 |
Page History
...
Nano-TAB Extensions---Since the material file does not exist in the ISA-TAB specification, the entire file is considered an extension.
The MATERIAL section allows for the description of the nanomaterial formulation and any materials (including material parts) associated with the nanomaterial formulation. A formulation is the nanomaterial and any other components or medium. A formulation can also be any non-biological material sample (for example, small molecule) analyzed in experiment. The MATERIAL section supports the following types of information:
...
(4) Intended application of the material
...
MATERIAL
The MATERIAL section allows for the description of the nanomaterial formulation and any materials (including material parts) associated with the nanomaterial formulation. A formulation is the nanomaterial and any other components or medium. A formulation can also be any non-biological material sample (e.g. small molecule) used in experimentation. The Material Section supports the following types of information:
s
- the material identifier, material name, material type, and material description
...
- a description of the synthesis and rationale for design
...
- the chemical name and characteristics of the material
...
- the intended application of the material
Exhibit 4.12 shows an example of how a material is described within the Material section.
...
A
...
B
...
MATERIAL
...
...
Material Identifier
...
NCL-23
...
Material Name
...
g45_coona_dendrimer_magnevist_complex
...
Material Description
...
G4.5 COONa terminated PAMAM dendrimer-Magnevist® complex
...
Material Synthesis
...
Material Design Rationale
...
Material Design RationaleTerm Accession Number
...
Material Design Rationale Term Source REF
...
Material Type
...
nanoparticle sample
...
Material Type Term Accession Number
...
NPO_1404
...
Material Type Term Source REF
...
NPO
...
Material Chemical Name
...
Material Chemical Term Accession Number
...
Material Chemical Term Source REF
...
Material Characteristic
...
Material Characteristic Term Accession Number
...
Material Characteristic Term Source REF
...
Material Characteristic Value
...
Material Characteristic Value Term Accession Number
...
Material Characteristic Value Term Source REF
...
Material Characteristic Statistic
...
Material Characteristic Statistic Term Accession Number
...
Material Characteristic Statistic Term Source REF
...
Material Characteristic Unit
...
Material Characteristic Unit Term Accession Number
...
Material Characteristic Unit Term Source REF
...
Material Intended Application
...
MRI Contrast Agent
...
Material Intended Application Term Accession Number
...
NPO_581
...
Material Intended Application Term Source REF
...
NPO
Exhibit 4.12 Material Section Example
1.1.1.1 Material Identifier
Material Identifier refers to the unique internal identification of the materialMaterial source identifier--- The unique identification name of the source from which the material sample is derived. Its value is used as the value for source name in nano-TAB study files, thereby linking the nano-TAB material file and the study file. For example, NCL-23 (see Exhibit 4-12TABLE 2) is the name that identifies a material characterized by the NCI Nanotechnology Characterization Laboratory (NCL).
1.1.1.2 Material Name
Material Name is the unique name given to a material, and this name is used to identify or reference the sample across the nano-TAB files.
1.1.1.3 Material Type
Material Type refers to names that describe the type of material. For example, for the material formulation NCL-23, the Material Type has the value “nanoparticle sample”. The material formulation is a dendrimer-Magnevist complex and the materials within the formulation are of type “dendrimer” and “small molecule”. If terms are selected from an open controlled vocabulary or ontology, then the fields, Material Type Term Accession Number and Material Type Term Source REF must be given values. If there are multiple terms that define the type of Material, then these terms must be separated by semi-colons.
1.1.1.3.1 Material Type Term Accession Number
The Material Type Term Accession Number is the identification number used within an ontology or a controlled vocabulary. For example, the term “dendrimer” is a term selected from the NPO, and has the accession number NPO_735.
1.1.1.3.2 Type Term Source REF
Material Sample Type Term Source REF is used to enter the name of the ontology or the controlled vocabulary (as specified in the Investigation file) from which a term is selected as a value for Material Type (e.g., NPO).
1.1.1.4 Material Description
The Material Description field contains a text description of the formulation or associated materials. For example: “G4.5 COONa terminated PAMAM dendrimer-Magnevist® complex”.
1.1.1.5 Material Synthesis
This example indicates that the sample NCL-23 is a complex formed out of NCL-22 (a G4.5 PAMAM dendrimer terminated with carboxyl groups) and NCL-24 (magnevist).
