Material

Description

(1) The material file describes the composition of the material formulation and is not included in the ISA-TAB specification.  The material file is an important file that is designed to allow for nanomaterial comparison across nanotechnology resources. 

(2) An investigation typically involves the preparation of multiple materials that are tested.  These materials could be of the same chemical composition (same type and amount of chemical components in the sample) or different chemical compositions. Materials having the same chemical composition should be described using one material file. Materials of different chemical composition should be described separately using multiple materials files.

File Format

The material file format leverages a vertical-based spreadsheet format with columns representing multiple values.  TABLE 4 shows an the example subset of the material file.

TABLE 1 Example Subset of the Material File Format

Fields

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:

(1) Material identifier, material name, material type, and material description;

(2) Description of the synthesis and rationale for design;

(3) Chemical name and characteristics of the material; and

(4) Intended application of the material.

1.1.1.1       Description

The Material file describes the composition of the material formulation and is not included in the ISA-TAB specification.  The Material file is an important file that is designed to allow for nanomaterial comparison across nanotechnology resources.  The Material file also allows for the association with an optional Structure file for representing the 3D structure of the nanomaterial.

An investigation typically involves the preparation of multiple materials.  These materials could be of the same chemical composition (same type and amount of chemical components in the sample) or of different chemical compositions. Materials having the same chemical composition should be described using one Material file. Materials of different chemical composition could be described separately using multiple materials files or described in a single material file.

1.1.1.2       File Format

The Material file format leverages a vertical based spreadsheet format with columns representing multiple values.  In the example subset of the Material file below, column A indicates the field names and columns B and C are field values.

1.1.1.3       nano-TAB Extensions

Since the Material file does not exist in the ISA-TAB standard, the entire file is considered an extension.  This file is described in detail in Section 4.

1.1       Material file

The Material file looks similar to an Investigation file. It is a vertically oriented spreadsheet containing tab delimited column values. The file consists of three sections, as listed below:

s  MATERIAL

s  MATERIAL RELATIONSHIP

s  MATERIAL FILE

1.1.1       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

s  a description of the synthesis and rationale for design

s  the chemical name and  characteristics of the material

s  the intended application of the material

Exhibit 4.12 shows an example of how a material is described within the Material section.

Exhibit 4.12 Material Section Example

1.1.1.1       Material Identifier

Material Identifier refers to the unique internal identification of the material. For example, NCL-23 (see Exhibit 4-12) 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

The Material Synthesis field contains a text description of how the material was made. 

1.1.1.6       Material Design Rationale

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

The identification number of a term selected from an ontology or a controlled vocabulary, and entered as a value for the underlying Material Design Rationale.

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

The identification number used within an ontology or a controlled vocabulary for the term that is 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

The identification number of a term selected from an ontology or a controlled vocabulary, and entered as a name 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

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

The identification number of a term selected from an ontology or a controlled vocabulary, and entered as a value for the material characteristic.

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

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.

1.1.1.10.2       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

The identification number used within an ontology or a controlled vocabulary for the term that is 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

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 selected from an ontology or a controlled vocabulary, and 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).

1.1.2       MATERIAL RELATIONSHIP

The MATERIAL RELATIONSHIP section is meant for specifying the name and types of the relationships between materials including material parts and material linkages.  Material parts represent components within a material.  Material linkages represent association between materials (e.g. encapsulation, attachment, entrapment).

Exhibit 4.13 illustrates the row headers of the MATERIAL RELATIONSHIP section.

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 (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 entered as a value for Material Linkage Type.

1.1.2.4       Material Linkage Characteristic

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

The MATERIAL FILE section is allows for the association of any files (e.g. images) to the material.

Exhibit 4.14 illustrates the row headers of the MATERIAL FILE section.

Exhibit 4.14 Material file Section Example

1.1.3.1       Material file Name

The name of any files (e.g. Image, Structures file) containing information about the Material.

1.1.3.2       Material file Type

The name that defines the type of the 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 selected from an ontology or a controlled vocabulary, and is entered as a value for the file Type.

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

A text description providing additional information on the file.  This field can carry multiple terms as values separated by semi-colons for describing multiple files.