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image representing ISA-TAB-Nano Extension - Study, Investigation, Assay, Material

Info
titleISA-TAB Specification

ISA-TAB-Nano extends ISA-TAB, an existing specification developed by the ISA-commmunity.  Please refer to the ISA-TAB Specification

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for guidelines on the format of ISA-TAB.

Click here for ISA-TAB-Nano OVERVIEW PRESENTATION - a great place to start!

ISA-TAB-Nano Paper:

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BMC Biotechnology 2013, 13:2 Published: 14 January 2013

Commentary

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Nature Nanotechnology 2013, 8, 73-74 Published: 5 February 2013

Blog ISA-TAB-Nano Code Fest: Community building and coding to advance nanotechnology data exchange, Bethesda, Maryland, May 9-10, 2013

ISA-TAB-Nano: A Click for Select each File type template: Investigation | Study | Material | Assay

See each File pages page for more information and links to examples and glossaries.

Scope

This standard (ISA-TAB-Nano) specifies the format for representing and sharing information about nanomaterials, small molecules and biological specimens along with their assay characterization data (including metadata, and summary data) using spreadsheet or TAB-delimited files.

Prerequisites

Familiarity with the fields of nanotechnology and nanomedicine is a prerequisite for this specification. An understanding of ISA-TAB is recommended but not required as the ISA-TAB-Nano specification provides descriptive information on ISA-TAB as applied to nanotechnology.

Version

The current version of ISA-TAB-Nano is Version 1.2 (March 2014). Differences between Version 1.2 and 1.1 are described in the ISA-TAB-Nano 1.2 Release Notes. Differences between Version 1.1 and 1.0 are described in the ISA-TAB-Nano Code Fest De-Brief presentation and in the ISA-TAB-Nano 1.1 Release Notes.

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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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. ISA-TAB-Nano also serves to empower organizations to adopt standard methods for representing data in nanotechnology publications; and to provide researchers with guidelines for representing nanomaterials and characterizations to achieve cross-material comparison.

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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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, namely, the investigation/study/assay (ISA-TAB) format specification. The ISA-TAB format (http://isatab.sourceforge.net/)
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is used by the ‘omics’ (proteomics, genomics, metabolomics, and transcriptomics) communities to share data and metadata associated with different assays and technology types in their experiments. The ISA-TAB file structure relies on three primary files---investigation, study, and assay (ISA) files. Raw/derived data files and any other files (e.g., image files, protocol documents) specific to each assay are shared along with the three primary ISA-TAB files if the data files are referenced in the primary ISA-TAB files. ISA-TAB does not provide format specification for files other than the investigation, study, and assay files. The ISA-TAB investigation file is used for three purposes: (1) to record all declarative information referenced in other files; (2) to relate assay files to study files; and (3) to group multiple study files that are part of the same investigation. The ISA-TAB study file is used to record information about the source, sampling methodology, treatment, preparation, and characteristics of the subjects (biospecimens) studied using one or more assays under an investigation.

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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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, 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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is an ontology that is designed and developed within the framework of the Basic Formal Ontology (BFO) and implemented in the ontology web language (OWL). It is being developed to represent the knowledge underlying the description, preparation, and characterization of nanomaterials. NPO development began with the representation of knowledge underlying the chemical composition, preparation, physiochemical, and functional/biological characterization of nanoparticles that are formulated and tested for applications in cancer diagnostics and therapeutics. The NPO provided the knowledge framework for developing the ISA-TAB-Nano material file format. The NPO provides a subset of the terms and relationships for the description and characterization of nanomaterials in the ISA-TAB-Nano file format. The NPO is being further developed for the following purposes: (1) to provide terms for annotating nanotechnology research data; (2) to provide the knowledge framework required for developing data-sharing models and standards in nanomedicine; (3) to enable semantic integration of data; (4) to enable unambiguous interpretation of the description and characterization of nanomaterials; and (5) to enable knowledge-based searching and comparison of nanomaterial descriptions and characterization results.

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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

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

MATERIALInvestigationTo allow for the identification of materials used in the investigation and associated studies
Material File NameInvestigationTo identify the name of the Material File, which lists information about the composition and characteristics of the nanomaterials or other small molecules
Material Source NameInvestigationTo 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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and other resources will provide facilities for importing/exporting ISA-TAB-Nano files as the ISA-TAB-Nano specification evolves.

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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

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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:

ISA-TAB-Nano Curated Examples

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