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

Access 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:

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...

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.

    Italic Links

    If you are not logged in or do not have curator visibility, the Navigation Tree links appear in italics if no annotations are associated with the open sample.

    NAVIGATION TREE
    GENERAL INFO
    COMPOSITION
    CHARACTERIZATION
    PUBLICATION
    • General Info displays after you click the sample name and shows the Update Sample page.
    • Composition defines Nanomaterial Entity, Functionalizing Entity, and Chemical Associations.
    • Characterization defines essential physical characteristics that identify the material and structural properties via the Protocol and Physico-Chemical, In Vivo, and In Vitro Characterization.
    • Publication displays articles, books chapters, reviews and reports already added to a 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.

To enter an alternative to an option, select other if available and enter a value. The value is added to the list of options.

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Exporting Sample Information to JSON or XML

You can export a sample's General Information, Composition, Characterization, and Publication information to JSON and XML.

To export sample information from the Navigation Tree

  1. From the Navigation Tree, select General Info.

    NAVIGATION TREE
    GENERAL INFO
    COMPOSITION
    CHARACTERIZATION
    PUBLICATION
  2. Click Export (JSON) or Export (XML).
    Export sample information
  3. The information is downloaded, and you can save it to a location.

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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.

    Note:
     
    When you are defining the characterization, to select an existing, non-standard Assay Type, select the Characterization Name, other_pc
    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

    Add data findings and supporting documentation relating to the sample. Import as many .csv files as you wish or add derived data manually.

    Click Add to expand the section, and add data findings and add supporting documents to the 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 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.

Surface

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

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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.

    Note:
     
    When you are defining the characterization, to select an existing, non-standard Assay Type, select the Characterization Name, other_vt.
    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

    Add data findings and supporting documentation relating to the sample. Import as many .csv files as you wish or add derived data manually.

    Click Add to expand the section, and add data findings and add supporting documents to the 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 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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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 Vivo Characterizations tab and click Add next to In Vivo Characterization.

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

    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.

    Note:
     
    When you are defining the characterization, to select an existing, non-standard Assay Type, select the Characterization Name, other_vv.
    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. Import as many .csv files as you wish or add derived data manually.

    Click Add to expand the section, and add data findings and add supporting documents to the 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.

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

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Adding an Ex Vivo Characterization

To add an ex vivo characterization

  1. Access a sample and characterization.
  2. Click the All tab or the Ex Vivo Characterizations tab and click Add next to Ex Vivo Characterization.

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

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

    SectionWhat to Do
    Ex Vivo CharacterizationFill in the general information about the characterization.

    Note:
      When you are defining the characterization, to select an existing, non-standard Assay Type, select the Characterization Name, other_ex_vv
    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. Import as many .csv files as you wish or add derived data manually.

    Click Add to expand the section, and add data findings and add supporting documents to the 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.

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

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Adding an Other Ex Vivo Characterization

To add an other ex vivo characterization

  1. Access a sample and characterization.
  2. Click the All tab or the Other Ex Vivo Characterizations tab and click Add next to Ex Vivo Characterization.

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

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

    SectionWhat to Do
    Other Ex Vivo CharacterizationFill in the general information about the characterization.
    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. Import as many .csv files as you wish or add derived data manually.

    Click Add to expand the section, and add data findings and add supporting documents to the 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.

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

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Adding Information to a Characterization

The following procedures apply to any Characterization Type when you are adding or editing a characterization.

Defining the Characterization

When you are adding a characterization, fill in the following characterization information.

CompleteHow to
Characterization Type*

This is already filled in with Physico-Chemical, In Vivo, Ex Vivo, or Other Ex Vv (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).


Character Type Notes

  • Physico-Chemical: If you select Cytoxicity, Enzyme Reduction, Target, or Transfection, you have to complete additional properties. To create an existing, non-standard Assay Type, select other_pc.
  • In Vitro: 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.
  • In Vivo: To select an existing, non-standard Assay Type, select other_vv.
  • Ex Vivo: To select an existing, non-standard Assay Type, select 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
    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 Characterization Design and Methods

When you are adding a characterization, fill in the following design, methods, and techniques used.

Design and Methods FieldDescription

Design and Methods Description

Enter a description for the characterization design and methods.

Adding 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

Click Add to expand the page where you can select and enter information regarding the technique and instrument used to derive the sample.

Technique*

Select the technique (required).

