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Managing Sample Composition Annotations | caNanoLab User's Guide| Managing Publications in caNanoLab
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titleAccess to sample characterizations

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:

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Characterization
Characterization
[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.

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iconfalse
titleWith the appropriate security permissions...

With the appropriate security permissions, you can

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

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CharacterizationSummary
CharacterizationSummary
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.

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    Understanding the Navigation Tree Abrev
    Understanding the Navigation Tree Abrev

  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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SubmittingCharacterizations
SubmittingCharacterizations
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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PhysicoChemical
PhysicoChemical
Adding a Physico-Chemical Characterization

To add a physico-chemical characterization

  1. Access a sample and characterization.

  2. Click All or the Physico-Chemical Characterizations tab and click Add next to Physico-chemical Characterization. Both tabs display five sections, but All provides customizations based what you select in the Characterization Type* field.

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

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    AddPhysicoChemical
    AddPhysicoChemical

    SectionWhat to Do
    Physico-Chemical CharacterizationFill in the general information about the characterization.
    [Characterization] PropertiesDisplays only for Physical State, Shape and Solubility characterizations. Define properties for the characterization, if applicable.
    Design and MethodsComplete the fields describing techniques and instruments used to derive the data.
    Finding

    Add data findings and supporting documentation relating to the sample.

    Analysis and ConclusionsEnter any relevant analyses and conclusions reached by the data.
    Copy to other Samples...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.

  4. When you finish, click Submit to save the data to the sample.

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Defining the Physico-Chemical Characterization

Fill in the following characterization information.

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Other options
Other options

FieldDescription
Characterization Type*

The Characterization Type is already selected as Physico-Chemical Characterization.

Characterization Name*

You must select the name of the Characterization you want to add or select an "other" option to create a new or select from an existing, non-standard Assay Type.

  • To select an existing, non-standard Assay Type, based on Characterization Type, select other_pc.
  • To create a new, non-standard Assay Type, select other. Enter a New Characterization Name, and click Add.  The new characterization is added the Characterization Name list.
    Adding a New Characterization Name
Assay Type

The field populates automatically with your selection in Characterization Name.

  • With Characterization Name, other_pc, select from existing, non-standard Assay Types.
  • With Characterization Name, other, create a new, non-standard Assay Type.
Protocol Name – VersionIf this field is available, select from the drop-down list 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 from the drop-down list or enter the source from which the characterization data is derived, such as a vendor or a laboratory (NCL).
Characterization DateSelect from the calendar or enter the date the characterization was made. Acceptable format: dd/mm/yyyy.

Continue to define Physico-Chemical Properties.

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Physico-Chemical Characterization Properties
Physico-Chemical Characterization Properties
Defining Physico-Chemical [Characterization] Properties

The [Characterization] Properties section opens only for the characterizations listed in the table below. Fill in the following Properties information as needed.

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Other options
Other options

CharacterizationProperty FieldsField Options

Physical State

Type

Select the appropriate type from among the following options:

Shape Properties

Type (required)

Select from the drop-down list the appropriate shape type:

Shape Properties

Aspect Ratio

Enter the shape aspect ratio.

Shape Properties

Minimum,/Maximum Dimensions

Enter the minimum and maximum dimensions of the sample, as well as the units of measurement.

Solubility Properties

Solvent

Select from the options or enter the name.

  • alcohol
  • phosphate-buffered saline
  • saline
  • water
Solubility PropertiesCritical Concentration

Enter appropriate values for the critical concentration, then select the appropriate units for those values.

Solubility PropertiesIs Soluble?Select Yes or No as to whether the solvent is soluble.

Surface Properties

Is Hydrophobic?

Indicate with Yes or No whether the surface is hydrophobic.

Continue to define Physico-Chemical Design and Methods.

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Defining Physico-Chemical Design and Methods

Fill in the following Design and Methods information as needed.

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Other options
Other options

Design and Methods FieldDescription

Design and Methods Description

Enter a description for the characterization design and methods.

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titleExtra lines add

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

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Technique and instrument
Technique and instrument

Technique*

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Technique
Technique

Abbreviation

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Abbreviation
Abbreviation

DescriptionEnter a description of the technical and instrument.
Instrument

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Instrument
Instrument

Once you enter the data, click Save to save the information to the sample or Cancel to close the mini-window without saving data.

Continue to define Physico-Chemical Findings.

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Describing Findings for Physico-Chemical Characterization

In the Finding section, you can add one or more publications relevant to the sample, as well as data derived for the sample. You can add as many files and derived data as you wish, or you can 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

In the Data and Conditions segment of the window, you can create a matrix where you can enter data values and/or other information, such as laboratory conditions like pH or temperature that are part of your findings.

