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Nanomedicine informaticsDENNIS G. THOMAS, PACIFIC NORTHWEST NATIONAL LABALAN CHAPPELL, PACIFIC NORTHWEST NATIONAL LABELAINE FREUND, 3RD MILLENNIUMSHARON GAHEEN, SAICSTACEY HARPER, OREGON STATE UNIVERSITYJULI D. KLEMM, NIH/NCIDAVID S. PAIK, STANFORD UNIVERSITYNATHAN A. BAKER, PACIFIC NORTHWEST NATIONAL LAB, [email protected]
Pacific Northwest National Laboratory
NCI Nano Alliance - Nano WG July 5, 2012
National Cancer Institute caBIG® Nanotechnology Working Group
GovernmentNational Institutes of Health
NCI, NHLBI, NIBIB, NCL
Center for Disease Control
Food and Drug Administration
Environmental Protection Agency
…
AcademiaWashington University
Pacific Northwest National Lab
Oregon State
Stanford
MIT
Georgia Tech
UCLA
…
IndustryIntel
Pennsylvania NanoSystems
…
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Standards organizationsASTM E56ISO TC229
Alliances and organizationsInternational Alliance for NanoEHS HarmonizationOregon Nanoscience and Microtechnologies InstituteNational Nanotechnology InitiativeNational Nanomanufacturing NetworkNCI Nano Alliance
Working Group Scope
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Future
Biomedical Research Community
CCNEInvestigator
Alliance Investigator
caBIG™ caGrid
(Advertise, Discover, Query, Security -Data and Analytical Grid Services)
Animal ModelsClinical,Genomics, Proteomics,Tissue/Pathology,Imaging,caBIG™ Services
FuturecaNanoLab Portal
Characterizations and Protocols
Techniques, Assays, Protocols
Regulatory Agencies
caNanoLab Portal
NCL
caGrid Portal
Characterizations and Protocols
Characterizations and Protocols
Sharon Gaheen, SAIC
Shaw et al., 2008. PNAS, 105: 7387.
Nano WG current areas of focus
Nano-TAB development (enabling)Nanotechnology data sharing standards
Working draft ready
Community engaged
Need to focus on applications and standards
NPO support and expansion (enabling)Standard vocabulary and ontology for nanomedicine
Foundation established
Community engaged
Need to focus on support for nano-TAB and other annotation projects
Nano-QSAR (applying)Structure-activity relationships for nanomaterial-biological interactions
Community engaged; participants identified
Many potential areas of focus
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NANOTECHNOLOGY INFORMATICS CHALLENGES
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!
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McNeil SE. J Leukoc Biol, 2005. 78(3): p. 585-94.doi:10.1189/jlb.0205074
Size distribution data
Surface morphology data
Tissue biodistribution
Drug loading data
Anti-tumor activity
In vitro drug releaseZeta 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
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What is the problem? Disconnected resources and users
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Nanomedicine informatics needs
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
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NANOTECHNOLOGY ONTOLOGY
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Ontology enables resource integration
NanoParticle Ontology (NPO)
Capture knowledge underlying nanomaterial
PreparationChemical compositionPhysiochemical characterizationBiological function/behavior
Basic Formal Ontology structureInitial focus on cancer diagnosis and therapyCurrent growth to include a broader range of nanotechnology conceptsSupported by the caBIG® Nano WGAvailable through Bioportalhttp://purl.bioontology.org/ontology/NPO
http://www.nano-ontology.org/
Thomas DG, Pappu RV, Baker NA. NanoParticle Ontology for Cancer Nanotechnology Research. J Biomed Inform, in press. doi:10.1016/j.jbi.2010.03.001
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Example view into the NPO
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A more detailed view of
nanoparticle composition
using the NPO
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NANOTECHNOLOGY RESOURCE INTEGRATION
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NCBO + NPO enable resource integration
Bioportal, NCBO Resource Index, & PubNano
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NANOTECHNOLOGY DATA SHARING
Protocol ReferenceSample 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 7.4NCL-20 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS)Mastersizer 2000 7.4NCL-22 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS)Mastersizer 2000 7.4NCL-22 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS)Mastersizer 2000 7.4NCL-22 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS)Mastersizer 2000 7.4NCL-23 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS)Mastersizer 2000 7.4NCL-23 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS)Mastersizer 2000 7.4NCL-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] I mage File Derived Data File5.2 4.4 0.122 distribution20.jpg ncl_20.xls8.6 6.2 0.2118.5 6.0 0.200 distribution22.jpg ncl_22.xls6.6 5.2 0.2147.9 5.1 0.2827.4 5.3 0.235 distribution23.jpg ncl_23.xls8.4 6.1 0.2659.8 5.6 0.358
