1. ISA-TAB-Nano A specification to facilitate data exchange among nanotechnology researchers and resources ISA-TAB-Nano https://wiki.nci.nih.gov/display/ICR/ISA- TAB-Nano https://wiki.nci.nih.gov/display/ICR/ISA- TAB-Nano Stacey Harper, Oregon State University Sharon Gaheen, SAIC-Frederi ck

2. Target Audiences and Applications Audiences Biomedical researchers (Nano)-Materials scientists Toxicologists Regulatory scientists Industrial hygienists … Applications Synthesis Therapeutics, diagnostics, imaging Bionics and prosthetics Risk and exposure assessment Toxicity prediction and reduction Laboratory and occupational safety …

3. Challenges: Diversity Combinatorial complexity in nanoparticle formulation Diversity of test systems Ecosystem vs. organism vs. cell vs. test tube Species, cell line Age, gender, weight Diversity of measurements and assays Physical and chemical: size, potential, surface chemistry, shape, aggregation, … Biological: toxicity, recognition and association, uptake, delivery, … Exposure: dose and concentration, timing, duration, … Diversity of data resources with lack of common standard for data exchange

4. Diversity in Composition and Formulation McNeil SE. J Leukoc Biol, 2005. 78(3): p. 585-94. doi:10.1189/jlb.0205074 Aqueous Dry

5. Nanomaterials are Complex 3 rd Dimension to the Periodic Table

6. Photos adapted: Dr. Z Wang, Georgia Tech Nanomaterials are Complex Diversity of Zinc Oxide Nanoparticles

7. Assay and Data Diversity 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)

8. Data Resource Diversity

9. Goal of ISA-TAB-Nano Develop a specification to facilitate the exchange of data on nanomaterials and their characterizations to/from nanotechnology resources Develop a specification to facilitate the exchange of data on nanomaterials and their characterizations to/from nanotechnology resources

10. What is ISA-TAB-Nano? A standard tab-delimited format for describing data related to: Investigations Materials (Nanomaterials) Studies (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 ISA-TAB-Nano supports ontology-based curation Nanomaterials and concepts from the NanoParticle Ontology (NPO) as well as other ontologies

11. Uses and Benefits Address the data sharing challenges in nanomedicine Provide a standard means for identifying nanomaterials and characterizations Enable the submission and exchange of nanomaterial data to/from nanotechnology data resources ( e.g., NBI, caNanoLab, etc.) Empower organizations to adopt standards for representing data in nanotechnology publications Provide researchers with guidelines for representing nanomaterials and characterizations to achieve cross- material comparison

12. ISA-TAB-Nano Structure 1. Describe the Investigation and Studies 1. Describe the Investigation and Studies 2. Identify Study Samples 2. Identify Study Samples 3. Record Assay Conditions and Measurements 3. Record Assay Conditions and Measurements i_xxx.txt m_xxx.txt s_xxx.txt a_xxx.txt Investigation File Study File(s)Material File(s)Assay File(s)

13. ISA-TAB-Nano Structure 1. Describe the Investigation and Studies 2. Identify Study Samples 2. Identify Study Samples 3. Record Assay Conditions and Measurements 3. Record Assay Conditions and Measurements i_xxx.txt m_xxx.txt s_xxx.txt a_xxx.txt Investigation File Study File(s)Material File(s)Assay File(s)

14. ISA-TAB-Nano Investigation File Describes: Primary investigation Associated studies, assays, and protocols Descriptive information about the study includes: Design descriptors and factors Publications Assays and protocols Contacts Vertical-based spreadsheet format with columns representing multiple values

15. Investigation File Ontology References Investigation Description Investigation Contacts Investigation Publications

16. Investigation File (cont.) Study Description Study Design Study Contacts

17. Investigation File (cont.) Study Publications Study Assays Study Factors Study Protocols

18. ISA-TAB-Nano Structure: Identify Study Samples 1. Describe the Investigation and Studies 1. Describe the Investigation and Studies 2. Identify Study Samples 3. Record Assay Conditions and Measurements 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)

19. ISA-TAB-Nano Study File Provides mapping between the study samples, materials, and processing events Samples can be: Biological materials Nanomaterials Small molecules For physical-chemical characterizations of nanomaterials, the sample is the nanomaterial For in vitro and in vivo characterizations, the sample is the biological specimen (cell line, animal, etc.) Horizontal spreadsheet describing the biological materials and association with the nanomaterials described in the Material file

20. Study File Biological Sample Identifier Biological Sample Characteristics Protocol Biological Sample Study Factors

21. ISA-TAB-Nano Material File Primary file for describing: Nanomaterial composition and formulation Physical properties Structure Allows for: Comparison of nanomaterials across nanotechnology resources Association with optional files; e.g., a Structure file for representing the 3D structure of the nanomaterial Horizontal spreadsheet describing the nanomaterial sample, associated components, material characteristics, and material linkages

22. Material File Material Identifiers Material Description Intended Application Material Type Chemical Name Characteristics