Material name---The unique identification name for the sample and its different components. This name is used to identify or reference the different components across the nano-TAB files.
Material description---A textual description of the material sample.
Material synthesis---A text or a single term The Material Synthesis field contains a text description of how the material was made.
1.1.1.6 Material Design Rationale
The Material design rationale---A text description for the underlying design rationale is the property, process or phenomenon taken into consideration when formulating a nanoparticle or other substance in order to achieve the intended use of the formulation. The value can be a textual description or terms that may be obtained from an ontology or controlled vocabulary. The field can take multiple terms as values separated by semi-colons.
1.1.1.6.1 Material Design Rationale Term Accession Number
Material type---One or more terms used to classify the type of material sample. Multiple terms are entered as a semicolon-delimited list.
Material type term accession number---Identification The identification number of a term selected from an ontology or a controlled vocabulary, and if the term is entered as a value for the underlying Material Design Rationale material type.
1.1.1.6.2 Material Design Rationale Term Source REF
The name of the ontology or controlled vocabulary (as specified in the Investigation file) from which a term is selected and entered as a value for the underlying Material Design Rationale.
1.1.1.7 Material Chemical Name
The chemical name of the Material. This field can carry multiple terms as values separated by semi-colons for describing multiple files.
1.1.1.7.1 Material Chemical Name Term Accession Number
Material type term source REF---The name which identifies the source from where the term for material type is selected. This name should match one of the names entered in the terms source name field in the investigation file.
Material chemical name---The chemical name of the material or its constituent material.
Material chemical name term accession number---Identification number of a term selected from The identification number used within an ontology or a controlled vocabulary for , if the term that is entered as a value for the Material Chemical Name. For example, the term “diaminobutane” is a term selected from CJEBI, and has the Accession Number CHEBI.xxx.
1.1.1.7.2 Material Chemical Name Term Source REF
The name of the ontology or controlled vocabulary (as specified in the Investigation file) from which a term is selected and entered as a value for Material Chemical Name.
1.1.1.8 Material Characteristic
A list of names separated by semi-colons, which define specific attributes of the characteristics of the Material. These characteristics may be specific to the type of formulation (e.g. wall type for carbon nanotubes, branch for dendrimer). This field can support multiple terms as values separated by semi-colons.
1.1.1.8.1 Material Characteristic Term Accession Number
material chemical name.
Material chemical name term source REF---The name which identifies the source from where the term for material chemical name is selected. This name should match one of the name entered in the term source name field in the investigation file.
Material characteristic--- A semicolon-delimited list of terms that describe specific attributes of the sample or its constituents.
Material characteristic term accession number---Identification The identification number of a term selected from an ontology or a controlled vocabulary, and if the term is entered as a name value for the material characteristic.
1.1.1.8.2 Material Characteristic Term Source Ref
The name of the ontology or controlled vocabulary (as specified in the Investigation file) from which a term is selected and entered for the material characteristic.
1.1.1.9 Material Characteristic Value
Material characteristic term source REF---The name which identifies the source from where the term for Material Characteristic is selected. This name should match one of the names entered in the terms source name field in the investigation file.
Material characteristic value--- The value corresponding to a material characteristic name. For example, “single walled carbon nanotube” The value corresponding to the characteristic name associated with a Material. For example, “SWNT” is the value of the characteristic name “wall type” . This field can carry multiple terms as values separated by semi-colons.
1.1.1.9.1 Material Characteristic Value Term Accession Number
for the material chemical name “carbon nanotube”.
Material characteristic value term accession number--- Identification The identification number of a term selected from an ontology or a controlled vocabulary, and if the term is entered as a value for the material characteristic value.
1.1.1.9.2 Material Characteristic Value Term Source Ref
The name of the ontology or controlled vocabulary (as specified in the Investigation file) from which a term is selected and entered as a value for the material characteristic.
1.1.1.10 Material Characteristic Statistic
The mathematical statistic (e.g. mean, standard deviation) associated with the value of a material characteristic. This field can carry multiple terms as values separated by semi-colons.
1.1.1.10.1 Material Characteristic Statistic Term Accession Number
Material characteristic value term source REF--- The name which identifies the source from where the term for material characteristic value is selected. This name should match one of the names entered in the terms source name field in the investigation file.