To define the data and condition matrix

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Other options
Other options

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Data and conditions1
Data and conditions1

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Data and conditions2
Data and conditions2

After adding data and conditions to the sample, continue to add a Physico-Chemical Characterization.

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Adding a File

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Adding a file
Adding a file

After adding one or more files, add data and conditions or if you have no derived data to add, add a Physico-Chemical Characterization.

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InVitro
InVitro
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 All or the In Vitro Characterizations tab and click Add next to In Vitro Characterization. Both tabs display five sections, but the All tab provide customizations based what you select in the Characterization* field.

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

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    AddInVitroCharacterization
    AddInVitroCharacterization

    Field/SectionWhat to Do
    In Vitro CharacterizationFill in the general information about the characterization.
    [Characterization] Properties]Displays only for Cytotoxicity, Enzyme Induction and Transfection in vitro characterizations. Define properties for the characterization, if applicable.
    Design and MethodsComplete the fields describing techniques and instruments used to derive the data.
    Finding

    Add data findings and supporting documentation relating to the sample.

    Analysis and ConclusionsEnter any relevant analyses and conclusions reached by the data.
    Copy to Other Samples...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.

  4. When you finish, click Submit to save the data to the sample.

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Defining an In Vitro Characterization

Fill in the following characterization information.

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Other options
Other options

FieldDescription
Characterization Type*

The Characterization Type is already selected as In Vitro Characterization.

Characterization Name*

You must select the name of the Characterization you want to add or select an "other" option to create a new or select from an existing, non-standard Assay Type.

  • To select an existing, non-standard Assay Type, based on Characterization Type, select other_vt.
  • To create a new, non-standard Assay Type, select other. Enter a New Characterization Name, and click Add.  The new characterization is added the Characterization Name list.
    Adding a New Characterization Name
Assay Type

The field populates automatically with options displayed for in vitro characterization selections: Blood Contact, Cytotoxicity, Immune Cell Function, Oxidative Stress, Sterility and Targeting.

  • With Characterization Name, other_vt, select from existing, non-standard Assay Types.
  • With Characterization Name, other, create a new, non-standard Assay Type.
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 from the calendar or enter the date the characterization was made. Acceptable format: dd/mm/yyyy.

Continue to In Vitro Properties.

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Assay Type Options for In Vitro Characterizations

Specify one of the following in vitro Assay Type options or select [Other] to open a window where you can add a new assay type.

Characterization Selection

Assay Type Corresponding to Characterization

Blood Contact

Cytotoxicity

Immune Cell Function

Oxidative stress

Sterility

Targeting

Cell binding/Internalization

Transfection

Click [Other] to add an assay type.

Continue to define in vitro characterizations.

Defining In Vitro [Characterization] Properties

The [Characterization] Properties section opens only when you select the following characterizations in the Summary section. To define properties for each unique characterization, enter information for the following fields.

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Other options
Other options

For Cytotoxicity, enter the appropriate Cell Line.

  • For Enzyme Induction, enter your name of choice.
  • For Transfection, enter the appropriate Cell Line.

For Targeting, enter the appropriate Cell Line.

Continue to define In Vitro Design and Methods.

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Defining In Vitro Design and Methods

Fill in the following Design and Methods information as needed.

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Other options
Other options


Design and Methods FieldDescription
Design and Methods Description

Enter a description for the characterization design and methods.

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titleExtra lines add

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

Include Page
Technique and instrument
Technique and instrument

Technique*

Include Page
Technique
Technique

Abbreviation

Include Page
Abbreviation
Abbreviation

DescriptionEnter a description of the technique and instrument.
Instrument

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Instrument
Instrument

Once you enter the data, click Save to save the information to the sample or Cancel to close the mini-window without saving data.

Continue to define In Vitro Findings.

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Describing Findings for an In Vitro Characterization

In the Finding sections, you can add one or more publications relevant to the sample, as well as data derived for the sample. You can add as many files and derived data as you wish, or you can 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

In the Data and Conditions segment of the window, you can create a matrix where you can enter data values and/or other information, such as laboratory conditions that are part of your findings.

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Other options
Other options

To define the matrix for the data

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Data and conditions1
Data and conditions1

        • Column Type "Datum" is selected with this characterizationAutopopulated Column Name Option[s]

          Enzyme Induction

          % of Control

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Data and conditions2
Data and conditions2

After adding data and conditions to the sample, add an In Vitro Characterization.

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Adding a File

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Adding a file
Adding a file

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InVivo
InVivo
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 or In Vivo Characterizations tab and click Add next to In Vivo Characterizations. Both tabs display five sections, but the All tab provide customizations based what you select in the Characterization* field.

