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Managing Sample Composition Annotations | caNanoLab User's Guide| Managing Publications in caNanoLab
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If you have read-only permissions, see Access refer to Accessing 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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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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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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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
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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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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.
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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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To add a physico-chemical characterization
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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.
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Add data findings and supporting documentation relating to the sample.
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When you finish, click Submit to save the data to the sample.
Defining the Physico-Chemical Characterization
Fill in the following characterization information.
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The Characterization Type is already selected as Physico-Chemical Characterization.
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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.
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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.
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Continue to define Physico-Chemical Properties.
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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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Physical State
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Type
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Select the appropriate type from among the following options:
- colloid-emulsion
- colloid-gel
- colloid-sol
- fluid-gas
- fluid-liquid
- fluid-vapor
- solid-crystal
- solid-fibril
- solid-glass
- solid-granule
- solid-powder
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Shape Properties
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Type (required)
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Select from the drop-down list the appropriate shape type:
- 2D-circle
- 2D-diamond
- 2D-ellipse
- 2D-parallelogram
- 2D-polygon
- 2D-rectangle
- 2D-square
- 2D-trapezoid
- 2D-triangle
- 3D-cone
- 3D-cube
- 3D-cylinder
- 3D-disc
- 3D-fibril
- 3D-hexadron
- 3D-needle
- 3D-oblate spheroid
- 3D-polyhedron
- 3D-prolate spheroid
- 3D-rod
- 3D-sphere
- 3D-tetrahedron
- 3D-tetrapod
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Shape Properties
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Aspect Ratio
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Enter the shape aspect ratio.
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Shape Properties
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Minimum,/Maximum Dimensions
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Enter the minimum and maximum dimensions of the sample, as well as the units of measurement.
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Solubility Properties
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Solvent
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Select from the options or enter the name.
- alcohol
- phosphate-buffered saline
- saline
- water
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Enter appropriate values for the critical concentration, then select the appropriate units for those values.
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Surface Properties
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Is Hydrophobic?
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Indicate with Yes or No whether the surface is hydrophobic.
Continue to define Physico-Chemical Design and Methods.
Defining Physico-Chemical Design and Methods
Fill in the following Design and Methods information as needed.
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Design and Methods Description
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Enter a description for the characterization design and methods.
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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. |
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Technique and Instrument
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Technique*
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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.
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.
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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Molecular Weight
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Purity
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Relaxivity
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Size
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PD1, Peak N , RMS size, Z Average
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Surface
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After adding data and conditions to the sample, continue to add a Physico-Chemical Characterization.
Adding a File
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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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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
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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.
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Add data findings and supporting documentation relating to the sample.
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When you finish, click Submit to save the data to the sample.
Defining an In Vitro Characterization
Fill in the following characterization information.
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The Characterization Type is already selected as In Vitro Characterization.
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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.
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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.
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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).
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Continue to In Vitro Properties.
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.
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Characterization Selection
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Assay Type Corresponding to Characterization
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Blood Contact
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Cytotoxicity
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- Caspase 3 apoptosis
- Cell viability
- Gene expression
- Mitochondrial function
- Mitochondrial membrane potential
- Proliferation
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Immune Cell Function
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- CFU – GM
- Chemotaxis
- Cytokine induction
- Cytotoxic activity
- Leukocyte proliferation
- Oxidative Burst
- Phagocytosis
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Oxidative stress
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Sterility
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Targeting
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Transfection
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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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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.
Defining In Vitro Design and Methods
Fill in the following Design and Methods information as needed.
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Enter a description for the characterization design and methods.
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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. |
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Technique and Instrument
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Technique*
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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.
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.
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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To define the matrix for the data
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Enzyme Induction
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After adding data and conditions to the sample, add an In Vitro Characterization.
Adding a File
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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
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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.
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Add data findings and supporting documentation relating to the sample.
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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.
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When you finish, click Submit to save the data to the sample.
Defining an In Vivo Characterization
Fill in the following characterization information.
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The Characterization Type is already selected as In Vivo Characterization.
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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.
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| 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.
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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.
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Continue to define In Vivo Design and Methods.
Defining In Vivo Design and Methods
Fill in the following Design and Methods information as needed.
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Design and Methods Description
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Enter a description for the characterization design and methods.
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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. |
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Technique and Instrument
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Technique*
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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.
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.
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.
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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
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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.
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
Printing a Characterization
To print a characterization
- Access a sample and characterization.
- The All tab displays the characterizations summary.
Click Print at the top right of the page.
Info title Read only access? If the button described in this section does not display, you have read-only access to the data.
Exporting Characterizations
To export a characterization
- Access a sample and characterization.
- The All tab displays the characterizations summary.
Click Export at the top right of the page.
Info title Read only access? If the button described in this section does not display, you have read-only access to the data.
Editing Characterizations
To edit a characterization
- Access a sample and characterization.
- The All tab displays the characterizations summary.
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 title Read only access? If the button described in this section does not display, you have read-only access to the data.
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
- Access a sample and characterization.
- The All tab displays the characterizations summary.
- On the characterization summary page, click Edit at the right of the section you want to copy. This opens the corresponding Characterization page.
- 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).
- Click Also copy characterization results? .
Click Submit to copy the characterization.
Info title Read only access? If the button described in this section does not display, you have read-only access to the data.
Deleting a Characterization
To delete a characterization for a selected sample
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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. |
- Access a sample and characterization.
- The All tab displays the characterizations summary.
- Click Edit at the right of the section you want to delete. This opens the corresponding Characterization page.
Click Delete.
Info title Read 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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