Material characteristic unit--- The standard of measurement used if the value for material characteristic value is quantitative and dimensional.
Material characteristic unit term accession number--- Identification The identification number of a term selected from an ontology or a controlled vocabulary, and if the term is entered as a value for the statistic associated with the characteristic value.
1.1.1.10.2 Material Characteristic Statistic Term Source Ref
The name of the ontology or controlled vocabulary (as specified in the Investigation file) from which a term is selected and entered as a value for the statistic associated with the characteristic value.
1.1.1.11 Material Characteristic Unit
The unit associated with a quantitative characteristic value. This field can carry multiple terms as values separated by semi-colons.
1.1.1.11.1 Material Characteristic Unit Term Accession Number
material characteristic unit.
Material characteristic unit term source REF--- The name which identifies the source from where the term for material characteristic unit is selected.
Material characteristic statistic--- The type of statistical measure attributed to a numerical value (e.g., mean, standard deviation, z-average, etc.). This is a required field, if the material characteristic value is a statistical measure.
Material characteristic statistic term accession number--- Identification number of a term selected from The identification number used within an ontology or a controlled vocabulary for , if the term that is entered as a value for the Material Characteristic Value Unit.
1.1.1.11.2 Material Characteristic Unit Term Source Ref
The name of the ontology or controlled vocabulary (as specified in the Investigation file) from which a term is selected and entered as a value for the Material Characteristic Value Unit.
1.1.1.12 Material Intended Application
material characteristic statistic.
Material characteristic statistic term source REF--- Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for material characteristic statistic. This name should match one of the names entered in the terms source name field in the investigation file.
Material intended application---The Intended Application is the application for which a drug, nanoparticle or other substance is formulated and tested (e.g., MRI). This field can carry multiple terms as values separated by semi-colons.
1.1.1.12.1 Material Intended Application Term Accession Number
This field corresponds to the identification number of the term that is Material intended application 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 Intended Application. For example, the accession number for the term “MRI Contrast Agent” is NPO_581.
1.1.1.12.2 Material Intended Application Term Source REF
This field is used to enter the name of the ontology or the controlled vocabulary (as specified in the Investigation file) from which a term is selected as a value for Intended Application (e.g., NPO).
...
material intended application.
Material intended application term source REF---The name which identifies the source from where the term for material intended application is selected. This name should match one of the names entered in the terms source name field in the investigation file.
Material Relationship
The MATERIAL RELATIONSHIP section is meant for specifying used to record the name and types of the relationships between materials including material parts and material linkages. Material parts represent the components within a material. Material linkages represent association between materials (e.g. encapsulation, attachment, entrapment).
Exhibit 4.13 illustrates the row headers TABLE 3 illustrates an example of the MATERIAL RELATIONSHIP section.
...
A
...
B
...
MATERIAL RELATIONSHIP
...
Material Part Material Name
...
Material Linkage Material Name
...
magnevist
...
Material Linkage Type
...
attachment
...
Material Linkage Type Term Accession Number
...
Material Linkage Type Term Source REF
...
Material Linkage Characteristic
...
bond type
...
Material Linkage Characteristic Term Accession Number
...
NPO_776; NPO_224
...
Material Linkage Characteristic Term Source REF
...
NPO; NPO
...
Material Linkage Characteristic Value
...
covalent
The concepts used for describing the relationship are given below.
Material part material name---A unique identification name for each of the two components (whole or part) that are linked to each other in the nanoparticle sample. The names should be obtained from the entries for the material name field. This is a required field, if the field material linkage type is not empty.
Material linkage material name---A unique identification name used for the linkage between any two components of a nanoparticle sample. There should be only one name per cell.
Material linkage type---The
...
Material Linkage Characteristic Value Term Accession Number
...
Material Linkage Characteristic Value Term Source REF
...
Material Linkage Characteristic Statistic
...
Material Linkage Characteristic Statistic Term Accession Number
...
Material Linkage Characteristic Statistic Term Source REF
...
Material Linkage Characteristic Unit
...
Material Linkage Characteristic Unit Term Accession Number
...
Material Linkage Characteristic Unit Term Source REF
Exhibit 4.13 Material Linkage Section Example
1.1.2.1 Material Part Material Name
The unique identification name used to identify the name of a material that is a part of the described material. This name is consistent with the material name of the material functioning as the part.
