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Description
ISA-TAB-Nano introduced the Material file. The ISA-TAB specification does not include it.
- The 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..
Fields
1.1.1.3 Nano-TAB Extensions---Since the material file does not exist in the ISA-TAB specification, the entire file is considered an extension. This file is described in detail in Section 6.
Material File
Description
...
- file describes the composition of the material formulation
...
- .
...
- The
...
- Material file is an important file that is designed to allow for nanomaterial comparison across nanotechnology resources.
...
...
- 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 of different chemical composition or physical characteristics should be described
...
- in separate Material 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..
Nano-TAB Extensions---Since the material file does not exist in the ISA-TAB specification, the entire file is considered an extension. This file is described in detail in the Appendix.
1.1.1.1 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.
Material file looks similar to the Study and Assay files. It is a horizontally oriented spreadsheet containing tab delimited row values representing multiple values. The Material file contains information on the material, the relationship between material constituents, and a description of the material file. The following table provides an example subset of this format.
TABLE 4 Example Subset of the Material File Format
A | B | C |
|---|
D | |||
|---|---|---|---|
Material Source Name | Material Name | Manufacturer Lot Identifier | Material Description |
NCL-20-1 |
Material Name
g4_tris_dendrimer |
g4_tris_core
Material Description
G4 tris(hydroxyl) terminated PAMAM dendrimer |
Material Synthesis
Material Design Rationale
Material Type
nanoparticle sample; dendrimer
dendrimer core molecule
Material Type Term Accession Number
NPO_1404;NPO_735
NPO_803
Material Type Term Source REF
NPO;NPO
NPO
Material Chemical Name
diaminobutane
Material Chemical Name Term Accession Number
Material Chemical Name Term Source REF
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.
...
A
...
B
...
C
...
Material Identifier
...
NCL-23
...
Material Name
...
g45_coona_dendrimer_magnevist_complex
...
g45_coona_dendrimer
...
Material Description
...
G4.5 COONa terminated PAMAM dendrimer-Magnevist® complex
...
Material Synthesis
...
Material Design Rationale
...
Material Design Rationale Term Accession Number
...
Material Design Rationale Term Source REF
...
Material Type
...
nanomaterial
...
dendrimer
...
Material Type Term Accession Number
...
NPO_1404
...
NPO_735
...
Material Type Term Source REF
...
NPO
...
NPO
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.
...
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
NCL-20-1 | g4_tris_core |
For a detailed example leveraging data from the Nanotechnology Characterization Laboratory (NCL) NCL200612, refer to the Material File Examples wiki page.
Fields
Nodes
Material source name--- The unique identification name of the source from which the material sample is derived. This value should match that used for source name in ISA-TAB-Nano study files, thereby linking the ISA-TAB-Nano Material file and the Study file.
Material name---The unique identification name for the sample and its different components. This name identifies or references the different components across the ISA-TAB-Nano files.
Manufacturer lot identifier---A distinctive numeric, alpha, or alpha-numeric identification code assigned by the manufacturer or distributor. It is assigned to a specific quantity of manufactured material or product that is produced in a manner that is expected to render it homogeneous.
Material description---A textual description of the material sample.
Material synthesis---A text or a single term
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 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
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.
...
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
Attributes of Material Nodes
Material intended application---The application for which a drug, nanoparticle or other substance is formulated and tested (such as MRI).
Material type---One or more terms used to classify the type of material sample. Multiple terms are entered as a semicolon-delimited list.
Material chemical name---The chemical name of the material or its constituent material.
Characteristics [ ]--- An attribute of the sample and its constituents. The term for each characteristics [ ] attribute is written within brackets (for example, Characteristics [wall type], etc.). Nominal particle characteristics (or vendor supplied) should be included in the Material File as characteristics. Experimentally determined characteristics should be included in the Assay File.
Unit--- The standard of measurement used if the value for Material characteristic value is quantitative and dimensional.
Material consitituent--- The material name for each of the components within a material. The names should be obtained from the entries for the “Material Name” field. If there is a "Material Linkage Type", then only the two linked components should be specified.
In the example below, Material M is comprised of A, B, and C and within Material M, A and B are linked and A and C are linked.
| Material Source Name | Material Name | Material Constituent | Material Linkage Type |
|---|---|---|---|
| M-lab-1 | M | A;B;C | |
| M-lab-1 | M | A;B | covalent linkage |
| M-lab-1 | M | A; C | covalent linkage |
| M-lab-1 | A | ||
| M-lab-1 | B | ||
| M-lab-1 | C |
Material linkage type---The type of linkage present in a nanoparticle sample (for example
...
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 (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.
...
A
...
B
...
MATERIAL FILE
...
Material file Name
...
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
If the linkage type is an entrapment or encapsulation, the material type column can specify whether the constituent is entrapped or encapsulated.
Material data file --- The name of files (such as Image, Structures file) containing information about the material sample. There are a few ways to capture multiple files here. 1. Reference one file per row. 2. Create an archive (i.e. zip, tar.gz) file containing all the relevant files and reference the archive file name in one row. 3. Reference each file separated by a semi-colon in the Material Data File column (such as "file 1; file 2") and replicate that format in the Material data file type and Material data file description fields.
Material data file type--- The name that defines the type of the material file (such as image, graph).
Material data file description--- A textual description providing additional information on the material file.
Qualifiers for Material Nodes’ Attributes
Each node attribute may be qualified using the following concepts, if applicable.
Unit---The standard of measurement used if the values for characteristic [ ] columns are quantitative and dimensional. If the term for unit is from an ontology/controlled vocabulary, then its term accession number and the term source REF should be defined in the ISA-TAB-Nano Material File.
Term Accession Number---Identification number of a term
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 if the term 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
...
in material intended application, material type, material chemical name, characteristic [ ], material linkage type [ ], material data file type [ ], unit or factor value [ ] columns.
Term Source REF---The name which identifies the source from where a term is selected and entered in ISA-TAB-Nano study files. This name should match one of the names entered in the term source name field in the ISA-TAB-Nano Investigation File.
Other Material Fields
Comment [ ]---Any comment that provides additional information, which is added only when no other appropriate field exists. This field can be added any where within the Material File.
