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ISA-TAB-Nano Extensions---Since the material file does not exist in the ISA-TAB specification, the entire file is considered an extension.
Material
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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
(4) Intended application of the material
Material source identifiersource name--- 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 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 is used to identify or reference the different components across the ISA-TAB-Nano files.
Manufacturer lot identifer---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.This concept is introduced in ISA-TAB-Nano.
Material description---A textual description of the material sample.
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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.
Material intended application---The application for which a drug, nanoparticle or other substance is formulated and tested (e.g., MRI).
Material intended application 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 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 type---One or more terms used to classify the type of material sample. Multiple terms are entered as a semicolon-delimited list.
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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 characteristicCharacteristics--- A semicolon-delimited list of terms that describe specific attributes of the sample or its constituents.
Material characteristic Characteristic 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 characteristic.
Material characteristic Characteristics 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 Characteristics value--- The value corresponding to a material characteristic name. For example, “single walled carbon nanotube” is the value of the characteristic name “wall type” for the material chemical name “carbon nanotube”.
Material characteristic Characteristics value 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 characteristic value.
Material characteristic Characteristics 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 unitUnit--- The standard of measurement used if the value for material characteristic value is quantitative and dimensional.
Material characteristic unit Unit 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 characteristic unit.
Material characteristic unit Unit term source REF--- The name which identifies the source from where the term for material characteristic unit is selected.
Material characteristic statisticStatistic--- 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 Statistic 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 characteristic statistic.
Material characteristic statistic 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 application for which a drug, nanoparticle or other substance is formulated and tested (e.g., MRI).
Material intended application 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 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.
TABLE 17 Example Subset of the Material File Format
A | B | C | D | E | F | G | H |
|---|---|---|---|---|---|---|---|
Material Source Identifier | Material Name | Material Description | Material Synthesis | Material Design Rationale | Material Intended Application | Material Intended Application Term Accession Number | Material Intended Application Term Source REF |
LAB-1 | g4.5_carboxyl-terminated dendrimer | g4.5 carboxyl-terminated dendrimer | --- | --- | delivery of image contrast agent | --- | --- |
LAB-1 | g4.5_core | --- | --- | --- | --- | --- | --- |
LAB-1 | g4.5_branch | --- | --- | --- | --- | --- | --- |
LAB-1 | g4.5_carboxyl_group | --- | --- | --- | --- | --- | --- |
I | J | K | L | M | N |
|---|---|---|---|---|---|
Material Type | Material Type Term Accession Number | Material Type Term Source REF | Material Chemical Name | Material Chemical Name Term Accession Number | Material Chemical Name Term Source REF |
nanoparticle sample; dendrimer | NPO_1404;NPO_735 | NPO;NPO | --- | --- | --- |
dendrimer core molecule | NPO_803 | NPO | diaminobutane | --- | --- |
dendrimer branch | NPO_776 | NPO | poly(amidoamine) | 53199 | CHEBI |
terminal group | NPO_695 | NPO | carboxyl group | 46883 | CHEBI |
O | P | Q | R | S |
|---|---|---|---|---|
Material Characteristic [dendrimer generation] | Material Characteristic [molecular weight] | Material Characteristic [molecular weight] Unit | Material Characteristic [molecular weight] Unit Term Accession | Material Characteristic[molecular weight] Unit Term Source REF |
4.5 | 27 | kDa | UO_0000222 | UO |
Material Relationship
The MATERIAL RELATIONSHIP section is used to record the name and types of relationships between materials including material parts and material linkages. Material parts represent the components within a material. Material linkages represent association between materials (for example, encapsulation, attachment, entrapment). TABLE 18 illustrates an example of the MATERIAL RELATIONSHIP section. The concepts used for describing the relationship are given below.
Material part name---A consitituent---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 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.
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Material linkage type 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.Table 18. Examples illustrates the MATERIAL RELATIONSHIP section of the material file.
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A
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B
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C
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D
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E
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F
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G
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H
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Material Part Name
Material
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Material Linkage Type
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Material Linkage Type Term Accession
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Material Linkage Type Term Source REF
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Material File Name
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Material File Type
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Material File Type Term Accession
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g4.5_carboxyl-terminated_dendrimer; magnevist
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covalent_linkage
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NPO_563
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NPO
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magnevist_jpg
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image
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Material File
The material file section allows for the association of any files (for example, image files) to the ISA-TAB-Nano material file. Table 19 illustrates a MATERIAL FILE section.Material file name--- The name of files (for example, Image, Structures file) containing information about the material sample. There can be only one file name per cell.
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Material file description--- A textual description providing additional information on the material file.
Table 19. Example Material File section of the Material File
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Z
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AA
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AB
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AC
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AD
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AE
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Material File Name
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Material File Type
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Material File Type Term Accession
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Material File Type Term Source REF
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Material File Version
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Material File Description
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magnevist_jpg
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image
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