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. 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.
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
- Click Samples and Search Existing Samples.
- Fill in criteria, and click Search.
- Click Edit in the search results.
The Navigation Tree appears on the left sidebar and comprises functions which you can use to add annotations to the sample.
NAVIGATION TREE GENERAL INFO COMPOSITION CHARACTERIZATION PUBLICATION - General Info appears 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.
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.
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
- Adding an Ex Vivo Characterization
- Adding an Other Ex Vv
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.
Adding a Physico-Chemical Characterization
To add a physico-chemical characterization
- Access a sample and characterization.
Click the All tab or the Physico-Chemical Characterizations tab and click Add next to Physico-chemical Characterization.
Both tabs provide customizations based on your Characterization Type* selection.
Follow these steps to fill in the characterization. Links are provided for additional details.
Step... | What to Do... |
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Physico-Chemical Characterization | Fill in the general information about the characterization. |
Characterization Properties | If you select one of the following characterization types, you need to fill in additional properties.
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Design and Methods | Complete 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 a file to a physico-chemical characterization. |
Analysis and Conclusions | Enter 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.
Defining the Physico-Chemical Characterization
Define the following characterization information.
Complete... | How to... |
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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). To select an existing, non-standard Assay Type, select other_pc. To create a new, non-standard Assay Type
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Assay Type | Select an assay type from the list that populates automatically based on the Characterization Name. To add a new Assay Type
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Protocol Name – Version | If 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 Source | Select or enter the source from which the characterization data is derived, such as a vendor or a laboratory (NCL). |
Characterization Date | Select 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 Type | Properties to Complete |
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Physical State | Select the Type of physical state. |
Shape |
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Solubility |
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Surface | Specify Yes or No to indicate whether the surface Is Hydrophobic?. |
Defining Physico-Chemical Design and Methods
Define the following Design and Methods information.
Design and Methods Field | Description |
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Design and Methods Description | Enter a description for the characterization design and methods. Extra 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 | 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. |
Description | Enter a description of the technical and instrument. |
Instrument | Click Add to expand the Instruments panel. Enter or select identifying information about the instrument used to obtain data.
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When you are finished, click Save or Cancel to close the section without saving.
Describing Findings for Physico-Chemical Characterization
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.
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
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). Select a Column Type, Datum or Condition. Select a Column Name or select other and add a new one. Column Notes For Column Type, Datum, the following characterization(s) display customized Column Name options. Enzyme Induction – % of Control 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. N/A media type, serum percentage bandwidth, frequency, time, wavelength N/A lyophilized, time time N/A N/A lyophilized, time ion concentration, ionic strength, molecular formula, osmolality, serum percentage, with serum number of pulses, pulse duration N/A To further identify a column, select a Column Value Type. If you want the same value to fill all rows in a column, add a Constant Value. For Column Value Type, boolean 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.
The Column Definition panel displays.Characterization Type Column Type and Column Name Option(s) Physico-Chemical In Vitro In Vivo Click Other to name the column yourself. Column Type, Condition Autopopulates Column Name Column Name Autopopulates
Condition Property
Column Type "Datum" is selected with this characterization Autopopulated Column Name Option[s] Molecular Weight
Purity
Relaxivity
Size
Surface
For Column Type, Condition, all characterizations provide the Column Name options in the left column of the following table. Select a Column Name and the Condition Property options in the right column are available. N/A media type, serum percentage bandwidth, frequency, time, wavelength N/A lyophilized, time time N/A N/A lyophilized, time ion concentration, ionic strength, molecular formula, osmolality, serum percentage, with serum number of pulses, pulse duration N/A To further identify a column, select a Column Value Type. Constant Value – 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. 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.Column Type, Condition autopopulates
Column NameColumn Name autopopulates
Condition Property
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
- Access a sample and characterization.
Click the All tab or the In Vitro Characterizations tab and click Add next to In Vitro Characterization.
Both tabs provide customizations based on your Characterization Type* selection.
Follow these steps to fill in the characterization. Links are provided for additional details.
Step... | What to Do... |
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In Vitro Characterization | Fill in the general information about the characterization. |
In Vitro Characterization Properties | If you select one of the following characterization names, you need to fill in additional properties.
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Design and Methods | Complete 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 a file to an in vitro characterization. |
Analysis and Conclusions | Enter 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. |
When you are finished, click Submit to save the data to the sample.
Defining an In Vitro Characterization
Fill in the following characterization information.
Complete... | How to... |
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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). To select an existing, non-standard Assay Type, select other_vt. To create a new, non-standard Assay Type
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Assay Type | Select an assay type from the list that populates automatically based on the Characterization Name. To add a new Assay Type
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Protocol Name – Version | If available, select the protocol from which the data is derived.
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Characterization Source | Select or enter the source from which the characterization data is derived, such as a vendor or a laboratory (NCL). |
Characterization Date | Select or enter the date the characterization was made (dd/mm/yyyy). |
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 Name | Properties to Complete |
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Cytotoxicity | Enter the appropriate Cell Line. |
Enzyme Induction | Enter the Enzyme Name of your choice. |
Targeting | Enter the appropriate Cell Line. |
Transfection | Enter the appropriate Cell Line. |
Defining In Vitro Design and Methods
Fill in the following Design and Methods information as needed.
