Community of Research NATHAN A. BAKER1, HUBERT RAUSCHER2 Computational and Statistical Analytics, Pacific Northwest National Laboratory1; DG Joint Research Centre Unit Nanobiosciences, European Comission2 March 2013, Society of Toxicology 52nd Annual Meeting
Nanomaterials are small and diverse The promise: High density Improved biodistribution Multi-modal applications The problems: Combinatorial diversity Difficult characterization An important challenge! 3 McNeil SE. J Leukoc Biol, 2005. 78(3): p. 585-94. doi:10.1189/jlb.0205074
data Anti-tumor activity In vitro drug release Zeta Potential Preparation Chemical composition of nanoparticle formulation Source: Chawla JS et al, Int J Pharm, 249, 127-38 (2002), Son YJ et al, J Control Release, 91, 135-145 (2003) What is the problem? Diversity of data
for nanomaterial informatics Systematically describe nanomaterials Structure and composition Physico-chemical properties … Understand nanomaterial interactions Interaction with immediate milieu Fate and transport in environment Impact on human health Search for existing data on nanoparticle synthesis and properties Exchange nanomaterial chemical, physical, and biological data (comparability) Design nanomaterials with custom properties for specific applications March 6, 2014 6
US, EU, and other countries focused on the environmental, health, and safety issues associated with nanotechnology Three main goals engaging in an active discussion about environmental, health, and safety questions for nano-enabled products encouraging joint programs of work that would leverage resources establishing communities of practice, including identification of key points-of- contact / interest groups / themes between key US and EU researchers and key US and EU funding sources for near-term and future collaborations March 6, 2014 8 http://www.us-eu.org/
(Mar 2012, San Francisco) Intended as specific platforms to develop a shared repertoire of protocols and methods to overcome research gaps and barriers and to enhance their professional relationships Six CoRs: Risk Assessment Databases & Ontologies Ecotoxicity Testing & Predictive Models Predictive Modeling for Human Health Exposure through Life Cycle Risk Management & Control March 6, 2014 9
communicating and agreed information systems covering nanoscale material descriptions nanomaterial properties (intrinsic & context-dependent) and their effects, including environmental and health-related The goals of this CoR are to enable the sharing, searching, and analysis of NM characterization data across a wide range of active and archived experimental sources to give advice on how to structure these data to enable their widest possible use Realization of these goals will allow integration of pertinent risk assessment data among labs provide situational awareness of data coverage across nanomaterial categories enable predictive computational models for bridging physical properties and biological outcomes with exposure, dispersal and fate March 6, 2014 10
to support the above activities and representation of those concepts in an ontological framework Data elements: Identification of the data elements necessary to establish common data-sharing model(s) for this domain Data exchange: Specification of requirements for sharing data between research groups and repositories in human- and machine- interpretable forms March 6, 2014 11
to support the above activities and representation of those concepts in an ontological framework Data elements: Identification of the data elements necessary to establish common data-sharing model(s) for this domain Data exchange: Specification of requirements for sharing data between research groups and repositories in human- and machine- interpretable forms March 6, 2014 13
knowledge underlying the description, preparation, and characterization of nanomaterials Includes terms from other biomedical ontologies Provides logical relations between terms Purpose Common vocabulary and data elements Structured and unstructured data annotation Semantic integration of data Unambiguous interpretation of data Knowledge-based searching Knowledge-framework for developing data sharing models and standards http://www.nano-ontology.org/ March 6, 2014 14
to support the above activities and representation of those concepts in an ontological framework Data elements: Identification of the data elements necessary to establish common data-sharing model(s) for this domain Data exchange: Specification of requirements for sharing data between research groups and repositories in human- and machine- interpretable forms March 6, 2014 16
information on nanomaterials in a standardized structure for reporting results of studies on nanomaterials derived from IUCLID 5 (database used for registration of substances according to REACH – the European Chemicals Regulation) the dataformat builds on OECD Harmonised Templates (OHTs) features additional nanomaterial- specific endpoints consists of independent, consortium specific installations, including OECD WPMN aims at compatibility to (EU) regulatory requirements March 6, 2014 17 Individual
sharing in the research community to expedite and validate the use of nanomaterials in biomedicine •caNanoLab provides support for the annotation of nanomaterials with composition information, characterizations, and protocols •caNanoLab leverages and extends concepts from the NCI’s Enterprise Vocabulary Services (EVS) and the NanoParticle Ontology (NPO) Composition Characterizations Protocols
to support the above activities and representation of those concepts in an ontological framework Data elements: Identification of the data elements necessary to establish common data-sharing model(s) for this domain Data exchange: Specification of requirements for sharing data between research groups and repositories in human- and machine- interpretable forms March 6, 2014 20
and extends the Investigation/Study/Assay (ISA-TAB) format (http://www.isa-tools.org/) Standard tab-delimited file format Developed by the European Bioinformatics Institute (EBI) for representing a variety of assays and technology types ISA-TAB-Nano supports ontology-based curation Nanomaterials and concepts from the NanoParticle Ontology (NPO) as well as other ontologies 22
Data types Nanomaterial coverage Modeling tools Collecting results into a special journal issue: http://j.mp/15tPAdK Identifying initial driving problems and use cases Exploratory data analysis Predictive modeling Data sharing needs Your input is needed! March 6, 2014 25
government, academia, industry Objectives: Identification of the data elements necessary to establish common data- sharing model(s) Specification of requirements for sharing data between research groups and repositories in human- and machine-interpretable forms Definition of concepts necessary to support the above activities and representation of those concepts in an ontological framework Get involved Monthly calls http://www.us-eu.org/ March 6, 2014 26
NCI-Fredrick Stacey Harper, OSU Fred Klaessig, PA Bio Juli Klemm, NCI Iseult Lynch, UC Dublin European Union Nano Safety Cluster National Nanotechnology Initiative National Nanotechnology Coordinating Office National Institutes of Health March 6, 2014 27