NCI Nano WG &ISA-TAB-Nano Overview

March 2014

What is the caBIG® Nanotechnology Working Group?

• NCI: National Cancer Institute– caBIG®: Cancer Biomedical Informatics Grid

• ICR WS: Integrated Cancer Research Workspace– Nano WG: Nanotechnology Working Group

• Composition– Academia

• Stanford, Oregon State, MIT, Georgia Tech, Georgetown– Industry

• SAIC, BAH, RTI, I-A-I– Government

• DOE, NIH, NIST, EPA, CDC, FDA, DoD, Army Corps– International

• IANH, Univ College Dublin, IITB– Standards

• ISO, ASTM, OECD– Other

• NNN, IANH

2

Nano WG Scope

3

Nano WG High-Level Objectives

• Applying informatics to nanomedicine– Predictive models for nanomaterial activity– Rational design of nanomaterials

• Enabling nanomedicine informatics applications– Facilitating data exchange– Supporting data curation– Building a community of interest

4

Nano WG Current Areas of Focus• ISA-TAB-Nano 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 ISA-TAB-Nano and other annotation

projects• Nano-QSAR (applying)

– Structure-activity relationships for nanomaterial-biological interactions– New start with Nanoinformatics 2010 pilot project– Community engaged; participants identified– Many potential areas of focus

5

ISA-TAB-Nano for Nanomaterial Data Sharing

May 2013

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

7

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

8

Diversity in Composition and Formulation

9

Nanomaterials are Complex 3rd Dimension to the Periodic Table

10

Nanomaterials are ComplexDiversity of Zinc Oxide Particle

11

Assay and Data Diversity

12

Data Resource Diversity

ISA-TAB-Nano Goal

14

Develop a specification to facilitate the import/export of

data 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

15

ISA-TAB Extensions for Nanotechnology

ISA-TAB Extension Field Name ISA-TAB File PurposeInvestigation Disease Investigation To capture and retrieve investigations associated with specific disease modalities such as cancerInvestigation Disease Term Accession Number Investigation To enable semantic interoperability for disease terms

Investigation Disease Term Source REF Investigation To enable semantic interoperability for disease terms

Investigation Outcome Investigation To enable researchers to review the outcomes of investigations for assessing the utility of the investigation in achieving scientific endpoints

MATERIAL Investigation Section header for the Material section. This section allows for the identification of materials used in the investigation and associated studies.

Material File Name Investigation The name of the ISA-TAB-Nano Material File, which lists information about the composition and characteristics of the nanomaterials or other small molecules. There can be only one file per cell.

Material Source Name Investigation A name of the nanomaterial or small molecule associated with the Material File. There can be only one Material Source Name per column.

Study Disease Investigation To capture and retrieve studies associated with specific disease modalities such as cancer

Study Disease Term Accession Number Investigation To enable semantic interoperability for disease terms

Study Disease Term Source REF Investigation To enable semantic interoperability for disease terms

Study Outcome Investigation To enable researchers to review the outcomes of studies for assessing the utility of the investigation in achieving scientific endpoints

Study Assay Measurement Name Investigation To capture the variables measured in an assay to support cross study analysis

Study Assay Measurement Name Term Accession Number Investigation To enable semantic interoperability for assay measurement names

Study Assay Measurement Name Term Source REF Investigation To enable semantic interoperability for assay measurement names

Measurement Value Assay To record the endpoint value of an assay measurement within the assay fileAll Fields Material To describe nanomaterials and small molecules

16

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

17

ISA-TAB-Nano Structure

18

ISA-TAB-Nano Structure (1)

19

ISA-TAB-Nano Investigation File

• Describes:– Primary investigation– Associated materials, 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

20

Investigation File (1 of 4)ONTOLOGY SOURCE REFERENCE Term Source Name MO NPO

Term Source File http://purl.bioontology.org/ontology/MO http://purl.bioontology.org/ontology/npoTerm Source Version v. 1.3.1.1 v. 2011-02-12Term Source Description MGED Ontology NanoParticle OntologyINVESTIGATION Investigation Identifier NCL200612A Investigation 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 contrast agent.

