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Description
The ISA-TAB-Nano investigation file leverages the ISA-TAB investigation file, and it
1.1.1.1 Description
The ISA-TAB Investigation file allows for the description of the primary investigation and associated studies including assays and protocols. . An investigation can have one or more studies. For example, an investigation title may be “Dendrimertitled “Dendrimer-Based MRI Contrast Agents” and associated studies may be “Characterizing Agents” may have two studies titled as “Characterizing the Size of Dendrimer based MRI Contrast Agents” Agents” and “Determining the Hemolytic Properties “Determining the cytotoxicity property of Dendrimer based MRI Contrast Agents ”. in porcine proximal tubule cells” Each study can have one or more assays depending on the endpoint measured and the technique used. For example, a cytoxicity study may be conducted using an MTT assay and a LDH release assay. While a size characterization study can include two types of assays based on the technique used – one using DLS and the other using AFM.
The ISA-TAB specification provides flexibility in representing the level of granularity in information associated with a study; however, the level of granularity should factor in the effective representation of assays and protocols in conformance with the specification. For example, a study focusing on “Size Characterizations” “Size Characterizations” will have multiple size assay measurements (e.g. for example, Z-Average Size, Hydrodynamic Sizeaverage size, hydrodynamic size) and may involve the use of multiple protocols (e.g. Size techniques (for example, size by DLS, Size size by AFFMAFM). These can be represented effectively in the ISA-TAB file structure . A study focusing on “Physico-Chemical Characterizations” would have numerous and diverse assay measurements (e.g. Size, Molecular Weight, Surface, etc.) and protocols and it may be challenging to represent and group the assay measurements and protocols associated with each characterization type.
that ISA-TAB-Nano uses.
The investigation file provides descriptive information about studies Studies within the Investigation file provide descriptive information about the study including design descriptors, publications, factors, assays, protocols, and contacts. This descriptive information lays the foundation for other ISA-TAB-Nano files. For example, the Study Factors the following table shows a subset of the Investigation File, which is the study factors section of the Investigation investigation file. This section provides details the names of the factors (e.g. media solventfor example, temperature, solvent medium) used in the study . The value and their associated units of measurement (if the factors are quantitative). The values of these factors (e.g. for example, PBS, 25 Celsius) is then are specified either in the study or the Assay assay file.
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File Format
The Investigation ISA-TAB-Nano investigation file leverages the ISA-TAB file format leverages , which is a vertical-based spreadsheet format with columns representing multiple values. In the example subset of the Investigation file below, column row headers in the first column, as shown in the following table. The fields are divided into sections. Therefore, the field values in the investigation file are entered in column order. For instance, in the following table, Column A indicates the field names and columns Columns B and C are contain the field values.
Example Subset of the Investigation File Format
A | B | C |
|---|---|---|
STUDY FACTORS | N/A | N/A |
Study Factor Name | temperature |
solvent |
Study Factor Type |
temperature |
solvent medium | ||
Study Factor Type Term Accession Number | PATO_0000146 | NPO_1855 |
Study Factor Type Term Source REF |
1.1.1.3 nano-TAB Extensions
In support of nano-TAB, the following extensions and constraints were applied to the ISA-TAB Investigation file and are further described in Section 4.
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
PATO | NPO |
Fields
The field names in an investigation file are organized vertically in the first column. These fields are divided into 11 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. These sections are:s
- ONTOLOGY SOURCE REFERENCE
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- INVESTIGATION
...
- INVESTIGATION
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- PUBLICATIONS
...
- INVESTIGATION CONTACTS
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- MATERIAL
- STUDY
...
- STUDY DESIGN DESCRIPTORS
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- STUDY PUBLICATIONS
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- STUDY FACTORS
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- STUDY ASSAYS
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- STUDY PROTOCOLS
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- STUDY CONTACTS
An investigation can contain multiple studies. As such the entire study section is typically repeated.
1.1.1 ONTOLOGY SOURCE REFERENCE
ISA-TAB-Nano Extensions--- ISA-TAB-Nano extends the ISA-TAB Investigation File specification by introducing new fields. The following sections define all fields.
