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

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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.

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 2013Blog

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

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

See each File 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 1.3 (February 2016March 2020). Differences For differences between Version 1.3 and 1.2 are described in , refer to the ISA-TAB-Nano 1.3 Release Notes.

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The field of nanomedicine faces many challenges in the development of standards to support meaningful data submission and information exchange. Nanomaterial characterization requires numerous physico-chemical, in-vitro, and in-vivo assays where measurements mostly depend on non-standardized protocols and diverse technology types. Unfortunately, information describing the nanomaterial, including functionalizing entities and three-dimensional (3D) structure, is often represented in an undisciplined fashion. In addition, there has been no standard way to associate this information with the data and metadata from characterization studies. This lack of standardization has been a significant deterrent to meaningful data sharing across the nanotechnology community; few publications contain sufficient information to enable adequate interpretation of results and successful achievement of experimental reproducibility. Furthermore, there has been very limited success in using non-standardized data to represent or derive structure-activity-relationships (SARs) that are critical for understanding the effects of nanomaterial structure on biological activity in nanomedicine.

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The ISA-TAB-Nano project is an effort of the National Cancer Institute (NCI) Nanotechnology 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-commmunitycommunity

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, namely, the investigation/study/assay (ISA-TAB) format specification. The ISA-TAB format
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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., such as image files , or 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 has 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 records 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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The NCI EVS is a project of the NCI Center for Biomedical Informatics and Information Technology (CBIIT). EVS provides controlled terminologies and ontologies in support of the biomedical research and informatics activities of the NCI and its partners. The activities of the EVS include development of terminologies, development of terminology-related software, and operations support to address the broad spectrum of terminology needs in the cancer research enterprise. Among the vocabularies that EVS supports is the NanoParticle Ontology (NPO), by providing terminology development facilities and terminology servers, which are made available both via the web and programmatically through EVS server APIs. Additionally, the NPO is presented to the public by EVS both in a standalone format and as a component of the NCI Metathesaurus, where its concepts are mapped to the concepts of other vocabularies used by the NCI community. Also, the EVS-managed NCI Thesaurus (NCIt) includes nanotechnology concepts that have been utilized in the development of the NCI caNanoLab. Data from caNanoLab has been utilized in the ISA-TAB-Nano example files.

Life Sciences Domain Analysis Model (LS DAM)

LS DAM provides a shared view of the semantics of different life sciences domains. It has a 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 the development of the NCI caNanoLab. Data from caNanoLab has been utilized in the ISA-TAB-Nano with the LS DAMexample files.

NanoParticle Ontology (NPO)

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

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, which is maintained by the National Center for Biomedical Ontologies maintains. 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 and NanoParticle Ontology elements.

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In nanotechnology, samples from biological and non-biological sources can be the primary subjects of a study. Therefore, in ISA-TAB-Nano, samples derived from biological sources are called biological specimens or biospecimens (for example, cell line, body fluids, organs, etc.). Whereas, samples derived from non-biological sources are simply called material samples (for example, nanomaterials, nanoparticle formulations, small molecules). For physico-chemical characterizations of nanomaterials, the sample is the nanomaterial. For in-vitro and in-vivo characterizations, the sample is the biological specimen (cell line, animal, and so forth). Hence, in ISA-TAB-Nano, the concept of a sample (as used in ISA-TAB specification) is redefined to include both biological specimens and material samples. The ISA-TAB study file can only be used to record the source and characteristics of biospecimens studied in an assay, and cannot support the representation of materials. Therefore, in ISA-TAB-Nano, the material file is used to describe describes material samples, while the study file is used to describe describes biospecimens.

Extensions to ISA-TAB Files

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ISA-TAB-Nano uses the three primary files of ISA-TAB-- investigation file, study file, and assay file; and, introduces a fourth file called the material file (FIG Figure 1). Other files such as raw/derived data files, image files, protocol documents, etc., referenced in the ISA-TAB-Nano files have to be shared along with the ISA-TAB-Nano files.

FIG Figure 1. ISA-TAB-Nano File Structure
diagram of file structure

ISA-TAB specifies that the names of the primary files end with .txt extensions. ISA-TAB-Nano file names may end in either .txt or .xls extensions. The ISA-TAB-Nano files used as examples in this document were prepared in excel Microsoft Excel spreadsheets, and so their filenames have the .xls extension.

In FIG Figure 2 , describes the ISA-TAB-Nano file development process is described.
Typically, the investigation file is developed first and describes the overall investigation, associated studies and assays. The investigation file is a text file with a naming convention of “i_xxx.txt” or “i_xxx.xls,” in which xxx can be any name provided by the investigator. Once the investigation file has been completed, one or more study files (following the convention “s_xxx.txt” or “s_xxx.xls”) can be created. Similarly, one or more material files can be created. The material file describes the nanomaterial (or small molecule) and its components including structural information and follows the naming convention “m_xxx.txt” or “m_xxx.xls”. Assay files (following the convention “a_xxx.txt” or “a_xxx.xls”) are created for all assays performed. Each assay is defined by the endpoint measured and the technique used to measure that endpoint. Data files (raw or derived) specific to each type of assay can be associated to the respective assay files by referencing the names of the data files in the assay files.

FIG Figure 2. ISA-TAB-Nano File Development Process

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ISA-TAB-Nano File Templates

Templates The following pages provide templates for each ISA-TAB-Nano file are provided below:

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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

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  • (NCL21) G4 pyrrolidinone terminated PAMAM dendrimer

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  • (NCL22) G4.5 COONa terminated PAMAM dendrimer

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  • (NCL23) G4.5 COONa terminated PAMAM dendrimer-Magnevist® complex

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  • (NCL25) G4 tris (hydroxyl) terminated PAMAM dendrimer-Magnevist® complex

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  • (NCL26) G4 pyrrolidinone terminated PAMAM dendrimer-Magnevist® complex

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Commercially available Magnevist® (NCL24) was used as a control. NCL studies addressed in this report can be divided into three main The NCL example files encompass three categories: physicochemical characterization; immunotoxicology; in vitro toxicology.


Example Files

ISA-TAB-Nano Curated Examples

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