isa-tab-nano weekly meeting may 1, 2012 use of informatics to expedite and validate the application...

ISA-TAB-Nano Weekly Meeting

May 1, 2012

Use of Informatics to Expedite and Validate the

Application of Nanotechnology in

Biomedicine

Agenda

• Continued discussion on Material and Manufacturer Lot IDs

• Continued discussion on versioning and governance

• Walkthrough of the ISA-TAB-Nano Wiki

• ISA-TAB-Nano XML Specification

Lot IDs

• Re-Cap from Last Week

• Add a Manufacturer Lot ID to the Material File

• Use the Material Source Identifier to record the Material Lot ID

• Seek guidance from Fred Klaessig regarding adding a Certificate of Analysis/MSDS number

• Modify the Factor Value [nanoparticle sample] in the Cytotoxicity Study file to Factor Value [material source identifier] to support file linkage

Lot ID Reference Updated Material File

Material Source Identifier Manufacturer Lot Identifer Material Name Material Description Material Synthesis Material Design Rationale

NCL-22-1 g45_coona_dendrimerG4.5 COONa terminated PAMAM dendrimer

NCL-23-1g45_coona_dendrimer_magnevist_complex

G4.5 COONa terminated PAMAM dendrimer-Magnevist® complex

NCL-23-2g45_coona_dendrimer_magnevist_complex

G4.5 COONa terminated PAMAM dendrimer-Magnevist® complex

NCL-23-3g45_coona_dendrimer_magnevist_complex

G4.5 COONa terminated PAMAM dendrimer-Magnevist® complex

NCL-24-1 123456 magnevistgadolinium based image contrast agent

Material Lot ID Reference Assay File

• Size by DLS Assay File

• Cytotoxicity Assay File

Sample Name Protocol REF Performer Assay Name Measurement Value[cell viability]Unit Term Accession NumberLLC-PK1-6h-NCL22-1 Time-6-24-48 plate MTT assay Marina Dobrovolskaia MTT assay percentage UO_0000187LLC-PK1-6h-NCL22-2 Time-6-24-48 plate MTT assay Marina Dobrovolskaia MTT assay percentage UO_0000187LLC-PK1-6h-NCL22-3 Time-6-24-48 plate MTT assay Marina Dobrovolskaia MTT assay percentage UO_0000187LLC-PK1-6h-NCL22-4 Time-6-24-48 plate MTT assay Marina Dobrovolskaia MTT assay percentage UO_0000187LLC-PK1-6h-NCL22-5 Time-6-24-48 plate MTT assay Marina Dobrovolskaia MTT assay percentage UO_0000187LLC-PK1-6h-NCL22-6 Time-6-24-48 plate MTT assay Marina Dobrovolskaia MTT assay percentage UO_0000187LLC-PK1-6h-NCL22-7 Time-6-24-48 plate MTT assay Marina Dobrovolskaia MTT assay percentage UO_0000187LLC-PK1-6h-NCL22-8 Time-6-24-48 plate MTT assay Marina Dobrovolskaia MTT assay percentage UO_0000187LLC-PK1-6h-NCL22-9 Time-6-24-48 plate MTT assay Marina Dobrovolskaia MTT assay percentage UO_0000187LLC-PK1-6h-NCL23-1 Time-6-24-48 plate MTT assay Marina Dobrovolskaia MTT assay percentage UO_0000187LLC-PK1-6h-NCL23-2 Time-6-24-48 plate MTT assay Marina Dobrovolskaia MTT assay percentage UO_0000187LLC-PK1-6h-NCL23-3 Time-6-24-48 plate MTT assay Marina Dobrovolskaia MTT assay percentage UO_0000187LLC-PK1-6h-NCL23-4 Time-6-24-48 plate MTT assay Marina Dobrovolskaia MTT assay percentage UO_0000187

Source Name Assay Name Factor Value[temperature]

Term Accession Number

Term Source Ref

Unit Term Accession Number

Term Source Ref

Factor Value[solvent medium]

Measurement Value[hydrodynamic diameter]

