1 Nanotechnology Working Group Nathan Baker Report to Integrative Cancer Research Workspace January 11, 2012

2 Working Group Current Composition (June to present) Academia Stanford, Oregon State, U Mass, UCLA, Jackson Lab Industry Pa NanoBIO, I-A-I, NNN, 3 rd Millennium, Lockheed, Sapient, SAIC Government PNNL, EPA, CDC, DoD, Army Corps, NCI-F/NCL, NIEHS NTP, NIEHS CEBS, NIBIB, NCI NanoAlliance, NCI CBIIT Standards ISO, ASTM 2

3 Working group high-level objectives Enabling nanomedicine informatics applications Develop data exchange standards Develop ontologies Build a community of interest To support ultimate goals of informatics in nanomedicine Predictive models for nanomaterial activity Rational design of nanomaterials

4 Working Group Scope Shaw et al., PNAS, 105: 7387.

5 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! McNeil SE. J Leukoc Biol, (3): p doi: /jlb

6 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, (2002), Son YJ et al, J Control Release, 91, (2003) What is the problem? Diversity of data

7 What is the problem? Disconnected resources and users

8 What does the community need? The nanomedicine community has an immediate need for nanomaterial informatics: Understand nanomaterial toxicity and other biological properties Search for existing data on nanoparticle synthesis and properties Systematically represent nanomaterial structure and composition Exchange nanomaterial chemical, physical, and biological data Design nanoparticles, and other materials with custom properties for specific biological applications

9 Our focus Information exchange and analysis through Data exchange standards Ontology Information resources Methodology development and applications in nanomaterial prediction: Biological activities Chemical and physical characteristics

10 NanoParticle Ontology (NPO) Capture knowledge underlying nanomaterial Preparation Chemical composition Physiochemical characterization Biological function/behavior Basic Formal Ontology structure Initial focus on cancer diagnosis and therapy Current growth to include a broader range of nanotechnology concepts Supported by the caBIG ® Nano WG Available through Bioportal Thomas DG, Pappu RV, Baker NA. NanoParticle Ontology for Cancer Nanotechnology Research. J Biomed Inform, in press. doi: /j.jbi /j.jbi

11 Example view into the NPO

12 A more detailed view of nanoparticle composition using the NPO

13 Protocol Reference Sample Identifiers Study Factors Assay Measurements Assay Files Assay Name Data Repositories NTP (NIEHS) NCL (NCI, FDA, NIST) NBI (ONAMI) InterNano (NNN) NIL (NIOSH) STANDARDIZED Goal of nano-TAB Develop a specification to facilitate the import/export of data on nanomaterials and their characterizations to/from nanotechnology resources

14 What is nano-TAB? A standard tab-delimited format for describing data related to Investigations Nanomaterials Specimens Assays Leverages and extends the Investigation/Study/Assay (ISA- TAB) format Standard tab-delimited file format Developed by the European Bioinformatics Institute (EBI) for representing a variety of assays and technology types Example: MAGE-TAB Nano-TAB supports ontology-based curation Nanomaterials and concepts from the NanoParticle Ontology (NPO) as well as other ontologies

15 nano-TAB structure 1. Describe the Investigation and Studies 2. Identify Study Samples 3. Record Assay Conditions and Measurements i_xxx.txt m_xxx.txts_xxx.txt a_xxx.txt Investigation File Study File(s)Material File(s)Assay File(s)

16 Nano WG meetings Weekly on Thursdays at 1 pm ET x77412 # Adobeconnect Meeting: nanowg nanowg Subgroups caNanoLab Users Group Meeting Bimonthly in Nano WG time slot beginning Feb 2 nano-TAB Weekly on Tuesdays at 11 am ET x # Adobeconnect Meeting:

17 Outreach (June to present) ISA-TAB Nanoinformatics Roadmap/NNN FDA NIEHS CEBS OBI BioPortal/PubNano NEHI European Nanosafety Cluster 17

18 Peer Reviewed Publications Thomas DG, Gaheen S, et.al., NANO-TAB: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format, manuscript submitted to BMC Bioinformatics, Nov 2011 Thomas DG, Klaessig F, et. al. Informatics and standards for nanomedicine technology. Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology. Volume 3, Issue 5, pages 511–532, September/October 2011 Klaessig, F., Marrapese, M., et. al.; Current Perspectives in Nanotechnology Terminology and Nomenclature; Nanotechnology Standards, Nanostructure Science and Technology, 2011,Springer New York. doi: / _2 Maojo,V., García-Remesal,M., et.al., anoinformatics: Developing Advanced Informatics Applications for Nanomedicine. In: Intracellular Delivery;Fundamental Biomedical Technologies. Netherlands: Springer; Volume 5, Part 3, Thomas, D.G., Pappu, R.V., Baker, N.A. NanoParticle Ontology for cancer nanotechnology research. Journal of Biomedical Informatics Volume 44, Issue 1, February 2011, Pages Gonzalez-Nilo, F., Perez-Acle, T., et al. Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology. Biological research, Vol. 44, No. 1. (0 2011), pp

19 Tool Use Metrics InstitutionLevel of UseQuantity of Data/Project nano-TAB OSUProduction214 data files PNNL/Wash UProduction23 nanoparticles Army, I-A-I, OSUPilotNEIMiner EU NanoSafety ClusterPilotNapiraHub NNNPilot caNanoLabInitial Review NPO Nano-TAB projectsvarious EMBL-EBI, University of Groningen ProductionIncorp into OntoCAT Stanford, NCBO, PNNLPubNano

20 Summary Introduction to the caBIG® Nanotechnology Working Group Overview of nanotechnology informatics challenges Research projects Ontology development Data exchange standards PubNano resource Structure-property-activity modeling Current participants Jessica Adamick, Nathan Baker, Amy Bednar, Alan Chappell, Yoram Cohen, Brad Collins, Joe Fisher, Jennifer Fostel, Denis Fourches, Gilberto Fragoso, Elaine Freund, Marty Fritts, Sharon Gaheen, Sumit Gangwal, Liz Hahn-Dantona, Stacey Harper, Mark Hoover, Fred Klaessig, Juli Klemm, Sharon Ku, Carole LeBlanc, James Luo, Andre Nel, David Paik, Sue Pan, Jens Poschet, Krzysztof Ptak, Robert Rallo, Grace Stafford, Kaizhi Tang, Dennis Thomas, Amy Wang, Denise Warzel, Trish Whetzel Current participants Jessica Adamick, Nathan Baker, Amy Bednar, Alan Chappell, Yoram Cohen, Brad Collins, Joe Fisher, Jennifer Fostel, Denis Fourches, Gilberto Fragoso, Elaine Freund, Marty Fritts, Sharon Gaheen, Sumit Gangwal, Liz Hahn-Dantona, Stacey Harper, Mark Hoover, Fred Klaessig, Juli Klemm, Sharon Ku, Carole LeBlanc, James Luo, Andre Nel, David Paik, Sue Pan, Jens Poschet, Krzysztof Ptak, Robert Rallo, Grace Stafford, Kaizhi Tang, Dennis Thomas, Amy Wang, Denise Warzel, Trish Whetzel Funding NIH NCI caBIG ® ICR Workspace Funding NIH NCI caBIG ® ICR Workspace