Study FactorsPerformer Date Assay Name Factor Value[temperature] Unit Term Source RefTerm Accession NumberFactor Value[media solvent]Anil Patri 2010:05:12 Size by DLS 25 celsius UO salineAnil Patri 2010:05:12 Size by DLS 25 celsius UO PBSAnil Patri 2010:05:12 Size by DLS 25 celsius UO salineAnil Patri 2010:05:12 Size by DLS 25 celsius UO PBSAnil Patri 2010:05:12 Size by DLS 37 celsius UO PBSAnil Patri 2010:05:12 Size by DLS 25 celsius UO salineAnil Patri 2010:05:12 Size by DLS 25 celsius UO PBSAnil Patri 2010:05:12 Size by DLS 37 celsius UO PBS
Assay Measurements Assay Files
Assay Name
Data RepositoriesNTP (NIEHS)
NCL (NCI, FDA, NIST)NBI (ONAMI)
InterNano (NNN)NIL (NIOSH)
STA
ND
AR
DIZ
ED S
TAN
DA
RD
IZE
D
Goal of nano-TAB
Develop a specification to facilitate the import/export of data on nanomaterials and their characterizations to/from nanotechnology resources
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
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)
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)
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
Investigation File
ONTOLOGY SOURCE REFERENCETerm Source Name MO NPO
Term Source File http: / /purl.bioontology.org/ontology/MOhttp: / /purl.bioontology.org/ontology/npo
Term Source Version v. 1.3.1.1 v. 2011-02-12Term Source Description MGED Ontology NanoParticle OntologyINVESTIGATION Investigation Identifier NCL200612AInvestigation Title Dendrimer-Based MRI Contrast Agents
Investigation Description
The goal of this investigation is to characterize a PAMAM dendrimer with an associated gadolinium chelate MRI Investigation Disease
Investigation Disease Term Accession NumberInvestigation Disease Term Source REFInvestigation OutcomeInvestigation Submission Date 2002-11-30Investigation Public Release Date 2002-11-30INVESTIGATION CONTACTSInvestigation Person Last Name McNeilInvestigation Person First Name ScottInvestigation Person Middle Initials EInvestigation Person Email [email protected] Person Phone 3018466939Investigation Person Fax
Investigation Person AddressMSC 1050 Boyles Street, Frederick, MD 21702
Investigation Person AffiliationNanotechnology Characterization Laboratory
Investigation Person Role investigatorInvestigation Person Role Term Accession NumberInvestigation Person Role Term Source REF MOINVESTIGATION PUBLICATIONSInvestigation PubMed ID 18095846Investigation Publication DOI 10.2217/17435889.2.6.789
Investigation Publication Author listHall J B; Dobrovolskaia MA; Patri AK; McNeil SE
Investigation Publication TitleCharacterization of nanoparticles for therapeutics
Investigation Publication Status publishedInvestigation Publication Status Term Accession NumberInvestigation Publication Status Term Source REF
Ontology References
Investigation Description
Investigation Contacts
Investigation Publications
STUDYStudy Identifier NCL200612A-Size
Study Title Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS)Study Submission Date 2002-11-30Study Public Release Date 2002-11-30
Study Description
Dynamic light scattering(DLS) technique was used to measure the hydrodynamic size of dendritic nanomaterials. The effects of sample concentration, buffer and temperature on the hydrodynamic size (stability) also were measured.
Study DiseaseStudy Disease Term Accession NumberStudy Disease Term Source REF
Study Outcome
Hydrodynamic size (diameter) of the dendrimer samples NCL22, NCL23 and NCL20 were measured in aqueous solutions using DLS at 25 °C and 37 °C. An instrument with a backscattering detector was used for these measurements in batch mode (no fractionation). This technique does not have the resolving power of differentiating monomers and dimers without fractionation. Samples were weighed, dissolved in deionized (DI) water, aliquoted, lyophilized and resuspended in desired buffer solutions to a final concentration of 1 mg/mL, and filtered through a 0.2-μm filter, unless otherwise indicated. The measurements were taken in saline (154 mM NaCl) and phosphate-buffered saline (PBS) at pH 7.4. Three measurements were taken for each sample. For NCL22, the size is slightly larger when dispersed in saline compared to PBS. In PBS, the size is independent of temperature. This is in contrast to NCL23, which is larger in PBS than in saline. NCL23 also shows temperature dependence, as its size decreases slightly with increased temperature in PBS. Finally, NCL20 is larger when dispersed in PBS compared to saline.
