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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:
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You can perform the procedures described in this section only if you are a curator. If you have read-only permissions, see Viewing a Characterization Summary. |
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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.
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To add characterizations to a sample |
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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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The All tab displays characterizations already added to the sample. The remaining tabs show annotations specific to those categories.
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If you are a curator, you can review existing characterizations, as well as Add, Edit, Delete, Copy, Print, and Export. If you have read-only access, see see Viewing Characterizations Summary. |
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Sample characterizations describing distinctive characteristics or essential features of the sample determined through analytical methods, record information associated with sample synthesis and properties. Samples can be characterized in caNanoLab by Physico-chemical characterizatics, or by data derived under In vitro and In vivo conditions.
To view a sample characterizations summary
- Perform a search for the sample.
- Click Edit in the search results row.
- In the Navigation Tree on the left sidebar, click the Characterizations link.
The All tab displays characterizations already added to the sampe by category. Additional tabs show annotations added to the sample under their corresponding Physical, In Vitro and In Vivo Characterization subcategories.
Info title Read only permissions? Based on your security permissions, you may have read-only access to characterizations and only be able to see a characterization summary and not be able to perform additional tasks.
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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 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.
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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
To define the general information about the characterization
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- The Characterization Type is already selected as Physico-Chemical Characterization.
- For the Characterization Name* select from the drop-down list the name of the Characterization you want to add (required).
- The Assay Type field populates automatically with your selection in the Characterization field.
- 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.
- 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).
- 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.
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The [Characterization] Properties section opens only for the characterizations listed in the table below. The following table lists and describes the Properties fields.
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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
The following table lists and describes the Design and Methods fields.
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Description
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Enter design and methods information not covered by other fields on the form.
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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 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 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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charge, surface area, zeta potential
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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 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.
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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
To continue defining this characterization
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In Characterization Date, select from the calendar or enter the date the characterization was made. Acceptable format: dd/mm/yyyy.
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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.
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.
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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.
Continue to define In Vitro Design and Methods.
Defining In Vitro Design and Methods
In the Design and Methods sections, complete the fields as described in the following table.
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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.
To define the matrix for the data, follow these steps.
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Enzyme Induction
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If you have read-only permissions, 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 in caNanoLab.
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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. 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
To define general information about the characterization
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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.
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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).
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Defining In Vivo Design and Methods.
Defining In Vivo Design and Methods
In the Design and Methods sections, complete the fields as described in the following table.
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Description
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Enter information not covered by other fields on the form.
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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.
Defining 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.
To define the matrix for the data
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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
- Open the sample of your choice.
- In the Navigation Tree on the left sidebar, click the Characterizations button. The All tab displays the characterizations summary.
Click the Print hyperlink at the top right of the page.
Info title Read only access? If buttons described in this section do not display, then you can assume that you have read-only access to the data.
Exporting Characterizations
To export a characterization
- Open the sample of your choice.
- In the Navigation Tree on the left sidebar, click the Characterizations button. The All tab displays the characterizations summary.
Click the Export hyperlink at the top right of the page.
Info title Read only access? If buttons described in this section do not display, then you can assume that you have read-only access to the data.
Editing Characterizations
To edit a characterization
- Open the sample of your choice.
- In the Navigation Tree on the left sidebar, click the Characterizations button. The All tab displays the characterizations summary.
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.
Info title Read only access? If buttons described in this section do not display, then you can assume that 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
- Open the sample of your choice.
- In the Navigation Tree on the left sidebar, click the Characterizations button. The All tab displays the characterizations summary.
- 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.
- 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 the Also copy characterization results? box.
Click Submit to execute the copy function.
Info title Read only access? If buttons described in this section do not display, then you can assume that 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) is copied for other samples, the characterization will not be deleted. |
- Open the sample of your choice.
- In the Navigation Tree on the left sidebar, click the Characterizations button. The All tab displays the characterizations summary.
- Click the Edit hyperlink at the right of the section you want to delete. This opens the corresponding Characterization page.
Click the Delete button at the bottom left of the page.
Info title Read only access? 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.
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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