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This page provides examples for an example of the ISA-TAB-Nano Investigation files, File leveraging data from the Nanotechnology Characterization Laboratory (NCL) as an example (NCL200612A).The
ISA-TAB Investigation File
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Extensions
- ONTOLOGY SOURCE REFERENCE
- INVESTIGATION
- INVESTIGATION CONTACTS
- INVESTIGATION PUBLICATION
- STUDY
- STUDY DESIGN DESCRIPTORS
- STUDY CONTACTS
- STUDY PUBLICATIONS
- STUDY ASSAYS
- STUDY FACTORS
- STUDY PROTOCOLS
The ISA-TAB Investigation file was extended to support ISA-TAB-Nano. TABLE 1 represents extensions made to each section of the ISA-TAB Investigation file in support of ISA-TAB-Nano.
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Section | Field | Field Status (if applicable) |
|---|---|---|
INVESTIGATION | Investigation Disease | Optional |
INVESTIGATION | Investigation Disease Term Accession Number | Optional |
INVESTIGATION | Investigation Disease Term Source REF | Optional |
INVESTIGATION | Investigation Outcome | Optional |
STUDY | Study Disease | Optional |
STUDY | Study Disease Term Accession Number | Optional |
STUDY | Study Disease Term Source REF | Optional |
STUDY | Study Outcome | Optional |
| STUDY FACTORS | Study Factor Name Term Accessions Number | Optional |
| STUDY FACTORS | Study Factor Name Term Source REF | Optional |
STUDY ASSAYS | Study Assay Measurement Name | Optional |
STUDY ASSAYS | Study Assay Measurement Name Term Accession Number | Optional |
STUDY ASSAYS | Study Assay Measurement Name Term Source REF | Optional |
Investigation File Example
The The sub-sections that follow identify the fields associated with each ISA-TAB -Nano Investigation File section.Investigation File consists of the following sections:
- ONTOLOGY SOURCE REFERENCE
- INVESTIGATION
- INVESTIGATION CONTACTS
- INVESTIGATION PUBLICATION
- STUDY
- STUDY DESIGN DESCRIPTORS
- STUDY CONTACTS
- STUDY PUBLICATIONS
- STUDY ASSAYS
- STUDY FACTORS
- STUDY PROTOCOLS
An example of each section is provided below.
Ontology Source Reference
TABLE 2: Example Investigation File Ontology Source Reference Section
| ONTOLOGY SOURCE REFERENCE | ||||||
| Term Source Name | MO | NPO | UO | ChEBI | PATO | NCIt |
| Term Source File | http://purl.bioontology.org/ontology/MO | http://purl.bioontology.org/ontology/npo | http://purl.bioontology.org/ontology/UO | http://purl.bioontology.org/ontology/CHEBI | http://purl.bioontology.org/ontology/PATO | http://ncit.nci.nih.gov/ |
| Term Source Version | v.1.3.1.1 | v.2011-02-12 | v.80 | v.11.11d | ||
| Term Source Description | MGED Ontology | NanoParticle Ontology | Unit Ontology | Chemical Entities of Biological Interest | Phenotype Ontology | NCI Thesaurus |
Investigation
TABLE 3: Example Investigation File Investigation Section
| INVESTIGATION | |
| Investigation Identifier | NCL200612A |
| Investigation Title | Dendrimer-Based MRI Contrast Agents |
| Investigation Description | The goal of this investigation is to characterize a PAMAM dendrimer with an associated gadolinium chelate MRI contrast agent. |
| Investigation Disease | |
| Investigation Disease Term Accession Number | |
| Investigation Disease Term Source REF | |
| Investigation Outcome | |
| Investigation Submission Date | 2002-11-30 |
| Investigation Public Release Date | 2002-11-30 |
Investigation Contacts
TABLE 4: Example Investigation File Investigation Contacts Section
| INVESTIGATION CONTACTS | |
| Investigation Person Last Name | McNeil |
| Investigation Person First Name | Scott |
| Investigation Person Mid Initials | E |
| Investigation Person Email | mcneils@mail.nih.gov |
| Investigation Person Phone | 3018466939 |
| Investigation Person Fax | |
| Investigation Person Address | MSC 1050 Boyles Street, Frederick, MD 21702 |
| Investigation Person Affiliation | Nanotechnology Characterization Laboratory |
| Investigation Person Roles | investigator |
| Investigation Person Roles Term Accession Number | |
| Investigation Person Roles Term Source REF | MO |
Investigation Publication
TABLE 5. Example Investigation Publication Section
| INVESTIGATION PUBLICATIONS | |