Abbreviation

When you select a technique, Abbreviation populates automatically if an abbreviation is known. If not, enter an abbreviation.

DescriptionEnter a description of the technique and instrument.
Instrument

Click Add to expand the Instruments panel. Enter or select identifying information about the instrument used to obtain data.
  • Select the instrument Manufacturer.
  • Enter the instrument Model Name.
  • Enter the model Type.

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

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Adding Data Findings to a Characterization

To add findings to a characterization, you can add data directly to Data and Conditions by creating columns and adding data manually or you can import as many .csv files as needed. Information can include laboratory conditions, pH, or temperature. You can add as many files as you wish.

  1. Add data values to Data and Conditions.
    1. To import a file of data values
      1. Save the spreadsheet of data values to a csv (comma-separated value) file.
      2. Click Import csv and select and follow the prompts to add the data file to the Findings Info.
        Import CSV button
      3. The columns and data are added to Data and Conditions.
    2. To add the data values manually
      1. Specify the number of columns and rows for the matrix, and click Update.
        Manually adding Data and Conditions data values
      2. Add the data values to the rows.

    Whether you imported or added information manually, you can preface each data value with one of the following: Maintain the default, equal to (=), or select greater than (>), less than (<), or infinity (approximate).
    Adding Data and Conditions values to the table

  2. To define a column, click an underlined column heading.
    Clicking column
    The Column Definition panel displays.
    Defining the Findings column definition
  3. Select a Column Type, Datum or Condition.
  4. Select a Column Name or select other and add a new one.

    Column Notes

    You can add up to three cell viability Column Names, including cell viability, cell viability B, and cell viability C. You can further identify the column with the Column Value Type.


    1. For Column Type, Datum, the following characterization(s) display customized Column Name options.

      Characterization TypeColumn Type and Column Name Option(s)
      Physico-Chemical
      • MolecularMolecular Weight
      • Purity% purity for sample
      • RelaxivityR1, R2, T1, T2
      • SizePD1, Peak N , RMS size, Z Average
      • Surfacecharge, zeta potential
      In Vitro

      Enzyme Induction – % of Control

      In VivoClick Other to name the column yourself.
    2. For Column Type, Condition, all characterizations provide the Column Name options in the left column of the following table. The Column Name autopopulates the Condition Property options in the right column.

      Column Type, Condition Autopopulates Column NameColumn Name Autopopulates
      Condition Property

      Centrifugation

      N/A

      Culture Media

      media type, serum percentage

      Electromagnetic Radiation

      bandwidth, frequency, time, wavelength

      Freeze Thaw

      N/A

      Long Term Storage

      lyophilized, time

      Lyophilization

      time

      pH

      N/A

      Sample concentration

      N/A

      Short Term Storage

      lyophilized, time

      Solvent Media

      ion concentration, ionic strength, molecular formula, osmolality, serum percentage, with serum

      Sonication

      number of pulses, pulse duration

      Temperature

      N/A

  5. To further identify a column, select a Column Value Type.

    Once the column information is saved, the Column Type is shown in parentheses after the Column Name, such as cell viability (mean).
  6. Select a Column Value Unit, or select other and add one.
  7. If you want the same value to fill all rows in a column, add a Constant Value.

    For Column Value Type, boolean

    For Column Value Type, boolean, enter a Constant Value of 1 for true and 0 for false.
  8. Click Save, and the column(s) are updated.

    If needed, click Set Column Order to change the order of the column headings in the matrix.


  9. Click Save in the Finding section.

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Adding Supporting Documents to a Characterization

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

You can add as many files as you wish.

  1. In the Finding section of the characterization, next to Files, click Add.
  2. Upload, browse, and select the file or enter the file's URL where the document is located.
  3. 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.
  4. Click Submit to add the file(s) to the sample.

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Copying to Samples in the Same Primary Organization

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

  1. 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.
  2. Click Also copy finding data and conditions?.
  3. Click Submit to copy the characterization.

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Additional Characterization Tasks

The following table lists tasks that require Curator privileges.

If a button does not display, you have read-only access to the data.
TaskHow to

Printing Characterization(s)

To print the characterization(s), from the All tab characterization summary, click Print at the top right of the page.

Exporting Characterization(s) to a Spreadsheet

To export the characterization(s) to a spreadsheet, from the All tab characterization summary, click Export at the top right of the page.

To export all sample information to JSON or XML, see Exporting Sample Information to JSON or XML

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.

Deleting a 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.

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