Managing Sample Composition Annotations | caNanoLab User's Guide| Managing Publications in caNanoLab

If you have read-only permissions, see Access the Sample Characterization Summary. If you are a curator with appropriate security permissions, you can create, update, and delete characterizations.

This chapter describes how to review or ascribe characterizations to samples save in caNanoLab. Topics in this chapter include:

Sample Characterization Overview

Sample characterization describe distinctive characteristics or essential features of the sample determined through analytical methods and records information associated with sample synthesis and properties. Samples can be characterized in caNanoLab by physical or chemical characteristics or by data derived under in vitro and in vivo conditions.

With the appropriate security permissions, you can

  • Add a Physico-Chemical, In Vitro, In Vivo, Ex Vivo, or Other Ex Vv to a sample.
  • Print, export, edit, copy, or delete a characterization and add a file to a characterization.

If the buttons do not display, you have read-only access to the item.

Accessing the Sample Characterization Summary

With read-only access, you can review a summary of characterization information and annotations added to the sample.

To access characterization functions in the Navigation Tree

  1. Click Samples and Search Existing Samples.
  2. Fill in criteria, and click Search.
  3. Click Edit in the search results.

  4. The Navigation Tree appears on the left sidebar and comprises functions which you can use to add annotations to the sample.

  5. Click Characterization. 
    The All tab displays characterizations already added to the sample by category. Additional tabs show annotations added to the sample for each subcategory.
    Characterization Summary

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Submitting Characterizations

Once you access Characterizations in the Navigation Tree, you can add different types of information to the sample.

If you have read-only access, you can View a Characterizations Summary.

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Adding a Physico-Chemical Characterization

To add a physico-chemical characterization

  1. Access a sample and characterization.

  2. Click the All tab or the Physico-Chemical Characterizations tab and click Add next to Physico-chemical Characterization.

  3. Both tabs provide customizations based on your Characterization Type* selection.

  4. Follow these steps to fill in the characterization. Links are provided for additional details.

SectionWhat to Do
Physico-Chemical CharacterizationFill in the general information about the characterization.
Properties

If you select one of the following characterization types, you need to fill in additional properties.

  • Physical State
  • Shape
  • Solubility
  • Surface
Design and MethodsComplete the fields describing techniques and instruments used to derive the data.
Finding

In the Finding section, add one or more publications relevant to the sample, as well as data derived for the sample. Add as many files and derived data as you wish or add derived data without adding files.

Click Add to expand the section, then add data and conditions and add a file.

Add data findings and supporting documentation relating to the sample.

In the Finding section, you can also add files to a physico-chemical characterization.

Analysis and ConclusionEnter any relevant analyses and conclusions reached by the data.

Copy to Other Samples with the Same Primary Organization

Select samples in the list to which you want this physico-chemical data transferrred. This option copies files and data to one or more selected samples "owned" by the same point of contact.

When you are finished, click Submit to save the data to the sample.

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Defining the Physico-Chemical Characterization

Define the following characterization information.

CompleteHow to
Characterization Type*

This is already filled in with Physico-Chemical Characterization (required) when you click the tab of the same name or add one from the All tab.

Characterization Name*

Select the name of the characterization (required). 

Note: If you select Cytoxicity, Enzyme Reduction, Target, or Transfection, you have to complete additional properties.

To select an existing, non-standard Assay Type, select other_pc.

To create a new, non-standard Assay Type

    1. Select other.
    2. Enter a New Characterization Name and click Add, and the new characterization is added the Characterization Name list.
      Adding a New Characterization Name
Assay Type

Select an assay type from the list that populates automatically based on the Characterization Name.

To add a new Assay Type

    1. Select other.
    2. Enter a New Assay Type and click Add, and the new Assay Type is added to the list.
Protocol Name – VersionIf available, select a protocol from which the data is derived. If displayed, click the hyperlink to the protocol text file to open or save the file.
Characterization SourceSelect or enter the source from which the characterization data is derived, such as a vendor or a laboratory (NCL).
Characterization DateSelect or enter the date the characterization was made (dd/mm/yyyy).

Defining Physico-Chemical Characterization Properties

If you selected one of the Characterization Names listed in the following table, the Properties section opens, and you must fill in additional information.

Characterization NameProperties to Complete

Physical State

Select the Type of physical state.

Shape

  1. Select the Type of shape.
  2. Enter the shape Aspect Ratio.
  3. Enter the Minimum and Maximum Dimensions of the sample, and the units of measurement.

Solubility

  1. Select from the options or enter the name of the Solvent.
    • 3D-cube
    • 3D-cylinder
    • alcohol
    • phosphate-buffered saline
    • saline
    • THF
    • water
  2. Enter appropriate values for the Critical Concentration, then select the appropriate units for those values.
  3. Specify Yes or No to indicate whether the solvent Is Soluble?.

Surface

Specify Yes or No to indicate whether the surface Is Hydrophobic?.