| Investigation PubMed ID | 18095846 |
| Investigation Publication DOI | 10.2217/17435889.2.6.789 |
| Investigation Publication Author list | Hall JB; Dobrovolskaia MA; Patri AK; McNeil SE |
| Investigation Publication Title | Characterization of nanoparticles for therapeutics |
| Investigation Publication Status | published |
| Investigation Publication Status Term Accession Number | |
| Investigation Publication Status Term Source REF |
Study
TABLE 6. Example Investigation File Study Section
| STUDY | |
| Study Identifier | NCL200612A-CytoxicityLLC-PK1 |
| Study Title | Cytotoxicity characterization in LLC-PK1 cells |
| Study Submission Date | 2002-11-30 |
| Study Public Release Date | 2002-11-30 |
| Study Description | Nanoparticle biocompatibility was evaluated in the porcine renal proximal tubule cell line, LLC-PK1. Cytotoxicity was determined as described in the NCL protocol for LLC-PK1 Kidney Cytotoxicity Assay(GTA-1). Briefly, test materials were diluted to the desired assay concentrations in cell culture media. Cells were preincubated for 24 h prior to adding test material, reaching an approximate confluence of 80%. Cells were exposed to test material for 6, 24 and 48 h, and cytotoxicity was determined using the MTT cell viability and LDH membrane integrity assays. |
| Study Disease | |
| Study Dise Term Accession Number | |
| Study Disease Term Source REF | |
| Study Outcome | NCL22, NCL23 and NCL24 were found to be minimally cytotoxic, under the testing conditions utilized. |
| Study File Name | s_cytotoxicity-LLC-PK1.xls |
Study Design Descriptors
TABLE 7. Example Investigation File Study Design Descriptors Section
| STUDY DESIGN DESCRIPTORS | |
| Study Design Type | comparison |
| Study Design Type Term Accession Number | |
| Study Design Type Term Source REF |
Study Contacts
TABLE 8. Example Investigation File Study Contacts Section
| STUDY CONTACTS | |
| Study Person Last Name | Dobrovolskaia |
| Study Person First Name | Marina |
| Study Person Mid Initials | A |
| Study Person Email | marina@mail.nih.gov |
| Study Person Phone | 3018466352 |
| Study Person Fax | |
| Study Person Address | MSC 1050 Boyles Street, Frederick, MD 21702 |
| Study Person Affiliation | Nanotechnology Characterization Laboratory |
| Study Person Roles | investigator |
| Study Person Roles Term Accession Number | |
| Study Person Roles Term Source REF | MO |
Study Publications
TABLE 9. Example Investigation File Study Publications Section
| STUDY PUBLICATIONS | |
| Study PubMed ID | 18095846 |
| Study Publication DOI | 10.2217/17435889.2.6.789 |
| Study Publication Author list | Hall JB; Dobrovolskaia MA; Patri AK; McNeil SE |
| Study Publication Title | Characterization of nanoparticles for therapeutics |
| Study Publication Status | published |
| Study Publication Status Term Accession Number | |
| Study Publication Status Term Source REF |
Study Assays
TABLE 10. Example Investigation File Study Assays Section
| STUDY ASSAYS | ||
| Study Assay Measurement Type | MTT Assay | LDH Release Assay |
| Study Assay Measurement Type Term Accession Number | NPO_1709 | |
| Study Assay Measurement Type Term Source REF | NPO | |
| Study Assay Technology Type | ||
| Study Assay Technology Type Term Accession Number | ||
| Study Assay Technology Type Term Source REF | ||
| Study Assay Technology Platform | ||
| Study Assay Measurement Name | cell viability | LDH release |
| Study Assay Measurement Name Term Accession Number | NPO_1343 | |
| Study Assay Measurement Name Term Source REF | NPO | |
| Study Assay File Name | a_MTT-LLCPK1.xls | a_LDH-LLCPK1.xls |
Study Factors
TABLE 11. Example Investigation File Study Factors Section
| STUDY FACTORS | |||
| Study Factor Name | nanoparticle sample | particle concentration | time of exposure |
| Study Factor Name Term Accession Number | NPO_1404 | NPO_1830 | NPO_1819 |
| Study Factor Name Term Source REF | NPO | NPO | NPO |
| Study Factor Type | |||
| Study Factor Type Term Accession Number | |||
| Study Factor Type Term Source REF |
Study Protocols
TABLE 12. Example Investigation File Study Protocols Section
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