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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.
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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
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:
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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.
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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.
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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.
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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.
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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 |
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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 |
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O | P | Q | R | S | ||
|---|---|---|---|---|---|---|
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="4cb04186de479262-dee85a01-4cf14c95-a38997ba-3ebfc0500cd74cc6814bb14a"><ac:plain-text-body><![CDATA[ | 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 | ]]></ac:plain-text-body></ac:structured-macro> |
4.5 | 27 | kDa | UO_0000222 | UO |
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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 (e.g. 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.
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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.
Material linkage type---The type of linkage present in a nanoparticle sample (e.g.for example, attachment, encapsulation, entrapment etc.).
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Table 18. Examples illustrates the MATERIAL RELATIONSHIP section of the material file.
A | B | C | D | E | F | G | H |
|---|---|---|---|---|---|---|---|
Material Part Name | Material Linkage Name | Material Linkage Type | Material Linkage Type Term Accession | Material Linkage Type Term Source REF | Material File Name | Material File Type | Material File Type Term Accession |
g4.5_carboxyl-terminated_dendrimer; magnevist |
| covalent_linkage | NPO_563 | NPO | magnevist_jpg | image |
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The material file section allows for the association of any files (e.g. for example, image files) to the ISA-TAB-Nano material file. Table 19 illustrates a a MATERIAL FILE section.
Material file name--- The name of files (e.g. 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
Z | AA | AB | AC | AD | AE |
|---|---|---|---|---|---|
Material File Name | Material File Type | Material File Type Term Accession | Material File Type Term Source REF | Material File Version | Material File Description |
magnevist_jpg | image | v. 1.0 | molecular structure of magnevist |
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