Design and Methods Field | Description |
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Design and Methods Description | Enter a description for the characterization design and methods. Extra 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 | 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. |
Description | Enter 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.
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When you are finished, click Save or Cancel to close the section without saving.
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.
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
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). Select a Column Type, Datum or Condition. Select a Column Name or select other and add a new one. Column Notes For Column Type, Datum, the following characterization(s) display customized Column Name options. Enzyme Induction – % of Control 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. N/A media type, serum percentage bandwidth, frequency, time, wavelength N/A lyophilized, time time N/A N/A lyophilized, time ion concentration, ionic strength, molecular formula, osmolality, serum percentage, with serum number of pulses, pulse duration N/A To further identify a column, select a Column Value Type. If you want the same value to fill all rows in a column, add a Constant Value. For Column Value Type, boolean 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.
The Column Definition panel displays.Characterization Type Column Type and Column Name Option(s) Physico-Chemical In Vitro In Vivo Click Other to name the column yourself. Column Type, Condition Autopopulates Column Name Column Name Autopopulates
Condition Property
Column Type "Datum" is selected with this characterization Autopopulated Column Name Option[s] Enzyme Induction
For Column Type, Condition, all characterizations provide the Column Name options in the left column of the following table. Select a Column Name and the Condition Property options in the right column are available. N/A media type, serum percentage bandwidth, frequency, time, wavelength N/A lyophilized, time time N/A N/A lyophilized, time ion concentration, ionic strength, molecular formula, osmolality, serum percentage, with serum number of pulses, pulse duration N/A To further identify a column, select a Column Value Type. Constant Value – 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. 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.Column Type, Condition autopopulates
Column NameColumn Name autopopulates
Condition Property
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
- Access a sample and characterization.
Click the All tab or the In Vitro Characterizations tab and click Add next to In Vitro Characterization.
Both tabs provide customizations based on your Characterization Type* selection.
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. In Vivo Characterization Properties Displays for in vivo characterizations. Design and Methods Complete 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 a file to an in vivo characterization.
Analysis and Conclusions Enter 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.
When you are finished, click Submit to save the data to the sample.
Defining an In Vivo Characterization
Fill in the following characterization information.
Field | Description |
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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
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Assay Type | Select an assay type from the list that populates automatically based on the Characterization Name. To add a new Assay Type
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Protocol Name – Version | Select 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 Source | Select or enter the source from which the characterization data is derived, such as a vendor or a laboratory (NCL). |
Characterization Date | Select or enter the date the characterization was made (dd/mm/yyyy). |
Defining In Vivo Design and Methods
Fill in the following Design and Methods information, as needed.
Design and Methods Field | Description |
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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. |
Description | Enter 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.
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When you are finished, click Save or Cancel to close the section without saving.
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.
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
- Add data values to Data and Conditions.
- To import a file of data values
- Save the spreadsheet of data values to a csv (comma-separated value) file.
- Click Import csv and select and follow the prompts to add the data file to the Findings Info.
- The columns and data are added to Data and Conditions.
- To add the data values manually
- Specify the number of columns and rows for the matrix, and click Update.
- Add the data values to the rows.
- Specify the number of columns and rows for the matrix, and click Update.
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).
- To import a file of data values
- To define a column, click an underlined column heading.
The Column Definition panel displays.
Select a Column Type, Datum or Condition.
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.For Column Type, Datum, the following characterization(s) display customized Column Name options.
Characterization Type Column Type and Column Name Option(s) Physico-Chemical - Molecular – Molecular Weight
- Purity – % purity for sample
- Relaxivity – R1, R2, T1, T2
- Size – PD1, Peak N , RMS size, Z Average
- Surface – charge, zeta potential
In Vitro Enzyme Induction – % of Control
In Vivo Click Other to name the column yourself. 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 Name Column Name Autopopulates
Condition PropertyN/A
media type, serum percentage
bandwidth, frequency, time, wavelength
N/A
lyophilized, time
time
N/A
N/A
lyophilized, time
ion concentration, ionic strength, molecular formula, osmolality, serum percentage, with serum
number of pulses, pulse duration
N/A
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).- Select a Column Value Unit, or select other and add one.
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.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.
- Click Save in the Finding section.
For an in vivo characterization, click [Other] to name the column yourself.
For Column Type, Condition, all characterizations provide the Column Name options in the left column of the following table. Select a Column Name and the Condition Property options in the right column are available.
Column Type, Condition autopopulates
Column NameColumn Name autopopulates
Condition PropertyN/A
media type, serum percentage
bandwidth, frequency, time, wavelength
N/A
lyophilized, time
time
N/A
N/A
lyophilized, time
ion concentration, ionic strength, molecular formula, osmolality, serum percentage, with serum
number of pulses, pulse duration
N/A
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).- Column Value Unit – Select a value unit, or select other and add one.
Constant Value – 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.
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.
- Click Save on the Finding Info panel.
Characterization Tasks
To perform the following tasks, you must have curator privileges.
Read only access?
If a button described in this section does not display, you have read-only access to the data.
What you can do | How you can do it |
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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
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 |
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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.
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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
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