Embed Size (px)
Citation preview
ISA-TAB-Nano
A specification to facilitate data exchange among
nanotechnology researchers and resources
ISA-TAB-Nanohttps://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano
Stacey Harper, Oregon State University
Sharon Gaheen, SAIC-Frederick
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• …
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
Diversity in Composition and Formulation
McNeil SE. J Leukoc Biol, 2005. 78(3): p. 585-94.doi:10.1189/jlb.0205074
Aqueous
Dry
Nanomaterials are Complex 3rd Dimension to the Periodic Table
Photos adapted: Dr. Z Wang, Georgia Tech
Nanomaterials are Complex Diversity of Zinc Oxide Nanoparticles
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)
Data Resource Diversity
Goal of ISA-TAB-Nano
Develop a specification to facilitate the exchange ofdata on nanomaterials and their characterizations
to/from nanotechnology resources
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
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
ISA-TAB-Nano 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 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 References
Investigation Description
Investigation Contacts
Investigation Publications
Investigation File (cont.)
Study Description
Study Design
Study Contacts
Investigation File (cont.)
Study Publications
Study Assays
Study Factors
Study Protocols
ISA-TAB-Nano Structure: Identify Study Samples
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 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
Study File
Biological Sample Identifier Biological Sample Characteristics Protocol
Biological Sample Study Factors
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
Material File
Material Identifiers Material Description Intended Application
Material Type Chemical Name Characteristics
Material File (cont.)
Material Linkage Material File
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
ISA-TAB-Nano 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:• 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!
ISA-TAB-Nano 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
Sample Names Protocol Parameters Assay Factors
Assay Measurements Assay Files
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
Assay Examples
Hemolysis
Pharmacokinetics
Tissue Distribution
Pharmacokinetics
Cytotoxicity
Size by Dynamic Light Scattering
Caspase Apoptosis
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/
Getting Started
1. Contact us for help! [email protected]
2. Use ISA-TAB-Nano template to create ISA-TAB-Nano files: 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
4. View example files: https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano
5. Navigate the BioPortal ontology for terms: http://purl.bioontology.org/ontology/NPO
6. Complete ISA-TAB-Nano files and send to the ISA-TAB-Nano Listserv: [email protected]
7. http://nbi.oregonstate.edu/
NCI Nano WG ISA-TAB-Nano Site: https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano
ISA-TAB-Nano is a Community-Driven Effort
Nanotechnology Toxicology Assays ISA-TAB-Nano
NCI caNanoLab
ONAMINBI
Your Organization
Here!
NIOSHNIL
NIBIBNano-
Registry
NIEHSNTP
NCICSN
Nanomaterials, Characterizations, Protocols
3D Nanomaterial Structures
Nanotechnology Safety Protocols
Nanotechnology Biological
Interactions
Curated Nanomaterial Biological, Environmental Interactions
References
• ISA-TAB-Nano Project Site: https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano
• ASTM nano-TAB Work Item WK28974: http://www.astm.org/DATABASE.CART/WORKITEMS/WK28974.htm
• ISA-TAB: http://isatab.sourceforge.net
• caBIG ICR Nano WG Data Standards Document: https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano
• NanoParticle Ontology (NPO): http://www.nano-ontology.org
• ISA-TAB-Nano Project Team• Nathan Baker, PNNL
• Dennis Thomas, PNNL• Amy Bednar, ERDC
• Elaine Freund, 3rd 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