Ontology Source Reference
This section records information about ontologies containing the terms referenced in the ISA-TAB-Nano files. The Investigation File Example page shows an An example of the ONTOLOGY SOURCE REFERENCE section along with example data. This section uses four ISA-TAB concepts:
Term Source Name---The name of the source of a term used in the ISA-TAB-Nano files. The source could be an ontology or a controlled vocabulary. The source name is the full name or the acronym of the spreadsheet is provided in Exhibit 4.1 along with example data.
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A
...
B
...
C
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ONTOLOGY SOURCE REFERENCE
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Term Source Name
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NPO
...
UO
...
Term Source file
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Term Source Version
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Term Source Description
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Nanoparticle Ontology
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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.
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A
...
B
...
C
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INVESTIGATION
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Investigation Identifier
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NCL200612A
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Investigation Title
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Dendrimer-Based MRI Contrast Agents
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Investigation Description
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The objective of the Dendritic Nanotechnologies, Inc. - NCL collaboration is to characterize a PAMAM dendrimer with an associated gadolinium chelate MRI contrast agent.
the ontology/controlled vocabulary. This is a required field if the term source name is referenced in any of the ISA-TAB-Nano files.
T erm Source File--- A file name or a URI of the source named in the Term Source Name field.
Term Source Version---Version number of the vocabulary source file. This is a required field if the field for Term Source File has a value.
Term Source Description---Text description to disambiguate resources when homologous acronyms are used.
Investigation
This section allows for the description of the investigation. An example of the INVESTIGATION section is in the Investigation File Example page. The INVESTIGATION section uses nine concepts and includes concepts from ISA-TAB and extensions made in support of ISA-TAB-Nano:
Investigation Identifier--- A locally unique identifier or an accession number provided by a repository.
Investigation Title---A concise phrase used as a title for the investigation.
Investigation Description---A textual description of the investigation.
Investigation Submission Date---The date on which the investigation was reported to a repository (format: YYYY-MM-DD).
Investigation Public Release Date---The date on which the investigation is publicly released or published (format: YYYY-MM-DD).
Investigation Disease---Disease(s) that are the subject of an investigation, if applicable. ISA-TAB-Nano introduced this concept to identify the disease(s) related to the subject of the investigation. (ISA-TAB Extension for ISA-TAB-Nano)
Investigation Disease Term Accession Number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for Investigation Disease. ISA-TAB-Nano introduced this concept to identify the term accession number for the disease. (ISA-TAB Extension for ISA-TAB-Nano)
Investigation Disease Term Source REF--- The name which identifies the source from where the term for investigation disease is selected. This name should match one of the names entered in the Term Source Name field. ISA-TAB-Nano introduced this concept to identify the term source ref for the disease. (ISA-TAB Extension for ISA-TAB-Nano)
Investigation Outcome---A textual description summarizing the conclusion of an investigation. ISA-TAB-Nano introduced this concept to identify the outcome of the investigation. (ISA-TAB Extension for ISA-TAB-Nano)
Investigation Publications
This section allows for the identification of articles (published) associated with the investigation. An example of the INVESTIGATION PUBLICATIONS section is in the Investigation File Example page. There are seven ISA-TAB concepts used in this section:
Investigation Pubmed ID---PubMed identifier of the publication associated with the investigation.
Investigation Publication DOI---A Digital Object Identifier (DOI) of the publication associated with the investigation.
Investigation Publication Author List---A semicolon-delimited (";") list of authors of a publication associated with the investigation.
Investigation Publication Title---A concise phrase used as a title for the publication associated with the investigation.
Investigation Publication Status---A term describing the status of a publication (that is, submitted, in preparation, published).
Investigation Publication Status Term Accession Number---The identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for Investigation Publication Status.
Investigation Publication Status Term Source REF---The name which identifies the source from where the term for Investigation Publication Status is selected. This name should match one of the names entered in the Term Source Name field.
Investigation Contacts
This section allows for the identification of the point(s) of contact for the investigation. An example of the INVESTIGATION CONTACTS section is in the Investigation File Example page. There are 11 ISA-TAB concepts used as field names:
Investigation Person Last Name---The last name of a person who is the point of contact for the investigation.
