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 looks similar to the Study and Assay files. It is a horizontally oriented spreadsheet containing tab delimited row values representing multiple values. The file consists of three sections: MATERIAL, MATERIAL RELATIONSHIP, and MATERIAL FILE.
Tables below illustrate fields in the material file. A detailed example leveraging data from the Nanotechnology Characterization Laboratory (NCL) NCL200612 is provided on the Material File Examples wiki page.
Fields
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:
(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 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 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.
Material description---A textual description of the material sample.
Material synthesis---A text or a single term description of how the material was made.
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 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 number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for material type.
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 an ontology or a controlled vocabulary, if the term is entered as a value for 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 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 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” is the value of the characteristic name “wall type” for the material chemical name “carbon nanotube”.
Material characteristic 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 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 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 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 an ontology or a controlled vocabulary, if the term is entered as a value for 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 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 |
||
|---|---|---|---|---|---|---|
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="769a07ba-9cb9-423c-855e-1c93abbbd893"><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 |
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 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.
Material linkage type---The type of linkage present in a nanoparticle sample (for example, attachment, encapsulation, entrapment etc.).
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 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.
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 |
|
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.
Material file type--- The name that defines the type of the material file (e.g. image, graph).
Material file 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 file type.
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 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 |