Investigation Submission Date 2002-11-30 Investigation Public Release Date 2002-11-30 Investigation Disease Investigation Disease Term Accession Number Investigation Disease Term Source REF Investigation Outcome INVESTIGATION PUBLICATIONS Investigation PubMed ID 18095846 Investigation Publication DOI 10.2217/17435889.2.6.789 Investigation Publication Author List 10.2217/17435889.2.6.789

Investigation Publication TitleCharacterization of nanoparticles for therapeutics

Investigation Publication Status published

Investigation Publication Status Term Accession Number Investigation Publication Status Term Source REF INVESTIGATION CONTACTS Investigation Person Last Name Doe Investigation Person First Name John Investigation Person Mid Initials E Investigation Person Email doej@mail.nih.gov Investigation Person Phone 1231231234 Investigation Person Fax

Investigation Person Address Laboratory Street, City, State 111111 Investigation Person Affiliation Doe Laboratories Investigation Person Roles investigator Investigation Person Roles Term Accession Number Investigation Person Roles Term Source REF MO

Investigation File (2 of 4)

MATERIAL Material File Name m_NCL-20.xls m_NCL-21.xls m_NCL-22.xls m_NCL-23.xls m_NCL-24.xls m_NCL-25.xls m_NCL-26.xlsMaterial Source Name NCL-20 NCL-21 NCL-22 NCL-23 NCL-24 NCL-25 NCL-26

Investigation File (3 of 4)STUDY Study Identifier NCL200612A-Size

Study Title Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS)

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 Submission Date 2002-11-30 Study Public Release Date 2002-11-30 Study Disease

Study Disease Term Accession Number Study 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. For each sample, the intensity weighted mean diameter (Z-avg) derived from the cumulants analysis and the diameter after conversion to volume-weighted distribution are provided on the following pages.

Study File Name s_size-DLS.xls STUDY DESIGN DESCRIPTORS Study Design Type comparison

Study Design Type Term Accession Number

Study Design Type Term Source REF STUDY PUBLICATIONS Study PubMed ID 18095846 Study Publication DOI 10.2217/17435889.2.6.789

Study Publication Author List Hall JB; Dobrovolskaia MA; Patri AK; McNeil SE

Study Publication Title Characterization of nanoparticles for therapeutics Study Publication Status published

Study Publication Status Term Accession Number

Study Publication Status Term Source REF STUDY FACTORS Study Factor Name temperature solvent mediumStudy Factor Type temperature solvent medium

Study Factor Type Term Accession Number PATO_0000146 NPO_1855

Study Factor Type Term Source REF PATO NPO

Investigation File (4 of 4)STUDY ASSAYS Study Assay Measurement Type hydrodynamic size

Study Assay Measurement Type Term Accession Number Study Assay Measurement Type Term Source REF Study 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 Platform Study Assay Measurement Name hydrodynamic diameter; peak size; PDI

Study Assay Measurement Name Term Accession Number ; ; NPO_1155

Study Assay Measurement Name Term Source REF ; ; NPOStudy Assay File Name a_size-DLS.xlsSTUDY PROTOCOLS

Study Protocol Name Measuring the size of nanoparticles in aqueous media using batch-mode dynamic light scatteringStudy Protocol Type sample preparation procedure; particle size measurement procedure

Study Protocol Type Term Accession Number Study 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 size is the primary determinant of the measured diffusion coefficient, other parameters can impact these measurements and influence the measured size. Therefore, guidelines for making successfully size measurements in the nanosize range are provided, as well as a discussion of relevant standards 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 1.1Study Protocol Parameters Name pH; NaCl concentration; particle concentration

Study Protocol Parameters Name Term Accession Number UO_0000196; ; NPO_1830

Study Protocol Parameters Name Term Source REF UO; ;NPOStudy Protocol Components Name Mastersizer 2000 (Malvern DLS)Study Protocol Components Type DLS instrument

Study Protocol Components Type Term Accession Number NPO_1766

Study Protocol Components Type Term Source REF NPOSTUDY CONTACTS Study Person Last Name SmithStudy Person First Name JaneStudy Person Mid Initials KStudy Person Email smithj@mail.nih.govStudy Person Phone 1231231235Study Person Fax Study Person Address Laboratory Street, City, State 111111Study Person Affiliation Doe LaboratoriesStudy Person Roles investigatorStudy Person Roles Term Accession Number Study Person Roles Term Source REF MO

