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US-EU Nanotechnology Databases and Ontology Com...

US-EU Nanotechnology Databases and Ontology Community of Research

Presented at the [2013 Society of Toxicology meeting](http://www.toxicology.org/ai/meet/am2013/).

Nathan Baker

March 12, 2013
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  1. March 6, 2014 PNNL-SA-93678 1 US-EU Nanotechnology Databases and Ontology

    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
  2. What is the problem? Unrealized potential due to combinatorial complexity

    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
  3. Size distribution data Surface morphology data Tissue biodistribution Drug loading

    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
  4. Nanotechnology informatics needs The nanotechnology community has an immediate needs

    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
  5. US-EU nanoEHS dialogue  A team of researchers from the

    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/
  6. US-EU Nanotechnology Communities of Research Launched at 51st SoT meeting

    (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
  7. Databases and Ontology CoR vision The community needs interconnected, freely

    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
  8. Initial focus of CoR Concept definitions: Definition of concepts necessary

    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
  9. Initial focus of CoR Concept definitions: Definition of concepts necessary

    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
  10. Describing nanoparticle formulations with the Nanoparticle Ontology Ontology for representing

    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
  11. Initial focus of CoR Concept definitions: Definition of concepts necessary

    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
  12. Managing nanomaterial information with NANOhub Platform for managing and exchanging

    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
  13. caNanoLab https://cananolab.nci.nih.gov •caNanoLab is a portal designed to facilitate data

    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
  14. A tool for the storing, sharing, and analysis of data

    from the nanomaterial community Web Address: www.nanomaterialregistry.org Funded by:
  15. Initial focus of CoR Concept definitions: Definition of concepts necessary

    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
  16. Protocol Reference Sample Identifiers Sample Material Name Protocol REF ParameterValue[instrument]

    ParameterValue[pH of solution] Parameter Value [NaCl concentration] NCL-20 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS) Mastersizer 2000 7.4 NCL-20 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS) Mastersizer 2000 7.4 NCL-22 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS) Mastersizer 2000 7.4 NCL-22 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS) Mastersizer 2000 7.4 NCL-22 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS) Mastersizer 2000 7.4 NCL-23 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS) Mastersizer 2000 7.4 NCL-23 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS) Mastersizer 2000 7.4 NCL-23 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS) Mastersizer 2000 7.4 Measurement Value[Z-avg (nm)] Measurement Value[Peak size (nm)] Measurement Value[pdl] Image File Derived Data File 5.2 4.4 0.122 distribution20.jpg ncl_20.xls 8.6 6.2 0.211 8.5 6.0 0.200 distribution22.jpg ncl_22.xls 6.6 5.2 0.214 7.9 5.1 0.282 7.4 5.3 0.235 distribution23.jpg ncl_23.xls 8.4 6.1 0.265 9.8 5.6 0.358 Study Factors Performer Date Assay Name Factor Value[temperature] Unit Term Source Ref Term Accession Number Factor Value[media solvent] Anil Patri 2010:05:12 Size by DLS 25 celsius UO saline Anil Patri 2010:05:12 Size by DLS 25 celsius UO PBS Anil Patri 2010:05:12 Size by DLS 25 celsius UO saline Anil Patri 2010:05:12 Size by DLS 25 celsius UO PBS Anil Patri 2010:05:12 Size by DLS 37 celsius UO PBS Anil Patri 2010:05:12 Size by DLS 25 celsius UO saline Anil Patri 2010:05:12 Size by DLS 25 celsius UO PBS Anil Patri 2010:05:12 Size by DLS 37 celsius UO PBS Assay Measurements Assay Files Assay Name Data Repositories NTP (NIEHS) NCL (NCI, FDA, NIST) NBI (ONAMI) InterNano (NNN) NIL (NIOSH) STANDARDIZED STANDARDIZED Goal of ISA-TAB-Nano Develop a specification to facilitate the import/export of data on nanomaterials and their characterizations to/from nanotechnology resources
  17. ISA-TAB-Nano A standard tab-delimited format for describing nanotechnology data Leverages

    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
  18. Initial focus of CoR Inventorying resources and methods Specific resources

    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
  19. Get involved! Membership: 35 registered participants Diverse international group from

    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
  20. Acknowledgments Marty Fritts, NIST Kenneth Dawson, UC Dublin Sharon Gaheen,

    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