23. Material File (cont.) Material Linkage Material File Characteristics

24. Structure File NCL Dendrimer-Based MRI Contrast Agents Atom Header

25. ISA-TAB-Nano Structure 1. Describe the Investigation and Studies 1. Describe the Investigation and Studies 2. Identify Study Samples 2. Identify Study Samples 3. Record Assay Conditions and Measurements i_xxx.txt m_xxx.txt s_xxx.txt a_xxx.txt Investigation File Study File(s)Material File(s)Assay File(s)

26. ISA-TAB-Nano Assay File Describes the protocol parameters and factors, including: Temperature Media/solvent Concentration Provides references or links to assay results, including: Measurements Instrumentation Derived data files Templates available for the “top Nano WG assays” Size by DLS (Physico-Chemical) Zeta Potential (Physico-Chemical) Hemolysis (In Vitro) Hepatocarcinoma Cytoxicity (MTT and LDH) (In Vitro) Caspase 3 Apoptosis (In Vitro) Toxicity (ADME, Single/Repeat Dose) (In Vivo) Your assay here!

27. ISA-TAB-Nano Assay File Horizontal-based spreadsheet format with the following sections: SAMPLE NAMES PROTOCOL PARAMETERS ASSAY FACTORS ASSAY MEASUREMENTS ASSAY FILES

28. Assay File Size by DLS Sample Names Protocol Parameters Assay Factors Assay Measurements Assay Files

29. ISA-TAB-Nano Site Walkthrough

30. Investigation File Example

31. Study File Examples

32. Material File Examples

33. Nanomaterial Examples Carbon Nanotube: Amine functionalized single wall nanotube with attached fluorescent oligonucleotide Dendrimer: G4.5 COONa terminated PAMAM dendrimer-Magnevist® complex Liposome: Liposome associated with 30% C6-ceramide Fullerene: C60 fullerene derivatives

34. Assay File Examples

35. Assay Examples Hemolysis Pharmacokinetics Tissue Distribution Pharmacokinetics Cytotoxicity Size by Dynamic Light Scattering Caspase Apoptosis

36. BioPortal Navigation

37. ISA-TAB Resources

38. ISA-TAB-Nano Future ISA-TAB-Nano ASTM Ballot Initial ballot for standard specification submitted May 2012 Re-balloted as a standard guide. Estimated ballot completion end of December 2012 ISA-TAB-Nano Manuscript Submitted manuscript to BMC Biotechnology on October 2012 Manuscript was accepted ISA-TAB-Nano Users Guide Basic descriptions of elements, glossary Organized collection of examples Tutorials Easier NPO Annotation/Integration List of most relevant terms List of missing terms Real World Applications “Client” engagement Friendly user support https://cananolab.nci.nih.gov/caNanoLab http://nbi.oregonstate.edu/

39. Getting Started 1.Contact us for help! nano-tab-l@list.nih.govnano-tab-l@list.nih.gov 2.Use ISA-TAB-Nano template to create ISA-TAB-Nano files: https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano 3.Leverage template glossary for definitions: https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano 4.View example files: https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano 5.Navigate the BioPortal ontology for terms: http://purl.bioontology.org/ontology/NPO http://purl.bioontology.org/ontology/NPO 6.Complete ISA-TAB-Nano files and send to the ISA-TAB-Nano Listserv: nano-tab-l@list.nih.govnano-tab-l@list.nih.gov 7.http://nbi.oregonstate.edu/http://nbi.oregonstate.edu/ NCI Nano WG ISA-TAB-Nano Site: https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano

40. ISA-TAB-Nano is a Community-Driven Effort Nanotechnology Toxicology Assays ISA-TAB- Nano NCI caNanoLab ONAMI NBI Your Organization Here! NIOSH NIL NIBIB Nano- Registry NIEHS NTP NCI CSN Nanomaterials, Characterizations, Protocols 3D Nanomaterial Structures Nanotechnology Safety Protocols Nanotechnology Biological Interactions Curated Nanomaterial Biological, Environmental Interactions

41. References ISA-TAB-Nano Project Site: https://wiki.nci.nih.gov/display/IC R/ISA-TAB-Nano https://wiki.nci.nih.gov/display/IC R/ISA-TAB-Nano ASTM nano-TAB Work Item WK28974: http://www.astm.org/DATABASE. CART/WORKITEMS/WK28974.ht m http://www.astm.org/DATABASE. CART/WORKITEMS/WK28974.ht m ISA-TAB: http://isatab.sourceforge.net http://isatab.sourceforge.net caBIG ICR Nano WG Data Standards Document: https://wiki.nci.nih.gov/display/IC R/ISA-TAB-Nano https://wiki.nci.nih.gov/display/IC R/ISA-TAB-Nano NanoParticle Ontology (NPO): http://www.nano-ontology.org http://www.nano-ontology.org ISA-TAB-Nano Project Team Nathan Baker, PNNL Dennis Thomas, PNNL Amy Bednar, ERDC Elaine Freund, 3 rd Millennium Marty Fritts, NCL Sharon Gaheen, SAIC Sue Pan, SAIC Liz Hahn-Dantona, Lockheed Martin Stacey Harper, Oregon State University Mark Hoover, NIOSH Fred Klaessig, Pennsylvania Bio Nano Systems Juli Klemm, NCI CBIIT Mervi Heiskanen, NCI CBIIT David Paik, Stanford University Grace Stafford, The Jackson Laboratory Todd Stokes, Georgia Tech