rare in the public domain and data sharing is only just commencing, given the absence of readily available solutions for that purpose. eNanomapper will address that issue, as the establishment of a universal standardisation schema and infrastructure for nanomaterials safety assessment is a key goal of the project. It will catalyze collaboration, integrated analysis, and discoveries from data organised within a knowledge-based framework. It will support the discovery of nanomaterial properties responsible for toxicity, the identification of toxicity pathways and nano-bio interactions from linked datasets, ontologies, omics data and external data sources.
By interfacing with statistical and data mining tools, eNanoMapper aims to provide scientifically sound guidelines for experimental design as well as computational models for predicting nanotoxicity. These computational models will help to design safe nanomaterials and improve the risk assessment of existing nanoparticles.
This presentation will provide an overview of the progress made in the initial 18 months of the project, including outlines of the initial development releases of the data platform and ontology.
Download eNanoMapper presentation: Download 150813 eNanoMapper ACS Boston
Using OpenTox to map toxicity data to AOPS
OpenTox provides a framework where data and model predictions can be retrieved from a federated set of data sources.
In this presentation we will discuss the concept of using relevant information (including its retrieval and organisation from multiple sources) in the development and application of Adverse Outcome Pathways (AOPs).
Analysis and discussion of the information obtained were used in conjunction with a collaborative wiki based approach to AOP development and interpretation.
We discuss the requirements and prospective solutions for the further computational development of AOPs e.g., using data and metadata to semantically annotate AOP nodes, challenge limitations in an AOP or propose new nodes for the AOP.
We will present meta analysis examples from the ToxBank data infrastructure project supporting integrated analysis across biochemical, functional and omics datasets supporting the safety assessment goals of the SEURAT-1 program which aims to develop alternatives to animal testing.
Download OpenTox, ToxBank and AOPS presentation Download 150819 OpenTox AOP 1.2