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

This chapter describes how to review or ascribe characterizations to samples save in caNanoLab. This section includes the following topics:

[Sample] Characterization Overview

Sample characterization, describing distinctive characteristics or essential features of the sample determined through analytical methods, 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.

Accessing a Sample Characterization

To access characterization functions in the Navigation Tree

1. Perform a search for the sample.
2. Click Edit in the search results row.

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

   

4. Click the Characterizations link. 

5. The All tab displays characterizations already added to the sample. The remaining tabs show annotations specific to those categories.

   

   If you are a curator, you can review existing characterizations, as well as add, edit, delete, and copy characterizations. If you have read-only access, see  Viewing Characterizations Summary.

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Viewing a Characterization Summary

With read-only access, you can review a summary of characterization information on the All tab and annotations added to the sample under the physico-chemical, In Vitro, and In Vivo subcategory tabs.

To view a sample characterizations summary

1. Perform a search for the sample.
2. Click Edit in the search results row.
3. In the Navigation Tree on the left sidebar, click the Characterizations link. 

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

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Submitting Characterizations

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

• Adding a Physico-chemical Characterization
• Adding an In Vitro Characterization
• Adding an In Vivo Characterization

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 the characterization functions.

2. Click the All or Physico-Chemical Characterizations tab. Both tabs display five sections, but the All tab provide 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.

   Section	What to Do
   Physico-Chemical Characterization	Fill in the general information about the characterization.
   [Characterization] Properties	Displays only for Physical State, Shape and Solubility characterizations. Define properties for the characterization, if applicable.
   Design and Methods	Complete the fields describing techniques and instruments used to derive the data.
   Finding	Add data findings and supporting documentation relating to the sample.
   Analysis and Conclusions	Enter 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

To define the general information about the characterization

1. The Characterization Type is already selected as Physico-Chemical Characterization.
2. For the Characterization Name* select from the drop-down list the name of the Characterization you want to add (required).
3. The Assay Type field populates automatically with your selection in the Characterization field.
4. If the Protocol Name – Version 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.
5. For Characterization Source, select from the drop-down list or enter the source from which the characterization data is derived, such as a vendor or a laboratory (NCL).
6. In the Characterization Date field, select from the calendar or enter the date the characterization was made. Acceptable format: dd/mm/yyyy.

Continue to define Physico-Chemical Properties.

Defining Physico-Chemical [Characterization] Properties

The [Characterization] Properties section opens only for the characterizations listed in the table below. The following table lists and describes the Properties fields.

Continue to define Physico-Chemical Design and Methods.

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Defining Physico-Chemical Design and Methods

The following table lists and describes the Design and Methods fields.

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 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 like pH or temperature that are part of your findings.

To define the data and condition matrix

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

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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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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 the characterization functions.

2. Click the All or In Vitro Characterizations tab. 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.

   Field/Section	What to Do
   In Vitro Characterization	Fill 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 Methods	Complete the fields describing techniques and instruments used to derive the data.
   Finding	Add data findings and supporting documentation relating to the sample.
   Analysis and Conclusions	Enter 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

To continue defining this characterization

1. The Characterization Type is already selected as In Vitro Characterization.
2. For the Characterization Name* select from the drop-down list the name of the Characterization you want to add (required).
3. The Assay Type populates automatically with options that display only for these in vitro characterization selections: Blood Contact, Cytotoxicity, Immune Cell Function, Oxidative Stress, Sterility and Targeting. Select an option, if appropriate, or if there are none or if you prefer, select [Other] to name the assay type.
4. If Protocol Name – Version is available, select from the drop-down list 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.
5. 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).
6. Select from the drop-down list or enter the Characterization Source from which the characterization data is derived, such as a vendor or a laboratory (NCL).

7. In Characterization Date, select 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.

Return to Defining 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.

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

Continue to define In Vitro Design and Methods.

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Defining In Vitro Design and Methods

In the Design and Methods sections, complete the fields as described in the following table.

