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ISA-TAB-Nano Introduction
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The ISA-TAB-Nano specification is intended to facilitate the submission and exchange of nanomaterial descriptions and characterization data (metadata and summary data) along with the other files (raw/derived data files, image files, protocol documents, etc.) among individual researchers and to/from nanotechnology resources like the NCI’s cancer Nanotechnology Laboratory (caNanoLab) portal [https://cananolab.nci.nih.gov/caNanoLab] and the Nanomaterial-Biological Interactions (NBI) knowledgebase [http://nbi.oregonstate.edu/
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] and the Nanomaterial-Biological Interactions (NBI) knowledgebase
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The ISA-TAB-Nano project is an effort of the National Cancer Institute (NCI) National Cancer Informatics Program (NCIP) Nanotechnology Informatics Working Group (Nano WG).
ISA-TAB-Nano Standards Re-Use
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The ISA-TAB-Nano format specification is based on an existing specification developed by the ISA-commmunity (http://www.isa-tools.org
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Life Sciences Domain Analysis Model (LS DAM)
LS DAM provides a shared view of the semantics of differenct life of different life sciences domains. It has a nanotechnolog nanotechnology subdomain, which was developed based on caNanoLab object model and NPO terms. LS DAM makes a distinction between biospecimens (for example, cell line, tissue samples, body fluid samples, organ parts) and materials that are not derived from a cell, tissue, organ, or body (for example, nanoparticle formulations, drug formulations, solvent, and so forth). This motivated the use of the term “material sample” in the ISA-TAB-Nano material file. Weekly Nano WG web-conferencing was used to ensure the alignment of ISA-TAB-Nano with the LS DAM.
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Like ISA-TAB, ISA-TAB-Nano provides fields for entering and referencing terms selected from ontologies and standard terminologies. The ontologies are available at BioPortal (http://www.bioontology.org
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NanoParticle Ontology (NPO) [http://www.nano-ontology.org
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The Table below represents extensions made to each ISA-TAB file in support of ISA-TAB-Nano.
ISA-TAB Extension Field Name | ISA-TAB File | Purpose | |||
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Investigation Disease | Investigation | To capture and retrieve investigations associated with specific disease modalities such as cancer | |||
Investigation Disease Term Accession Number | Investigation | To enable semantic interoperability for disease terms | |||
Investigation Disease Term Source REF | Investigation | To enable semantic interoperability for disease termsInvestigation Disease Term Source REF | |||
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 | To enable semantic interoperability for disease termsallow for the identification of materials used in the investigation and associated studies | |||
Material File Name | Investigation | To identify the name of the Material File, which lists information about the composition and characteristics of the nanomaterials or other small molecules | |||
Material Source Name | Investigation | To identify the name of the nanomaterial or small molecule associated with the Material File | Investigation Outcome | Investigation | To enable researchers to review the outcomes of investigations for assessing the utility of the investigation in achieving scientific endpoints |
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 Factor Name Term Accession Number | Investigation | To enable semantic interoperability for study factor name | |||
Study Factor Name Term Source REF | Investigation | To enable semantic interoperability for study factor namesthe 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 | |||
Material Source Name | Study, Material | To provide a reference for the material associated with the study | |||
Material File | Study | To provide a reference for the ISA-TAB-Nano material file that describes the material samples of a studymeasurement names | |||
Measurement Value | Assay | To record the endpoint value of an assay measurement within the assay file | Statistic | Assay | To capture the statistical measures (e.g. mean, SD) associated with a measurement or factor value |
All Fields | Material | To describe nanomaterials and small molecules |
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FIG 2. ISA-TAB-Nano File Development Process
When sharing primary ISA-TAB-Nano files, other files referenced in these files have to be shared along with the primary files. It is anticipated that content management systems will become available to facilitate the sharing and exchange of files. Until then, these files could be bundled together in a folder and shared as a zip file.
Once the ISA-TAB-Nano files have been created, the files can be validated and submitted into nanotechnology resources that support the ISA-TAB-Nano specification. It is anticipated that validation of the files may occur via a validation service that leverages a modified version of the ISA-TAB validator [http://isatab.sourceforge.net/ validator.html
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It is also anticipated that nanotechnology resources like caNanoLab (https://cananolab.nci.nih.gov/caNanoLab/ ), the Nanomaterial-Biological Interactions (NBI) knowledgebase (http://nbi.oregonstate.edu/
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Templates for each ISA-TAB-Nano file are provided below:
A definition Definitions of terms in each file are available in the ISA-TAB-Nano Glossary Files.
ISA-TAB-Nano Example Files
Below The following are example ISA-TAB-Nano files for a nanotechnology investigations investigation involving physico-chemical , and in vitro , and in vivo characterization studies.
Investigation Title: Nanotechnology Characterization Laboratory (NCL) Dendrimer-Based MRI Contrast Agent
Investigation Description: The objective of this investigation is to characterize a PAMAM dendrimer with an associated gadolinium chelate MRI contrast agent. The nanomaterials submitted for testing at the NCL were (NCL20) G4 tris (hydroxyl) terminated PAMAM dendrimer, (NCL21) G4 pyrrolidinone terminated PAMAM dendrimer, (NCL22) G4.5 COONa terminated PAMAM dendrimer, (NCL23) G4.5 COONa terminated PAMAM dendrimer-Magnevist® complex, (NCL25) G4 tris (hydroxyl) terminated PAMAM dendrimer-Magnevist® complex, and (NCL26) G4 pyrrolidinone terminated PAMAM dendrimer-Magnevist® complex. Commercially available Magnevist® (NCL24) was used as a control. NCL studies addressed in this report can be divided into three main categories: physicochemical characterization; immunotoxicology; in vitro toxicology.
Example Files
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- Investigation File: NCL Dendrimer-Based MRI Contrast Agent
- Study Files: Size by Dynamic Light Scattering (DLS) | Cytotoxicity Study
- Material Files: NCL-20 | NCL-21 | NCL-22 | NCL-23 | NCL-24 | NCL-25 | NCL-26
- Assay Files: Size by DLS Assay | Lactate Dehydrogenase (LDH) Assay | MTT Assay
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ISA-TAB-Nano XML Specification
An XML specification for ISA-TAB-Nano was derived from the
ISA-TAB-Nano Object Model to assist in validating the ISA-TAB-Nano file format.
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