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Field | Change | Description | Field Status |
Term Source Name | Use NPO | Reference the Nanoparticle Ontology (NPO) as the primary ontology supporting nanotechnology studies | Optional |
Investigation Outcome | Addition | Provides a textual description of the outcome(results) of the investigation | Optional |
Study Outcome | Addition | Provides a textual description of the outcome (results) of the study | Optional |
Study file Version | Addition | Indicates the version (e.g. 1.0) of a file | Optional |
Study file Description | Addition | Provides a textual description of the file | Optional |
1.1 Investigation file
The Investigation file is a vertically oriented spreadsheet containing tab delimited column values. The Investigation file consists of the following sections as defined by ISA-TAB:
s ONTOLOGY SOURCE REFERENCE
s INVESTIGATION
s INVESTIGATION PUBLICATION
s INVESTIGATION CONTACTS
s STUDY
º STUDY DESIGN DESCRIPTORS
º STUDY PUBLICATIONS
º STUDY FACTORS
º STUDY ASSAYS
º STUDY PROTOCOLS
º STUDY CONTACTS
An investigation can contain multiple studies. As such the entire study section is typically repeated.
1.1.1 ONTOLOGY SOURCE REFERENCE
An example of the ONTOLOGY SOURCE REFERENCE section of the spreadsheet is provided in Exhibit 4.1 along with example data.
A | B | C |
ONTOLOGY SOURCE REFERENCE | ||
Term Source Name | NPO | UO |
Term Source file | ||
Term Source Version | ||
Term Source Description | Nanoparticle Ontology | Unit Ontology |
Exhibit 4.1 Example ONTOLOGY SOURCE REFERENCE section
Definitions for concepts in the ONTOLOGY SOURCE REFERENCE section are provided below.
Term Source Name - List of ontologies containing terms referenced in the nano-TAB files.
Term Source file - The URI of the ontology.
Term Source Version - Version for each ontology referenced in the nano-TAB files.
Term Source Description - Description of each ontology referenced in the nano-TAB files.
1.1.2 INVESTIGATION
An example of the INVESTIGATION section of the spreadsheet is provided in Exhibit 4.2 along with example data.
A | B | C |
INVESTIGATION | ||
Investigation Identifier | NCL200612A | |
Investigation Title | Dendrimer-Based MRI Contrast Agents | |
Investigation Description | The objective of the Dendritic Nanotechnologies, Inc. - NCL collaboration 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 | 2006-12-01 | |
Investigation Public Release Date | 2006-12-01 |
Exhibit 4.2 Example INVESTIGATION Section
Definitions for concepts in the INVESTIGATION section are provided below.
Investigation Identifier - Name used as an identifier for the investigation.
Investigation Title - Name used as a title for the investigation.
Investigation Description – Text description of the investigation.
Investigation Disease - Disease(s) that are the subject of the investigation, if applicable. Note: This term is a nano-TAB extension.
Investigation Disease Term Accession Number – Identification number of a term selected from an ontology or a controlled vocabulary, and entered as a value for the Disease. Note: This term is a nano-TAB extension.
Investigation Disease Term Source REF - Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for the Disease. Note: This term is a nano-TAB extension.
Investigation Outcome - Text description of the outcome of the investigation. Note: This term is a nano-TAB extension.
Investigation Submission Date - Date the investigation was initiated in the format YYYY-MM-DD.
Investigation Public Release Date - Date the investigation was published or made publically available in the format YYYY-MM-DD.
1.1.3 INVESTIGATION PUBLICATIONS
An example of the INVESTIGATION PUBLICATION section of the spreadsheet is provided in Exhibit 4.3 along with example data.
A | B | C |
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 | peer reviewed | |
Investigation Publication Status Term Accession Number | ||
Investigation Publication Status Term Source REF | NPO |
Exhibit 4.3 Example INVESTIGATION PUBLICATIONS Section
Definitions for concepts in the INVESTIGATION PUBLICATIONS section are provided below.
Investigation PubMed ID - Identifier of the publication in the PubMed publication source.
Investigation Publication DOI - Publication Document Object Identifier.
Investigation Publication Author List - List of authors separated by semi-colons.
Investigation Publication Title - Name used as a title for the publication.
Investigation Publication Status - The status of the publication.
Investigation Publication Status Term Accession Number - Identification number of a term selected from an ontology or a controlled vocabulary, and entered as a value for the Publication Status.
Investigation Publication Status Term Source REF - Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for the Publication Status.
1.1.4 INVESTIGATION CONTACTS
An example of the INVESTIGATION CONTACTS section of the spreadsheet is provided in Exhibit 4.4 along with example data.
A | B | C |
INVESTIGATION CONTACTS | ||
Investigation Person Last Name | McNeil | |
Investigation Person First Name | Scott | |
Investigation Person Mid Initials | ||
Investigation Person Email | ||
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 |
Exhibit 4.4 Example INVESTIGATION CONTACTS Section
Definitions for concepts in the INVESTIGATION CONTACTS section are provided below.
Investigation Person Last Name - Last name of the point of contact.
Investigation Person First Name - First name of the point of contact.
Investigation Person Mid Initials – Middle Initials of the point of contact.
Investigation Person Email - Email address of the point of contact
Investigation Person Phone - Phone number of the point of contact.
Inv Investigation Person Fax - Fax number of the point of contact.
Investigation Person Address - Mailing address of the point of contact.
Investigation Person Affiliation - Organization in which the point of contact belongs.
Investigation Person Roles - Role of the point of contact in the investigation.
Investigation Person Roles Term Accession Number - Identification number of a term selected from an ontology or a controlled vocabulary, and entered as a value for Person Roles.
Investigation Person Roles Term Source REF - Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for Person Roles.