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

    Anchor
    Defining an In Vivo Characterization
    Defining an In Vivo Characterization

    Field/SectionWhat to Do
    In Vivo CharacterizationFill in the general information about the characterization.
    [Characterization] PropertiesDisplays for in vivo characterizations.
    Design and MethodsComplete the fields describing techniques and instruments used to derive the data.
    Findings

    Add data findings and supporting documentation relating to the sample.

    Analysis and ConclusionsEnter any relevant analyses and conclusions reached by the data.
    Copy to Other Samples...

    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.

  4. When you finish, click Submit to save the data to the sample.

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Defining an In Vivo Characterization

Fill in the following characterization information.

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Other options
Other options


FieldDescription
Characterization Type*

The Characterization Type is already selected as In Vivo Characterization.

Characterization Name*

You must select the name of the Characterization you want to add or select an "other" option to create a new or select from an existing, non-standard Assay Type.

Info
If you select Pharmacokinetics and Toxicity, there are no customizations on this Characterization page based on either of these selections.
  • To select an existing, non-standard Assay Type, based on Characterization Type, select other_vv or other_ex_vv.
  • To create a new, non-standard Assay Type, select other. Enter a New Characterization Name, and click Add.  The new characterization is added the Characterization Name list.
    Adding a New Characterization Name
Assay Type

Leave this blank or select a type.

  • With Characterization Name, other_vv or other_ex_vv, select from existing, non-standard Assay Types.
  • With Characterization Name, other, create a new, non-standard Assay Type.
Protocol Name – VersionSelect from the drop-down list 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 from the drop-down list or enter the source from which the characterization data is derived, such as a vendor or a laboratory (NCL).
Characterization DateSelect from the calendar or enter the date the characterization was made. Acceptable format: dd/mm/yyyy.

Continue to define In Vivo Design and Methods.

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Defining In Vivo Design and Methods

Fill in the following Design and Methods information as needed.

Include Page
Other options
Other options


Design and Methods FieldDescription

Design and Methods Description

Enter a description for the characterization design and methods.

Info
titleAdding extra lines

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

Include Page
Technique and instrument
Technique and instrument

Technique*

Include Page
Technique
Technique

Abbreviation

Include Page
Abbreviation
Abbreviation

DescriptionEnter a description of the technique and instrument.
Instrument

Include Page
Instrument
Instrument

Once you specify the data, click Save to save the information to the sample or Cancel to close the mini-window without saving data.

Continue to define In Vivo Findings.

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Describing Findings for In Vivo Characterizations

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

Complete the instructions as described in Adding Data and Conditions and Adding a File.

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Adding Data and Conditions

In the Data and Conditions segment of the window, you can create a matrix where you can enter data values and/or other information that are part of your findings.

Include Page
Data and conditions1
Data and conditions1

To define the matrix for the data

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

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Data and conditions2
Data and conditions2

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Adding a File

Include Page
Adding a file
Adding a file

After adding one or more files, continue by Adding Data and Conditions or if you have no derived data to add, return to the steps described in Adding an In Vivo Characterization.

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Characterization Tasks

From a characterization summary page, and with curator privileges, you can perform these tasks:

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Printing a Characterization

To print a characterization

  1. Access a sample and characterization.
  2. The All tab displays the characterizations summary.

  3. Click Print at the top right of the page.

    Info
    titleRead only access?

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

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Exporting Characterizations

To export a characterization

  1. Access a sample and characterization.
  2. The All tab displays the characterizations summary.

  3. Click Export at the top right of the page.

    Info
    titleRead only access?

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

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Editing Characterizations

To edit a characterization

  1. Access a sample and characterization.
  2. The All tab displays the characterizations summary.

  3. Click Edit at the right of the characterization section you want to change. This opens the corresponding Characterization page where you can edit the file by following the same directions as described for creating characterizations.

    Info
    titleRead only access?

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

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Copying Characterizations

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

To copy characterizations, open the sample characterization form that displays the characterization

  1. Access a sample and characterization.
  2. The All tab displays the characterizations summary.
  3. On the characterization summary page, click Edit at the right of the section you want to copy. This opens the corresponding Characterization page.
  4. At the bottom of the page, in the Copy to other samples... box, select one or more samples that have the same primary point of contact (those listed).
  5. Click Also copy characterization results? .

  6. Click Submit to copy the characterization.

    Info
    titleRead only access?

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

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Deleting a Characterization

To delete a characterization for a selected sample

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titleDeleting a characterization

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

  1. Access a sample and characterization.
  2. The All tab displays the characterizations summary.
  3. Click Edit at the right of the section you want to delete. This opens the corresponding Characterization page.

  4. Click Delete.

    Info
    titleRead only access?

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

    Deleted characterizations are placed in the sample archive for history purposes.

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