Study File Name s_size-DLS.xlsStudy File DescriptionSTUDY DESIGN DESCRIPTORSStudy Design Type comparisonStudy Design Type Term Accession NumberStudy Design Type Term Source REFSTUDY CONTACTSStudy Person Last Name PatriStudy Person First Name AnilStudy Person Middle Initials KStudy Person Email [email protected] Person Phone 3018465237Study Person Fax
Study Person Address MSC 1050 Boyles Street, Frederick, MD 21702
Study Person Affiliation Nanotechnology Characterization LaboratoryStudy Person Role investigatorStudy Person Role Term Accession NumberStudy Person Role Term Source REF MO
Investigation File (cont.)
Study Description
Study Design
Study Contacts
STUDY PUBLICATIONSStudy PubMed ID 18095846Study Publication DOI 10.2217/17435889.2.6.789
Study Publication Author list Hall J B; Dobrovolskaia MA; Patri AK; McNeil SE
Study Publication Title Characterization of nanoparticles for therapeuticsStudy Publication Status publishedStudy Publication Status Term Accession NumberStudy Publication Status Term Source REFSTUDY ASSAYSStudy Assay Measurement Type hydrodynamic sizeStudy Assay Measurement Type Term Accession NumberStudy Assay Measurement Type Term Source REFStudy Assay Technology Type dynamic light scattering(DLS)Study Assay Technology Type Term Accession Number NPO_1469Study Assay Technology Type Term Source REF NPOStudy Assay Technology PlatformStudy Assay Measurement Name hydrodynamic diameter; peak size; PDIStudy Assay Measurement Name Term Accession Number ; ; NPO_1155Study Assay Measurement Name Term Source REF ; ; NPOStudy Assay File Name a_size-DLS.xlsSTUDY FACTORSStudy Factor Name temperature solvent mediumStudy Factor Name Term Accession Number PATO_0000146 NPO_1855Study Factor Name Term Source REF PATO NPOStudy Factor Type condition conditionStudy Factor Type Term Accession NumberStudy Factor Type Term Source REFSTUDY PROTOCOLS
Study Protocol NameMeasuring the size of nanoparticles in aqueous media using batch-mode dynamic light scattering
Study Protocol Typesample preparation procedure; particle size measurement procedure
Study Protocol Type Term Accession NumberStudy Protocol Type Term Source REF
Study Protocol Description
This assay protocol outlines procedures for sample preparation and the determination of mean nanoparticle size (hydrodynamic diameter) using batch-mode dynamic light scattering (DLS) in dilute aqueous suspensions. Although particle sie is the primary determinant of the measured diffusion coefficient, other parameters can impact these measurements and influence the measured size. Therefore, guidelines for making successfuly size measurements in the nanosize range are provided, as well as a discussion of relevant standardss and data analysis. This protocol can be applied to any suitable DLS instrument with batch measurement capability.
Study Protocol URI NCL_Method_PCC-1.pdfStudy Protocol Version 1.1
Study Protocol Parameter Name pH; NaCl concentration; particle concentrationStudy Protocol Parameter Name Term Accession Number UO_0000196; ; NPO_1830Study Protocol Parameter Name Term Source REF UO; ;NPOStudy Protocol Component Name Mastersizer 2000 (Malvern DLS)Study Protocol Component Type DLS instrumentStudy Protocol Component Type Term Accession Number NPO_1766Study Protocol Component Type Term Source REF NPO
Investigation File (cont.)