ISA-TAB-Nano Structure (2)

25

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

26

Study File

27

Sample Name Factor Value[nanoparticle sample]Factor Value[particle concentration] Unit Term Accession Number Term Source Ref

Factor Value[time of exposure] Unit

LLC-PK1-6h-NCL22-1 NCL-22 0.004 mg/mL UO_0000176 UO 6 hour

LLC-PK1-6h-NCL22-2 NCL-22 0.008 mg/mL UO_0000176 UO 6 hour

LLC-PK1-6h-NCL22-3 NCL-22 0.016 mg/mL UO_0000176 UO 6 hour

LLC-PK1-6h-NCL22-4 NCL-22 0.032 mg/mL UO_0000176 UO 6 hour

LLC-PK1-6h-NCL22-5 NCL-22 0.064 mg/mL UO_0000176 UO 6 hour

LLC-PK1-6h-NCL22-6 NCL-22 0.128 mg/mL UO_0000176 UO 6 hour

LLC-PK1-6h-NCL22-7 NCL-22 0.256 mg/mL UO_0000176 UO 6 hour

LLC-PK1-6h-NCL22-8 NCL-22 0.512 mg/mL UO_0000176 UO 6 hour

LLC-PK1-6h-NCL22-9 NCL-23 1 mg/mL UO_0000176 UO 6 hour

Source Name Material Type Characteristics[cell type{NCIt:C12508}]Characteristics[ATCC#{NCIt:C15661}] Provider Protocol REF Performer

LLC-PK1 biospecimen porcine proximal tubule cells CL-101 Doe Technologies cell preparation in four 96-well plates Jane DoeLLC-PK1 biospecimen porcine proximal tubule cells CL-101 Doe Technologies cell preparation in four 96-well plates Jane DoeLLC-PK1 biospecimen porcine proximal tubule cells CL-101 Doe Technologies cell preparation in four 96-well plates Jane DoeLLC-PK1 biospecimen porcine proximal tubule cells CL-101 Doe Technologies cell preparation in four 96-well plates Jane DoeLLC-PK1 biospecimen porcine proximal tubule cells CL-101 Doe Technologies cell preparation in four 96-well plates Jane DoeLLC-PK1 biospecimen porcine proximal tubule cells CL-101 Doe Technologies cell preparation in four 96-well plates Jane DoeLLC-PK1 biospecimen porcine proximal tubule cells CL-101 Doe Technologies cell preparation in four 96-well plates Jane DoeLLC-PK1 biospecimen porcine proximal tubule cells CL-101 Doe Technologies cell preparation in four 96-well plates Jane DoeLLC-PK1 biospecimen porcine proximal tubule cells CL-101 Doe Technologies cell preparation in four 96-well plates Jane Doe

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

28

Material File (1 of 2)

Material Source Name Material Name Material Description Material SynthesisMaterial Design Rationale

Material Intended Application

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

NCL-24 magnevistgadolinium based image contrast agent MRI contrast agent

Material Type Term Accession Number Term Source REFMaterial Chemical Name

Term Accession Number Term Source REF

Characteristics[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

gadopentetate dimeglumine 31797 ChEBI

Material File (2 of 2)

Characteristics[dendrimer generation] Characteristics[molecular weight] Unit

Term Accession Number Term Source REF Characteristics[molecular formula]

4.5 26.28 kDa UO_0000222 UO

[Gd+3] .CNC[C@H] (O) [C@@H] (O) [C@H] (O) [C@H] (O) CO.CNC[C@H] (O) [C@@H] (O) [C@H] (O) [C@H] (O) CO.OC(=O) CN(CCN(CCN(CC(O) =O) CC([O- ] ) =O) CC([O- ] ) =O) CC([O- ] ) =O

Material Constituent

Material Linkage Type

Term Accession Number

Term Source REF

Material Data File

Material Data File Type

Term Accession Number

Term Source REF

Material Data File Version

Material Data File Description

g45_coona_dendrimer; magnevist covalent linkage NPO_563 NPO magnevist.jpg image NCIt_C48179 NCIt

Structure File (Optional)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;

ISA-TAB-Nano Structure (3)

32

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!