Investigation Person First Name---The first name of a person who is the point of contact for the investigation.
Investigation Person Mid Initials---The middle initial(s) of a person who is the point of contact for the investigation.
Investigation Person Email---The email address of a person who is the point of contact for the investigation.
Investigation Person Phone---The telephone number of a person who is the point of contact for the investigation.
Investigation Person Fax---The fax number of a person who is the point of contact for the investigation.
Investigation Person Address---The mailing address of a person who is the point of contact for the investigation.
Investigation Person Affiliation--- The name of the organization to which the point of contact belongs.
Investigation Person Roles--- The term which classifies the role(s) performed by person who is the point of contact for the investigation.
Investigation Person Roles Term Accession Number---
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Investigation Disease
...
Investigation Disease Term Accession Number
...
Investigation Disease Term Source REF
...
Investigation Outcome
...
Investigation Submission Date
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2006-12-01
...
Investigation Public Release Date
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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 if the term is entered as a value for the Disease. Note: This term is a nano-TAB extension. Investigation Person Role.
Investigation Person Roles 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.
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A
...
B
...
C
...
INVESTIGATION PUBLICATIONS
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Investigation PubMed ID
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18095846
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Investigation Publication DOI
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10.2217/17435889.2.6.789
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Investigation Publication Author List
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Hall JB; Dobrovolskaia MA; Patri AK; McNeil SE
Investigation Person Role.
Material
This section allows for the identification of materials used in the investigation and associated studies. There are two concepts used in the MATERIAL section. An example of the MATERIAL section is in the Investigation File Example page. ISA-TAB-Nano introduced the MATERIAL section. These concepts are described below:
Material File Name---The name of the ISA-TAB-Nano Material File, which lists information about the composition and characteristics of the nanomaterials or other small molecules. There can be only one file per cell. ISA-TAB-Nano introduced this concept to identify the name of the Material File. (ISA-TAB Extension for ISA-TAB-Nano)
Material Source Name---The name of the nanomaterial or small molecule associated with the Material File. There can be only one Material Source Name per column. ISA-TAB-Nano introduced this concept to identify source name of the material. (ISA-TAB Extension for ISA-TAB-Nano)
Study
This section allows for the description of one or more studies conducted as part of an investigation. An example of the STUDY section is in the Investigation File Example page. There are 11 concepts used in the STUDY section, seven of which are from ISA-TAB and four were added by ISA-TAB-Nano.
Study Identifier---A unique identifier used for the study. It is either a temporary identifier supplied by users or one generated by a repository or other database.
Study Title---A concise phrase used to encapsulate the purpose and goal of the study.
Study Description---A textual description of the study, with components such as objectives or goals.
Study Submission Date---The date on which the study is submitted to an archive (format: YYYY-MM-DD).
Study Public Release Date---The date on which the study is publicly released or published (format: YYYY-MM-DD).
Study Disease---Disease(s) that are the subject of the study, if applicable. ISA-TAB-Nano introduced this concept to identify the disease(s) related to the study. (ISA-TAB Extension for ISA-TAB-Nano)
Study Disease Term Accession Number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for Study Disease. (ISA-TAB Extension for ISA-TAB-Nano)
Study Disease Term Source REF---The name which identifies the source from where the term for Study Disease is selected. This name should match one of the names entered in the Term Source Name field. (ISA-TAB Extension for ISA-TAB-Nano)
Study Outcome---A textual description about the outcome(s) of the study. ISA-TAB-Nano introduced this concept to provide a summary or conclusion of a study. (ISA-TAB Extension for ISA-TAB-Nano)
Study File Name---The name of the ISA-TAB-Nano study file, which lists information about the biological specimens (cells, tissues, organs, animal model, body fluids), nanoparticles; small organic molecules, and other types of samples assayed in a study. There can be only one file name per cell.
Study Design Descriptors
This section allows for the identification of design type of the study. An example of the STUDY DESIGN DESCRIPTORS section is in the Investigation File Example page. There are three concepts used in the STUDY DESCRIPTORS section. These concepts are from ISA-TAB.