1.1.2.2 Material Linkage Material Name
The unique identification name used within the material file, and across the nano-TAB files to identify / reference a linkage in a nanoparticle.
1.1.2.3 Material Linkage Type
Material Linkage Type describes the type of linkage present in a nanoparticle sample (e.g., attachment, encapsulation, entrapment etc.).
1.1.2.3.1 Material Linkage Type Term Accession Number
The identification number used within ontology or a controlled vocabulary for the term that is a value for the Material Linkage Type.
1.1.2.3.2 Linkage Type Term Source REF
The name of the ontology or controlled vocabulary (as specified in the Investigation file) from which a term is selected and Material linkage 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 Material Linkage Type material linkage type.
...
Material
...
A list of names separated by semi-colons, which define specific attributes of a linkage . For example, the bond type may be a characteristic of a linkage of type attachment.
1.1.2.4.1 Material Linkage Characteristic Term Accession Number
The identification number used within an ontology or a controlled vocabulary for the term that is a value for the Material Linkage Characteristic.
1.1.2.4.2 Material Linkage Characteristic Term Source REF
The name of the ontology or controlled vocabulary (as specified in the Investigation file) from which a term is selected and entered as a value for the Material Linkage Characteristic.
1.1.2.5 Material Linkage Characteristic Value
The value corresponding to the characteristic associated with a linkage.
1.1.2.6 Material Linkage Characteristic Statistic
The mathematical statistic (e.g. mean, standard deviation) associated with the value of a material linkage characteristic. This field can carry multiple terms as values separated by semi-colons.
1.1.2.6.1 Material Linkage Characteristic Statistic Term Accession Number
The identification number of a term selected from an ontology or a controlled vocabulary, and entered as a value for the statistic associated with the characteristic value.
1.1.2.6.2 Material Linkage Characteristic Statistic Term Source Ref
The name of the ontology or controlled vocabulary (as specified in the Investigation file) from which a term is selected and entered as a value for the statistic associated with the characteristic value.
1.1.2.7 Material Linkage Characteristic Unit
The unit associated with a quantitative linkage parameter value.
1.1.2.7.1 Material Linkage Characteristic Unit Term Accession Number
The identification number used within an ontology or a controlled vocabulary for the term that is a value for the Material Linkage Characteristic Unit.
1.1.2.7.2 Material Linkage Characteristic Unit Term Source REF
The name of the ontology or controlled vocabulary (as specified in the Investigation file) from which a term is selected and entered as a value for the Material Linkage Characteristic Unit.
1.1.3 MATERIAL FILE
term source REF---The name which identifies the source from where the term for material linkage type is selected. This name should match one of the names entered in the term source name field in the investigation file.
Material File
The material file section The MATERIAL FILE section is allows for the association of any files (e.g. imagesimage files) to the nano-TAB material file.
Exhibit TABLE 4 .14 illustrates the row headers illustrates an example of the MATERIAL FILE section.
...
A
...
B
...
Material file
...
ncl-23_composition.png; ncl-23_structure.pdb
...
Material file Type
...
image; structure
...
Material file Type Term Accession Number
...
Material file Type Term Source REF
...
Material file Version
...
Material file Description
...
1.0; 1.0
Exhibit 4.14 Material file Section Example
1.1.3.1 Material file Name
The name of any name--- The name of files (e.g. Image, Structures file) containing information about the Material.
1.1.3.2 Material file Type
material sample. There can be only one file name per cell. .
Material file type--- The name that defines the type of the material file (e.g. image, graph).
1.1.3.2.1 Material file Type Term Accession Number
This field corresponds to the identification number of the term that is Material file type 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 material file Typetype.
1.1.3.2.2 Material file Type Term Source Ref
This field is used to enter the name of the ontology or the controlled vocabulary (as specified in the Investigation file) from which a term is selected as a value for the file Type (e.g., NPO).
1.1.3.3 Material file Version
The version number (e.g. 1.0) of the file. This field can carry multiple terms as values separated by semi-colons for providing version information for multiple files.
1.1.3.4 Material file Description
Material file type term source REF--- The name which identifies the source from where the term for material file type is selected.
Material file version--- The version number of the material file.
Material file description--- A textual A text description providing additional information on the file. This field can carry multiple terms as values separated by semi-colons for describing multiple filesmaterial file.