Study Publications
Study Assays
Study Factors
Study Protocols
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)
ISA-TAB-Nano Study File
Provides mapping between the study samples, materials, and processing events Samples can be:
Biological materialsNanomaterialsSmall molecules
For physical-chemical characterizations of nanomaterials, the sample is the nanomaterialFor 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
Study File
Source Name Material Type Characteristic[cell type] Characteristic[ATCC#] Protocol REF PerformerLLC-PK1 biospecimen porcine proximal tubule cells CL-101 cell preparation in four 96-well plates Marina DobrovolskaiaLLC-PK1 biospecimen porcine proximal tubule cells CL-101 cell preparation in four 96-well plates Marina DobrovolskaiaLLC-PK1 biospecimen porcine proximal tubule cells CL-101 cell preparation in four 96-well plates Marina DobrovolskaiaLLC-PK1 biospecimen porcine proximal tubule cells CL-101 cell preparation in four 96-well plates Marina DobrovolskaiaLLC-PK1 biospecimen porcine proximal tubule cells CL-101 cell preparation in four 96-well plates Marina DobrovolskaiaLLC-PK1 biospecimen porcine proximal tubule cells CL-101 cell preparation in four 96-well plates Marina DobrovolskaiaLLC-PK1 biospecimen porcine proximal tubule cells CL-101 cell preparation in four 96-well plates Marina DobrovolskaiaLLC-PK1 biospecimen porcine proximal tubule cells CL-101 cell preparation in four 96-well plates Marina DobrovolskaiaLLC-PK1 biospecimen porcine proximal tubule cells CL-101 cell preparation in four 96-well plates Marina Dobrovolskaia
Sample NameFactor Value[material source identifier]
Factor Value[particle concentration] Unit
Factor Value[time of exposure] Unit
LLC-PK1-6h-NCL22-1 NCL-22 0.004 mg/mL 6 hourLLC-PK1-6h-NCL22-2 NCL-22 0.008 mg/mL 6 hourLLC-PK1-6h-NCL22-3 NCL-22 0.016 mg/mL 6 hourLLC-PK1-6h-NCL22-4 NCL-22 0.032 mg/mL 6 hourLLC-PK1-6h-NCL22-5 NCL-22 0.064 mg/mL 6 hourLLC-PK1-6h-NCL22-6 NCL-22 0.128 mg/mL 6 hourLLC-PK1-6h-NCL22-7 NCL-22 0.256 mg/mL 6 hourLLC-PK1-6h-NCL22-8 NCL-22 0.512 mg/mL 6 hourLLC-PK1-6h-NCL22-9 NCL-22 1 mg/mL 6 hour
Biological Sample Identifier Biological Sample Characteristics Protocol
Biological Sample Study Factors
ISA-TAB-Nano Material File
Primary file for describing:Nanomaterial composition and formulationPhysical propertiesStructure
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
Material File
Material Source Identifier Material Name Material Description Material Synthesis
Material Design Rationale
Material I ntended Application
Material I ntended Application Term Accession Number
NCL-22 g45_coona_dendrimerG4.5 COONa terminated PAMAM dendrimer
delivery of image contrast agent
NCL-23g45_coona_dendrimer_magnevist_complex
G4.5 COONa terminated PAMAM dendrimer-Magnevist® complex MRI NPO_1483
NCL-24 magnevistgadolinium based image contrast agent MRI contrast agent NPO_581
Material TypeMaterial Type Term Acession Number
Material Type Term Source REF
Material Chemical Name
Material Chemical Name Term Acession Number
Material Chemical Name Term Source REF
Material Characteristic[dendrimer branch]
dendrimer; conjugated component NPO_735; NPO_1826 NPO;NPO 1-4
nanoparticle sample NPO_1404 NPO
small molecule; imaging payload agent; conjugated component
NCIt_C48809; NPO_1534; NPO_1826 NCIt;NPO;NPO magnevist 31797 ChEBI
Material Identifiers Material Description Intended Application
Material Type Chemical Name Characteristics
Material File (cont.)