33

Assay File Size by DLS

Sample Name

Protocol REF Performer Assay Name Factor Value[temperature]

Term Accession Number

Term Source Ref

Unit Term Accession Number

Term Source Ref

Factor Value[solvent medium]

NCL-20-1Measuring the size of nanoparticles in aqueous media using batch-mode dynamic light scattering John Doe

size by DLS assay 25 PATO_0000146 PATO celsius UO_0000027 UO saline

NCL-20-1Measuring the size of nanoparticles in aqueous media using batch-mode dynamic light scattering John Doe

size by DLS assay 25 PATO_0000146 PATO celsius UO_0000027 UO PBS

NCL-22-1Measuring the size of nanoparticles in aqueous media using batch-mode dynamic light scattering John Doe

size by DLS assay 25 PATO_0000146 PATO celsius UO_0000027 UO saline

NCL-22-1Measuring the size of nanoparticles in aqueous media using batch-mode dynamic light scattering John Doe

size by DLS assay 25 PATO_0000146 PATO celsius UO_0000027 UO PBS

NCL-22-1Measuring the size of nanoparticles in aqueous media using batch-mode dynamic light scattering John Doe

size by DLS assay 37 PATO_0000146 PATO celsius UO_0000027 UO PBS

Measurement Value[z-average(hydrodynamic diameter)]

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 nm UO_0000018 UO 4.4 nm UO_0000018 UO 0.122NCL-Dendrimer-Based_MRI_Contrast_Agent.pdf

8.6 nm UO_0000018 UO 6.2 nm UO_0000018 UO 0.211NCL-Dendrimer-Based_MRI_Contrast_Agent.pdf

8.5 nm UO_0000018 UO 6 nm UO_0000018 UO 0.2NCL-Dendrimer-Based_MRI_Contrast_Agent.pdf

6.6 nm UO_0000018 UO 5.2 nm UO_0000018 UO 0.214NCL-Dendrimer-Based_MRI_Contrast_Agent.pdf

7.9 nm UO_0000018 UO 5.1 nm UO_0000018 UO 0.282NCL-Dendrimer-Based_MRI_Contrast_Agent.pdf

Getting Started

NCI Nano WG ISA-TAB-Nano Site: https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano

1. Contact us for help! nano-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

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: nano-tab-l@list.nih.gov

35

ISA-TAB-Nano Template Glossary

36

Term Definition

Material Source Name

The unique identification name of the source from which the material sample is derived. Its value is used as the value for “Source Name” in ISA-TAB-Nano Study files, thereby linking the ISA-TAB-Nano Material file and the study file. This concept is introduced in ISA-TAB-Nano.

Material NameThe unique identification name for the sample and its different components.This concept is introduced in ISA-TAB-Nano.

Manufacturer Lot Identifier

A distinctive numeric, alpha, or alpha-numeric identification code assigned by the manufacturer or distributor. It is assigned to a specific quantity of manufactured material or product that is produced in a manner that is expected to render it homogeneous.This concept is introduced in ISA-TAB-Nano.

Material DescriptionA textual description of the material sample.This concept is introduced in ISA-TAB-Nano.

Material SynthesisA text or a single term description of how the material was made.This concept is introduced in ISA-TAB-Nano.

Material Design Rationale

A text description for the underlying design rationale is the property, process or phenomenon taken into consideration when formulating a nanoparticle or other substance in order to achieve the intended use of the formulation.This concept is introduced in ISA-TAB-Nano.

Material Intended Application

The application for which a drug, nanoparticle or other substance is formulated and tested (e.g., MRI). This concept is introduced in ISA-TAB-Nano.

Term Accession Number

Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for Material Intended Application.

Term Source REF

The name which identifies the source from where the term for Material Intended Application is selected. This name should match one of the names entered in the Term Source Name field..

Material TypeOne or more terms used to classify the type of material sample. Multiple terms are entered as a semicolon-delimited list.

ISA-TAB-Nano Future

37

• ASTM ballot–Target May 16–Format write-up

• User guide–Basic descriptions of elements,

glossary–Organized collection of

examples–Tutorials

• Easier NPO annotation/integration

https://cananolab.nci.nih.gov/caNanoLab

http://nbi.oregonstate.edu/

ISA-TAB-Nano is a Community-Driven Effort

38

References and Project Team

39

• 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