Statistic Unit

NCL-20-1 size by DLS assay 25 PATO_0000146 PATO celsius UO_0000027 UO saline 5.2 z-average nmNCL-20-1 size by DLS assay 25 PATO_0000146 PATO celsius UO_0000027 UO PBS 8.6 z-average nmNCL-22-1 size by DLS assay 25 PATO_0000146 PATO celsius UO_0000027 UO saline 8.5 z-average nmNCL-22-3 size by DLS assay 25 PATO_0000146 PATO celsius UO_0000027 UO PBS 6.6 z-average nmNCL-22-3 size by DLS assay 37 PATO_0000146 PATO celsius UO_0000027 UO PBS 7.9 z-average nmNCL-23-1 size by DLS assay 25 PATO_0000146 PATO celsius UO_0000027 UO saline 7.4 z-average nmNCL-23-1 size by DLS assay 25 PATO_0000146 PATO celsius UO_0000027 UO PBS 8.4 z-average nmNCL-23-1 size by DLS assay 37 PATO_0000146 PATO celsius UO_0000027 UO PBS 9.8 z-average nm

Material Lot ID Reference Study File

• Size by DLS Study File

• Cytotoxicity Study File

Source Name

Protocol REF Sample Name Performer Parameter Value[pH]

Parameter Value[particle concentration]

Unit ParameterValue[NaCl concentration]

Unit

NCL-20 Measuring the size of nanoparticles in aqueous media using batch-mode

NCL-20-1 Anil Patri 7.4 1 mg/mL 154 mM

NCL-22 Measuring the size of nanoparticles in aqueous media using batch-mode

NCL-22-1 Anil Patri 7.4 1 mg/mL 154 mM

NCL-23 Measuring the size of nanoparticles in aqueous media using batch-mode

NCL-23-1 Anil Patri 7.4 1 mg/mL 154 mM

Source Name Material Type Characteristic[cell type] Sample Name Factor Value[material source identifier]LLC-PK1 biospecimen porcine proximal tubule cells LLC-PK1-6h-NCL22-1 NCL-22-1LLC-PK1 biospecimen porcine proximal tubule cells LLC-PK1-6h-NCL22-2 NCL-22-2LLC-PK1 biospecimen porcine proximal tubule cells LLC-PK1-6h-NCL22-3 NCL-22-3LLC-PK1 biospecimen porcine proximal tubule cells LLC-PK1-6h-NCL22-4 NCL-22-4LLC-PK1 biospecimen porcine proximal tubule cells LLC-PK1-6h-NCL22-5 NCL-22-5LLC-PK1 biospecimen porcine proximal tubule cells LLC-PK1-6h-NCL22-6 NCL-22-6LLC-PK1 biospecimen porcine proximal tubule cells LLC-PK1-6h-NCL22-7 NCL-22-7LLC-PK1 biospecimen porcine proximal tubule cells LLC-PK1-6h-NCL22-8 NCL-22-8

ISA-TAB-Nano Versioning

• Current ISA-TAB-Nano Version References• ISA-TAB-Nano Wiki – References ISA-TAB-Nano Version 0.6 files and

structures• ISA-TAB-Nano ASTM Document – References Work Item No.: WK28974.

No Version Number referenced.• ISA-TAB-Nano Manuscript – No Version Number referenced

• ISA-TAB-Nano Version Discussion• Version 1.0? – Original Nano-TAB submitted to ASTM• Version 1.1? – Updated ISA-TAB-Nano version

• Modification of Material File to reflect a horizontal layout• Inclusion of Manufacturer ID (and other related elements)• Re-naming of Material Part Name and Material Linkage Name• Other?

• Discuss version control• Version control in the ISA-TAB-Nano Wiki• Version control in SVN (final file versions only)

ISA-TAB-Nano Governance

• ISA-TAB-Nano Membership

• ISA-TAB-Nano Standards Development Life Cycle (x Month?)• Standards Development Activities (4 Months?)

• Review feature requests in the ISA-TAB-Nano JIRA Tracker (Month 1)• Determine need for standards update and version number (Month 1)• Update example files in support of feature requests (Months 1-2)• Review/validate example file updates (Month 2)• Internal member voting (Month 3)• Review comments and finalize updates (Month 3)• Update ISA-TAB-Nano work products (Months 3-4)

• ASTM Ballot, Manuscript, Supporting Information, Wiki Page

• ASTM Submission (x Months?)• Submit updates to ASTM and request ballot submission (Month 4)• Support ASTM voting process (Months 4-6?)• Review comments and finalize updates (Month 7?)• Obtain final ASTM Approval (Month 8?)