Study Design Type---A term describing the classification of the study based on the overall study (experimental) design (for example, comparison study). The term can be free-text or taken from a controlled vocabulary/ontology.
Study Design Type Term Accession Number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for Study Design Type.
Study Design Type Term Source REF---The name which identifies the source from where the term for Study Design Type is selected. This name should match one of the names entered in the Term Source Name field.
Study Publications
This section allows for the identification of articles (published) associated with the study. An example of the STUDY PUBLICATIONS section is in the Investigation File Example page. This section uses seven ISA-TAB concepts.
Study Pubmed ID---PubMed identifier of the publication associated with the study.
Study Publication DOI---A Digital Object Identifier (DOI) of the publication associated with the study.
Study Publication Author List---A semicolon-delimited (";") list of authors of a publication associated with the study.
Study Publication Title---A concise phrase used as a title for the publication associated with the study.
Study Publication Status---A term describing the status of a publication (that is, submitted, in preparation, published), associated with the study.
Study Publication Status Term Accession Number---The identification
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Investigation Publication Title
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Characterization of nanoparticles for therapeutics
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Investigation Publication Status
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peer reviewed
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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 if the term is entered as a value for the Study Publication Status.Investigation
Study Publication Status Term Source REF---The name which identifies the source from where the term for Study Publications Status is selected. This name should match one of the names entered in the Term Source Name.
Study Factors
This section allows for the identification of factors associated with the study. An example of the STUDY FACTORS section is in the Investigation File Example page. This section has four concepts taken from ISA-TAB.
Study Factor Name---The name of one independent variable (factor) manipulated by the experimentalist with the intention to affect the subject of study (that is, Stressor). This is a required field, if there are factors in an assay study. Only one factor name is allowed per cell. The value of a factor is given either in the study or in the assay file.
Study Factor Type---A term used for the classification of factors associated with the study (for example, condition). This is a required field if there are factors in an assay study. More than one term is allowed per cell; multiple terms are separated by semicolons.
Study Factor Type Term Accession Number---Identification number of a term selected from an ontology or a controlled vocabulary from which a , if the 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.
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A
...
B
...
C
...
INVESTIGATION CONTACTS
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Investigation Person Last Name
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McNeil
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Investigation Person First Name
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Scott
...
Investigation Person Mid Initials
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Investigation Person Email
...
...
Investigation Person Phone
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3018466939
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Investigation Person Fax
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Investigation Person Address
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MSC 1050 Boyles Street, Frederick, MD 21702
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Investigation Person Affiliation
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Nanotechnology Characterization Laboratory
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Investigation Person Roles
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investigator
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Investigation Person Roles Term Accession Number
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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.
Study Factor Type.
Study Factor Type Term Source REF---The name which identifies the source from where the term for Study Factor Type is selected. This name should match one of the names entered in the Term Source Name field.
Study Assays
This section allows for the identification of type of measurement and the type of technology used for the measurement in an assay that is part of a study. An example of the STUDY ASSAYS section is in the Investigation File Example page. The STUDY ASSAYS section has 11 concepts. Out of these, eight concepts are from ISA-TAB. ISA-TAB-Nano introduced the remaining concepts.
Study Assay Measurement Type---A term to qualify the endpoint, or what is being measured.
Study Assay Measurement Type Term Accession Number---Identification number of the term selected from an ontology or a controlled vocabulary, if the term is entered as a value for Study Assay Measurement Type.
Study Assay Measurement Type Term Source REF---The name which identifies the source from where the term for Study Assay Measurement Type is selected. This name should match one of the names entered in the Term Source Name field.
Study Assay Technology Type---The type of technology (technique or method) used for the assay measurement (for example, Dynamic light scattering).
Study Assay Technology Type Term Accession Number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for Study Assay Technology Type.
Study Assay Technology Type Term Source REF---The name which identifies the source from where the term for Study Assay Technology Type is selected. This name should match one of the names entered in the Term Source Name field.
Study Technology Platform---The manufacturer and platform name of the instruments used in the study assay.