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.

To define the matrix for the data, follow these steps.

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 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 the characterization functions.

2. Click the All or In Vivo Characterizations tab. 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.

   Field/Section	What to Do
   In Vivo Characterization	Fill in the general information about the characterization.
   [Characterization] Properties	Displays for in vivo characterizations.
   Design and Methods	Complete the fields describing techniques and instruments used to derive the data.
   Findings	Add data findings and supporting documentation relating to the sample.
   Analysis and Conclusions	Enter 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

To define general information about the characterization

1. The Characterization Type is already selected.
2. For the Characterization Name*, select from the drop-down list the name of the Characterization you want to ad (required). The options for In Vivo Characterization are Pharmacokinetics and Toxicology. There are no customizations on this Characterization page based on either of these selections. 
3. You can leave the Assay Type field blank or specify an Assay Type.

4. If the Protocol Name – Version 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.

5. Select from the drop-down list or enter the Characterization Source from which the characterization data is derived, such as a vendor or a laboratory (NCL).

6. In the Characterization Date field, select from the calendar or enter the date the characterization was made. Acceptable format: dd/mm/yyyy.

Defining In Vivo Design and Methods.

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Defining In Vivo Design and Methods

In the Design and Methods sections, complete the fields as described in the following table.

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

Defining 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.

To define the matrix for the data

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

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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:

• Printing a Characterization
• Exporting Characterizations
• Editing Characterizations
• Copying Characterizations
• Deleting a Characterization

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Printing a Characterization

To print a characterization

1. Open the sample of your choice.
2. In the Navigation Tree on the left sidebar, click the Characterizations button. The All tab displays the characterizations summary.

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

   If buttons described in this section do not display, then you can assume that you have read-only access to the data.

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Exporting Characterizations

To export a characterization

1. Open the sample of your choice.
2. In the Navigation Tree on the left sidebar, click the Characterizations button. The All tab displays the characterizations summary.

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

   If buttons described in this section do not display, then you can assume that you have read-only access to the data.

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Editing Characterizations

To edit a characterization

1. Open the sample of your choice.
2. In the Navigation Tree on the left sidebar, click the Characterizations button. The All tab displays the characterizations summary.

3. Click the Edit hyperlink 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.

   If buttons described in this section do not display, then you can assume that 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. Open the sample of your choice.
2. In the Navigation Tree on the left sidebar, click the Characterizations button. The All tab displays the characterizations summary.
3. On the characterization summary page, click the Edit hyperlink 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 the Also copy characterization results? box.

6. Click Submit to execute the copy function.

   If buttons described in this section do not display, then you can assume that you have read-only access to the data.

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Deleting a Characterization

To delete a characterization for a selected sample

1. Open the sample of your choice.
2. In the Navigation Tree on the left sidebar, click the Characterizations button. The All tab displays the characterizations summary.
3. Click the Edit hyperlink at the right of the section you want to delete. This opens the corresponding Characterization page.

4. Click the Delete button at the bottom left of the page.

   If buttons described in this section do not display, then you can assume that you have read-only access to the data.

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

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Publication Tasks Associated with a Sample

Click the Publications button on the Navigation Tree. A Publication[s] summary page displays those publications associated with the sample, and the publication identifier, title, authors and year, where appropriate. Additionally, each publication category tab displays its corresponding publications.

From the Publications All tab or the subcategory tabs, you can perform the same tasks.

• To open a publication, click the Abstract/Download hyperlink.
• To add a publication to the open sample, click the Add button corresponding to the publication type on the All tab or select a publication type tab. The Submit Publication page opens which is identical one accessed Publications menu option with one exception:

If you work from the Publications menu option, you can associate multiple samples with a publication. Alternatively, if you add publications to an open sample using the Navigation Tree option, you can use the copy feature to associate the publication with other samples in the same way you copy characterizations to multiple samples. See Copying Characterizations.

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