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

Click for each File type template: Investigation | Study | Material | Assay

See each File pages 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 pre-requisite 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.

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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]. 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 Biomedical Informatics Grid Program (caBIG®NCIP) Nanotechnology Informatics Working Group (Nano WG).

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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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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, including the caBIG^®^ community. 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)

The caBIG® (cancer Bioinformatics Grid)  LS DAM provides a shared view of the semantics of the life of differenct life sciences domains that are represented by the different workspaces in the caBIG infrastructure. It has a nanotechnolog 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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), 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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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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), and other resources will provide facilities for importing/exporting ISA-TAB-Nano files as the ISA-TAB-Nano specification evolves.

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