Study Assay Measurement Name---A semicolon-delimited list of names of quantities whose values are the outputs of an assay measurement. (ISA-TAB Extension for ISA-TAB-Nano)
Study Assay Measurement Name Term Accession Number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for Study Assay Measurement Name. (ISA-TAB Extension for ISA-TAB-Nano)
Study Assay Measurement Name Term Source REF--- The name which identifies the source from where the term for Study Assay Measurement Name is selected. (ISA-TAB Extension for ISA-TAB-Nano)
Study Assay File Name--- Name of the ISA-TAB-Nano Assay file corresponding to the study assay. This is a required field. There can be only one assay file name per cell.
Study Protocols
This section allows for the identification of the type of protocols, and the parameters and components of a protocol used in a study. A protocol describes the formal plan of an experiment or research activity, including the objective, rationale, design, materials and methods for the conduct of the study; intervention description, and method of data analysis. An example of the STUDY PROTOCOLS section is in the Investigation File Example page. There are 14 concepts in this section taken from ISA-TAB.
Study Protocol Name---The name of the protocols used within a study and will be referenced in the ISA-TAB-Nano Study or Assay files.
Study Protocol Type---The term used to classify the protocol (for example, synthesis, assay, etc.).
Study Protocol Type Term Accession Number--- Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for Study Protocol Type
Study Protocol Type Term Source REF---Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for Study Protocol Type.
Study Protocol Description---A textual description of the protocol.
Study Protocol URI---Pointer to protocol documents or resources external to ISA-TAB-Nano, which can be accessed by their Uniform Resource Identifier (URI). If URI is not available, enter the protocol document file name and make the protocol document available along with ISA-TAB-Nano files.
Study Protocol Version---An identifier for the version to ensure protocol tracking.
Study Protocol Parameters Name---A semicolon-delimited (";") list of parameter names used as an identifier in the ISA-TAB-Nano Study or Assay files. A protocol parameter is an intrinsic experimental condition that may be varied or constant.
Study Protocol Parameters Name Term Accession Number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for the Study Protocol Parameter Name.
Study Protocol Parameters Name Term Source REF---The name which identifies the source from where the term for Study Protocol Parameter Name. This name should match one of the names entered in the Term Source Name field.
Study Protocol Components Name--- A semicolon-delimited (";") list of names identifying the components of a protocol. Component names include instrument names, software names, and reagent names.
Study Protocol Components Type--- The term to classify the protocol component, for example, instrument, software, and reagent.
Study Protocol Components Type Term Accession Number--- Identification number of a term seleced from an ontology or a controlled vocabulary, if the term is entered as a value for the Study Protocol Component Type.
Study Protocol Components Type Term Source REF--- The name which identifies the source from where the term for Study Protocol Component Type is selected. This name should match one of the names entered in the Term Source Name field.
Study Contacts
This section allows the identification of the point of contact for a study. An example of the STUDY CONTACTS section is in the Investigation File Example page. The STUDY CONTACTS section has 11 ISA-TAB concepts.
Study Person Last Name---The last name of a person who is the point of contact for the study.
Study Person First Name---The first name of a person who is the point of contact for the study.
Study Person Mid Initials---The middle initial(s) of a person who is the point of contact for the study.
Study Person Email---The email address of a person who is the point of contact for the study.
Study Person Phone---The telephone number of a person who is the point of contact for the study.
Study Person Fax--- The fax number of a person who is the point of contact for the study
Study Person address--- The mailing number of a person who is the point of contact for the study
Study Person Affiliation--- The name of the organization to Investigation Person Affiliation - Organization in which the point of contact belongs.
Investigation Study Person Roles - Role of --- The term which classifies the role(s) performed by person who is the point of contact in for the investigationstudy.
Investigation Study Person Roles Term Accession Number--- Identification number of a term selected from an ontology or a controlled vocabulary, and if the term is entered as a value for Study Person RolesRole.Investigation
Study 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.--- The name which identifies the source from where the term for Study Person Role is selected. This name should match one of the names entered in the Term Source Name field.
Files
The following pages provide the investigation file examples, template, and glossary:
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