Material Part NameMaterial Linkage Name Material Linkage Type
Material Linkage Type Term Accession
Material Linkage Type Term Source REF
Material File Name
Material File Type
Material File Version Material File Description
g45_coona_dendrimer; magnevist covalent linkage NPO_563 NPO magnevist.jpg image
Material Linkage Material File
Material Characteristic[dendrimer generation]
Material Characteristic[molecular weight]
Material Characteristic[molecular weight] Unit
Material Characteristic[molecular weight] Unit Term Accession
Material Characteristic[molecular weight] Unit Term Source REF
4.5 26.28 kDa UO_0000222 UO
Characteristics
Structure FileNCL Dendrimer-Based MRI Contrast Agents
ATOM 1770 C1 HANDS 1 0.451 -12.517 10.977 0 0 SEGO CATOM 1771 N2 HANDS 1 1.624 -12.647 10.091 0 0 SEGO NATOM 1772 C3 HANDS 1 2.489 -11.674 9.688 0 0 SEGO CATOM 1773 O4 HANDS 1 2.411 -10.485 10.019 0 0 SEGO OATOM 1774 C5 HANDS 1 3.639 -12.175 8.815 0 0 SEGO CATOM 1775 C6 HANDS 1 4.915 -12.278 9.679 0 0 SEGO CATOM 1776 H1 0 HANDS 1 1.879 -13.547 9.725 0 0 SEGO HATOM 1777 1H1 HANDS 1 3.753 -11.471 7.996 0 0 SEGO HATOM 1778 2H1 HANDS 1 3.369 -13.122 8.358 0 0 SEGO HATOM 1779 4H1 HANDS 1 4.724 -12.967 10.502 0 0 SEGO HATOM 1780 5H1 HANDS 1 5.066 -11.299 10.129 0 0 SEGO HTER 1781 HANDS 1ATOM 1782 C1 ARM1S 1 6.188 -12.716 8.918 0 0 SEGP CATOM 1783 N2 ARM1S 1 6.256 -11.808 7.767 0 0 SEGP NATOM 1784 C3 ARM1S 1 7.152 -10.838 7.49 0 0 SEGP CATOM 1785 O4 ARM1S 1 8.254 -10.714 8.012 0 0 SEGP OATOM 1786 C5 ARM1S 1 6.653 -9.788 6.524 0 0 SEGP CATOM 1787 C6 ARM1S 1 7.239 -9.935 5.119 0 0 SEGP CATOM 1788 C7 ARM1S 1 6.112 -9.762 4.124 0 0 SEGP CATOM 1789 O8 ARM1S 1 5.455 -11.03 4.034 0 0 SEGP OATOM 1790 O9 ARM1S 1 3.788 -10.808 5.448 0 0 SEGP OATOM 1791 C1 0 ARM1S 1 4.145 -10.919 4.278 0 0 SEGP CATOM 1792 H1 4 ARM1S 1 5.578 -11.888 7.023 0 0 SEGP HATOM 1793 5H1 ARM1S 1 6.892 -8.808 6.929 0 0 SEGP HATOM 1794 6H1 ARM1S 1 5.569 -9.845 6.51 0 0 SEGP HATOM 1795 7H1 ARM1S 1 7.66 -10.923 4.947 0 0 SEGP HATOM 1796 8H1 ARM1S 1 8.026 -9.201 4.949 0 0 SEGP HATOM 1797 9H1 ARM1S 1 6.474 -9.457 3.155 0 0 SEGP HATOM 1798 0H2 ARM1S 1 5.468 -8.959 4.482 0 0 SEGP HTER 1799 ARM1S 1ATOM 1800 C1 CARBS 1 3.262 -11.048 2.947 0 0 SEGQ CTER 1801 CARBS 1ENDHEADER D ENDR IMER -4 12-2007 DF 40KEYWDS D ENDR IMER FUL LER ENEAUTHOR U SER4COMPND M OL_I D:1;COMPND 2 MOLE CULE: DF 4;COMPND 3 CHAI N: FULLE REN E;COMPND 4 SYNO NYM: ;COMPND 5 EC: ;COMPND 6 ENGI NEERED: YES ;COMPND 7 BIOL OGICAL_UNIT : CARBOXY AMIDO FULL ERENE;
Atom
Header
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)
ISA-TAB-Nano Assay File
Describes the protocol parameters and factors, including:TemperatureMedia/solventConcentration
Provides references or links to assay results, including:MeasurementsInstrumentationDerived 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!