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Defining Physico-Chemical Design and Methods

Define the following Design and Methods information.

Design and Methods FieldDescription

Design and Methods Description

Enter a description for the characterization design and methods.

If you include an extra line between text in the Design and Methods Description, the line separation is preserved when you save or update the characterization.

Technique and Instrument

Technique*

Abbreviation

DescriptionEnter a description of the technical and instrument.
Instrument

When you are finished, click Save or Cancel to close the section without saving.

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Describing Findings for Physico-Chemical Characterization


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Adding Data and Conditions for a Physico-Chemical Characterization

In the Data and Conditions segment of the window, add or import data values and specify other information that is part of your findings (like laboratory conditions, pH, or temperature).

To define the data and conditions matrix

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Adding an In Vitro Characterization

In vitro characterization allows you to add characterizations for the nanomaterial component of the sample derived from analytical techniques performed under in vitro conditions.

To add an in vitro characterization

  1. Access a sample and characterization.

  2. Click the All tab or the In Vitro Characterizations tab and click Add next to In Vitro Characterization.

  3. Both tabs provide customizations based on your Characterization Type* selection.

  4. Follow these steps to fill in the characterization. Links are provided for additional details.

SectionWhat to Do
In Vitro CharacterizationFill in the general information about the characterization.
Properties

If you select one of the following characterization names, you need to fill in additional properties.

  • Cytotoxicity
  • Enzyme Induction
  • Transfection
Design and MethodsComplete the fields describing techniques and instruments used to derive the data.
Finding Info

Add data findings and supporting documentation relating to the sample.

In the Finding section, you can also add files to an in vitro characterization.

Analysis and ConclusionEnter any relevant analyses and conclusions reached by the data.
Copy to Other Samples with the Same Primary OrganizationSelect samples in the list to which you want this physico-chemical data transferred. This option copies files and data to one or more selected samples "owned" by the same point of contact.

When you are finished, click Submit to save the data to the sample.

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Defining an In Vitro Characterization

Fill in the following characterization information.

CompleteHow to
Characterization Type*

This is already filled in with In Vitro Characterization (required) when you click the tab of the same name or add one from the All tab.

Characterization Name*

Select the name of the characterization (required). 

Note: If you select Cytoxicity, Enzyme Reduction, Target, or Transfection, you have to complete additional properties.

To select an existing, non-standard Assay Type, select other_vt.

To create a new, non-standard Assay Type

    1. Select other.
    2. Enter a New Characterization Name and click Add, and the new characterization is added the Characterization Name list.
      Adding a New Characterization Name
Assay Type

Select an assay type from the list that populates automatically based on the Characterization Name.

To add a new Assay Type

    1. Select other.
    2. Enter a New Assay Type and click Add, and the new Assay Type is added to the list.
Protocol Name – Version

If available, select the protocol from which the data is derived.

  • A hyperlink to the protocol text file should appear (if the protocol is not private to the user and the protocol file exists). However, protocol files are not required. Click the hyperlink to open or save the file.
  • A hyperlink to the protocol text file should appear (if the protocol is not private to the user and the protocol file exists - ie. protocol files are not required).
Characterization SourceSelect or enter the source from which the characterization data is derived, such as a vendor or a laboratory (NCL).
Characterization DateSelect or enter the date the characterization was made (dd/mm/yyyy).

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Defining In Vitro Characterization Properties

If you selected one of the Characterization Names listed in the following table, the Properties section opens, and you must fill in additional information.

Characterization NameProperties to Complete

Cytotoxicity

Enter the appropriate Cell Line.

Enzyme Induction

Enter the Enzyme Name of your choice.

TargetingEnter the appropriate Cell Line.

Transfection

Enter the appropriate Cell Line.

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Defining In Vitro Design and Methods

Fill in the following Design and Methods information as needed.

Design and Methods FieldDescription
Design and Methods Description

Enter a description for the characterization design and methods.

If you include an extra line between text in the Design and Methods Description, the line separation is preserved when you save or update the characterization.

Technique and Instrument

Technique*

Abbreviation

DescriptionEnter a description of the technique and instrument.
Instrument

When you are finished, click Save or Cancel to close the section without saving.

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Describing Findings for an In Vitro Characterization

In the Finding sections, add one or more publications relevant to the sample, as well as data derived for the sample. Add as many files and derived data as you wish or add derived data without adding files.

Click Add to expand the section, then add data and conditions and add a file.

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Adding Data and Conditions for an In Vitro Characterization

In the Data and Conditions segment of the window, add or import data values and specify other information that is part of your findings (like laboratory conditions).

To define the matrix for the data

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Adding an In Vivo Characterization

In vivo characterization allows you to add characterizations for the nanomaterial component of the sample that were derived from analytical techniques performed under in vivo conditions.

