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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