nano-TAB Assay File
Horizontal-based spreadsheet format with the following sections:SAMPLE NAMES
PROTOCOL PARAMETERS
ASSAY FACTORS
ASSAY MEASUREMENTS
ASSAY FILES
Assay File Size by DLS
Source Name Protocol REF Parameter Value[pH of solution]
Performer Date Assay Name Factor Value[temperature]
Unit Term Accession Number
NCL-20 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering
7.4 Anil Patri 2010:05:12 Size by DLS 25 celsius UO_0000027
NCL-20 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering
7.4 Anil Patri 2010:05:12 Size by DLS 25 celsius UO_0000027NCL-22 Hydrodynamic Size/Size Distribution
via Dynamic Light Scattering7.4 Anil Patri 2010:05:12 Size by DLS 25 celsius UO_0000027
NCL-22 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering
7.4 Anil Patri 2010:05:12 Size by DLS 25 celsius UO_0000027NCL-22 Hydrodynamic Size/Size Distribution 7.4 Anil Patri 2010:05:12 Size by DLS 37 celsius UO_0000027NCL-23 Hydrodynamic Size/Size Distribution 7.4 Anil Patri 2010:05:12 Size by DLS 25 celsius UO_0000027
NCL-23 Hydrodynamic Size/Size Distribution via Dynamic Light Scattering
7.4 Anil Patri 2010:05:12 Size by DLS 25 celsius UO_0000027NCL-23 Hydrodynamic Size/Size Distribution 7.4 Anil Patri 2010:05:12 Size by DLS 37 celsius UO_0000027
Measurement Value[hydrodynamic diameter]
Statistic Unit Term Accession Number
Term Source Ref
Measurement Value[Peak Size]
Unit Term Accession Number
Term Source Ref
Measurement Value[PDI ]
Derived Data File
5.2 z-average nm UO_0000018 UO 4.4 nm UO_0000018 UO 0.122 NCL-DNT-Report.pdf8.6 z-average nm UO_0000018 UO 6.2 nm UO_0000018 UO 0.211 NCL-DNT-Report.pdf8.5 z-average nm UO_0000018 UO 6 nm UO_0000018 UO 0.2 NCL-DNT-Report.pdf6.6 z-average nm UO_0000018 UO 5.2 nm UO_0000018 UO 0.214 NCL-DNT-Report.pdf7.9 z-average nm UO_0000018 UO 5.1 nm UO_0000018 UO 0.282 NCL-DNT-Report.pdf7.4 z-average nm UO_0000018 UO 5.3 nm UO_0000018 UO 0.235 NCL-DNT-Report.pdf8.4 z-average nm UO_0000018 UO 6.1 nm UO_0000018 UO 0.265 NCL-DNT-Report.pdf9.8 z-average nm UO_0000018 UO 5.6 nm UO_0000018 UO 0.358 NCL-DNT-Report.pdf
Sample Names Protocol Parameters Assay Factors
Assay Measurements Assay Files
nano-TAB future
ASTM ballot
User guideBasic descriptions of elements, glossary
Organized collection of examples
Tutorials
Easier NPO annotation and integration
List of most relevant terms
List of missing terms
Real world applications“Client” engagement
Friendly user support
http://cananolab.nci.nih.gov/caNanoLab/welcome.do
http://nbi.oregonstate.edu/knowledgebase
Additional nano-TAB reading and project team
nano-TAB Project Site: http://goo.gl/yKFew
ASTM nano-TAB Work Item WK28974: http://goo.gl/OjSOX
ISA-TAB: http://isatab.sourceforge.net
caBIG ICR Nano WG Data Standards Document: http://goo.gl/sDEvp
NanoParticle Ontology (NPO): http://www.nano-ontology.org
Nano-TAB project team
Nathan Baker, PNNL
Amy Bednar, ERDC
Elaine Freund, 3rd Millennium
Marty Fritts, NCL
Sharon Gaheen, SAIC
Liz Hahn-Dantona, Lockheed Martin
Stacey Harper, Oregon State University
Mark Hoover, NIOSH
Fred Klaessig, Pennsylvania Bio Nano Systems
Juli Klemm, NCI CBIIT
David Paik, Stanford University
Sue Pan, SAIC
Grace Stafford, The Jackson Laboratory
Todd Stokes, Georgia Tech
Dennis Thomas, PNNL
Summary
Introduction to the caBIG® Nanotechnology Working Group
Overview of nanotechnology informatics challenges
Research projectsOntology development
PubNano resource
Data exchange standards
Structure-property-activity modeling
Funding
caBIG® ICR Workspace and the NIH NCI caBIG® Working Group, Pacific Northwest National Laboratory HHS sector LDRD funds, as well as NIH grants U54 HG004028 and U01 NS073457
Collaborators
caBIG® ICR Workspace, NCBO staff, ASTM, Raul Cachau, Gilbert Fragoso, Elaine Freund, Marty Fritts, Sam Gambhir, Sharon Gaheen, Liz Hahn-Dantona,Stacey Harper, Mark Hoover, Fred Klaessig, Juli Klemm, Michal Lijowski, David Paik, Sue Pan, Rohit Pappu, Persistent Systems Ltd, Daniel Rubin, Stan Shaw, Dennis Thomas, Eddie Xu, Kilian Weinberger, Trish Whetzel, …and many more!
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