To add an in vivo characterization

  1. Access a sample and characterization.

  2. Click the All tab or the In Vitro Characterizations tab and click Add next to In Vitro Characterization.

  3. Both tabs provide customizations based on your Characterization Type* selection.

  4. Follow these steps to fill in the characterization. Links are provided for additional details.

    SectionWhat to Do
    In Vivo CharacterizationFill in the general information about the characterization.
    PropertiesDisplays for in vivo characterizations.
    Design and MethodsComplete the fields describing techniques and instruments used to derive the data.
    Finding Info

    Add data findings and supporting documentation relating to the sample.

    In the Finding section, you can also add files to an in vivo characterization.

    Analysis and ConclusionEnter any relevant analyses and conclusions reached by the data.
    Copy to Other Samples with the Same Primary Organization

    Select samples in the list to which you want this physico-chemical data transferred. This option copies files and data to one or more selected samples "owned" by the same point of contact.

  5. When you are finished, click Submit to save the data to the sample.

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Defining an In Vivo Characterization

Fill in the following characterization information.

CompleteHow to
Characterization Type*

This is already filled in with In Vivo Characterization (required) when you click the tab of the same name or add one from the All tab.

Characterization Name*

Select the name of the characterization (required). 

To select an existing, non-standard Assay Type, select other_vv or other_ex_vv.

To create a new, non-standard Assay Type

    1. Select other.
    2. Enter a New Characterization Name and click Add, and the new characterization is added the Characterization Name list.
      Adding a New Characterization Name
Assay Type

Select an assay type from the list that populates automatically based on the Characterization Name.

To add a new Assay Type

    1. Select other.
    2. Enter a New Assay Type and click Add, and the new Assay Type is added to the list.
Protocol Name – VersionSelect the protocol from which the data is derived. A hyperlink of the protocol text file may appear. Click the hyperlink to open or save the file.
Characterization SourceSelect or enter the source from which the characterization data is derived, such as a vendor or a laboratory (NCL).
Characterization DateSelect or enter the date the characterization was made (dd/mm/yyyy).

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Defining In Vivo Design and Methods

Fill in the following Design and Methods information, as needed.

Design and Methods FieldDescription

Design and Methods Description

Enter a description for the characterization design and methods.

If you include an extra line between text in the Characterizations free text, Design and Methods Description, the line separation is preserved when you save or update the characterization.

Technique and Instrument

Technique*

Abbreviation

DescriptionEnter a description of the technique and instrument.
Instrument

When you are finished, click Save or Cancel to close the section without saving.

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Describing Findings for In Vivo Characterizations

In the Finding sections, add one or more publications relevant to the sample, as well as data derived for the sample. Add as many files and derived data as you wish add derived data without adding files.

Click Add to expand the section, then add data and conditions and add a file to the characterization.

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Adding Data and Conditions to an In Vivo Characterization

In the Data and Conditions segment of the window, add or import data values and specify other information that is part of your findings.

To define the matrix for the data

For an in vivo characterization, click [Other] to name the column yourself.

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Characterization Tasks

To perform the following tasks, you must have curator privileges.

If a button described in this section does not display, you have read-only access to the data.

TaskHow to

Add a file to a characterization

To add results in the form of supporting documents, such as a graphic, spreadsheet or images to a characterization

  1. Edit the characterization.
  2. From the In the Finding section, next to Files, click Add.
  3. Upload, browse, and select the file or enter the file's URL where the document is located.
  4. Complete the following.
    1. Select the File Type (required), Document, Graph, Image, Movie, or Spreadsheet.
    2. Enter the File Title (required).
    3. Specify Keywords to associate with the file
    4. Enter a Description of additional information of the file.

  5. Click Submit to add the file(s) to the sample.

You can add as many files as you wish.

Printing a characterization

From the All tab's characterizations summary, click Print at the top right of the page.

Exporting characterizations

From the All tab's characterizations summary, click Export at the top right of the page.

Editing a characterization

  1. From the All tab's characterizations summary, click Edit at the right of the characterization section you want to change.
  2. The Characterization opens and you can edit it as needed.

Copying a characterization

The characterization files and/or derived data for a sample can be copied to other samples from the same primary point of contact.

  1. From the All tab's characterizations summary, click Edit at the right of a characterization section.
  2. The Characterization opens and at the bottom of the page, in the Copy to other samples... section, select one or more samples with the same primary point of contact.
  3. Click Also copy characterization results?.

  4. Click Submit to copy the characterization.

Deleting a characterization

This deletes a characterization(s) from the selected sample. If the characterization(s) was copied to other samples, the characterization is not removed from those samples.

To delete a characterization for a selected sample

  1. From the All tab's characterizations summary, click Edit at the right of a characterization section.
  2. The Characterization opens, and click Delete.
  3. The deleted characterization is placed in the sample archive for historical purposes.
Managing Sample Composition Annotations | caNanoLab User's Guide| Managing Publications in caNanoLab