ISA-TAB-Nano Wikihttps://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano

• Discuss overall structure/content

• Wiki and relationship to ASTM specification

• Discuss consistency

• Representing file example pages

• Discuss Wiki access

• Wiki write access

ISA-TAB-Nano-ML

class ISA-TAB-Nano-ML

Inv estigationFile

StudyFile

MaterialFile

AssayFile

ISA-TAB-Nano-ML

1

1..*

1..*

1..*

04/20/23

C:\NCI ICR\Meetings\Project Area 1 caBIO

Investigation File

class InvestigationFile

isa-tab-nano::InvestigationFile

isa-tab-nano::OntologySourceReference

isa-tab-nano::Investigation

isa-tab-nano::Study

- description :String- fi leDescription :String- fi leName :String- identifier :String- publicReleaseDate :Date- studyOutcome :String- submissionDate :Date- title :String

isa-tab-nano::Publication

isa-tab-nano::Assay

isa-tab-nano::Factor

- name :String- nameTermReference :TermReference- type :String- typeTermReference :TermReference

isa-tab-nano::Protocol

isa-tab-nano::Contact

isa-tab-nano::Disease

- termReference :TermReference- value :String

isa-tab-nano::Measurement

- name :String- nameTermReference :TermReference- type :String- typeTermReference :TermReference

isa-tab-nano::Technology

isa-tab-nano::Parameter

isa-tab-nano::DesignDescriptor

isa-tab-nano::PersonRole

isa-tab-nano::Component

isa-tab-nano::Author

1..*1

1..*

0..*

0..*

1..*

0..*

1..*

1..*

1..*

0..*0..*

1

11..*

1..*

0..*

1..*

1..*

04/20/23

Study File

class StudyFile

isa-tab-nano::StudyFile

isa-tab-nano::SampleSource

isa-tab-nano::Characteristics

- name :String- nameTermReference :TermReference- unit :String- unitTermReference :TermReference- value :String- valueTermReference :TermReference

isa-tab-nano::MaterialType

isa-tab-nano::Sample

isa-tab-nano::Prov ider

isa-tab-nano::Comment

isa-tab-nano::ProtocolReference

isa-tab-nano::ParameterValue

isa-tab-nano::FactorValue

isa-tab-nano::MaterialFileReference

- fi leUri :String

1..*

1..*

1

1..*

1..*

1

0..1

0..*

0..*

1..*

1..*

1..*

0..1

0..1

0..*

04/20/23

Material File

class MaterialFile

isa-tab-nano::MaterialFile

- description :String- name :String- type :String- typeTermReference :TermReference- version :String

isa-tab-nano::Material

- chemicalName :String- chemicalNameTermReference :TermReference- description :String- designRationale :String- designRationaleTermReference :TermReference- intendedApplication :String- intendedApplicationTermReference :TermReference- name :String- sourceIdentifier :String- synthesis :String

isa-tab-nano::MaterialType

- termReference :TermReference- value :String

isa-tab-nano::Characteristics

- name :String- nameTermReference :TermReference- unit :String- unitTermReference :TermReference- value :String- valueTermReference :TermReference

isa-tab-nano::MaterialLinkage

- name :String- type :String- typeTermReference :TermReference

isa-tab-nano::MaterialComposition

isa-tab-nano::TermReference

- accessionNumber :String- sourceReference :String

MaterialPart

- name :String

1..*

1..*

0..*

0..*

1..*

1..*

1..*

04/20/23

Assay File

class AssayFile

isa-tab-nano::AssayFile

isa-tab-nano::SourceName

isa-tab-nano::Sample

isa-tab-nano::ProtocolReference

isa-tab-nano::Characteristics

- name :String- nameTermReference :TermReference- unit :String- unitTermReference :TermReference- value :String- valueTermReference :TermReference

isa-tab-nano::MaterialType

- termReference :TermReference- value :String

isa-tab-nano::MeasurementValue

- measurementName :String- statistics :String- statisticsTermReference :TermReference- unit :String- unitTermReference :TermReference- value :String

isa-tab-nano::AssayName

isa-tab-nano::ImageFileReference

isa-tab-nano::ParameterValue

isa-tab-nano::DataTransformationName

isa-tab-nano::Deriv edDataFileReference

isa-tab-nano::RawDataFileReference

isa-tab-nano::Comment

isa-tab-nano::TermReference

- accessionNumber :String- sourceReference :String

0..*

1..*

0..*

1..*

1..*

1

0..*

1..*

0..*

1..*

0..*

1..*

0..*

0..*

0..*

0..*

0..*0..*

0..*

0..*

1..*

04/20/23