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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 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 \[[http://nbi.oregonstate.edu/]\]. 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) Cancer Biomedical Informatics Grid (caBIG®) Nanotechnology Informatics Working Group (Nano WG).
ISA-TAB-Nano Standards Re-Use
ISA-TABTAB
The ISA-TAB-Nano format specification is based on an existing specification developed by the ISA-commmunity (www.isa-tools.org), namely, the investigation/study/assay (ISA-TAB) format specification. The ISA-TAB format (http://isatab.sourceforge.net/) 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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