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* [Material File Examples|ICR:Material File Examples]
* [Material File Template|ISA-TAB-Nano^m_xxxx.xls]
* [Material File Glossary|ISA-TAB-Nano^MaterialFileTermGlossary.xls]
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h2. 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.

h2. 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 [ICR:Material File Examples] wiki page.

h2. Fields

ISA-TAB-Nano _Extensions_\---Since the material file does not exist in the ISA-TAB specification, the entire file is considered an extension.

h3. 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.&nbsp; 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 ||
| *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 |

h3. 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.&nbsp; 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 | \--\- \\ |

h3. 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 |