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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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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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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), which is maintained by the National Center for Biomedical Ontologies. Though the investigator may use alternative ontology and vocabulary sources, the ability to evaluate and share data require that all parties have access to those being used (they should be available to the investigators). All terms and fields used in this standard utilize the NCI EVS (http://evs.nci.nih.gov) and NanoParticle Ontology elements.
NanoParticle Ontology (NPO) [http://www.nano-ontology.org]
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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 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 | To allow 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 |
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 file |
All Fields | Material | To describe nanomaterials and small molecules |
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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/tools.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/) and
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Templates for each ISA-TAB-Nano file are provided below:
- Investigation File (login required)
- Study File (login required)
- Material File (login required)
- Assay File (login required)
A definition of terms in each file are available in ISA-TAB-Nano Glossary Files (login required).
ISA-TAB-Nano Example Files
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- Investigation File: NCL Dendrimer-Based MRI Contrast Agent (login required)
- Study Files: Size by Dynamic Light Scattering (DLS) | Cytotoxicity Study (login required)
- Material Files: NCL-20 | NCL-21 | NCL-22 | NCL-23 | NCL-24 | NCL-25 | NCL-26 (login required)
- Assay Files: Size by DLS Assay | Lactate Dehydrogenase (LDH) Assay | MTT Assay (login required)
- Report: Dentrimer-Based MRI Image Contrast Agent (login required)