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This section chapter describes how to manage samples in caNanoLab with the Samples function. Topics in this chapter include:
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When a sample is defined as a formulation of a base nanoparticle platform and any additional components that contribute to the function(s) of the nanoparticle. A sample can also be a control used in comparative analysis. These samples are used in biomedical applications in which they serve as drug carriers or imaging agents. Samples can be targeting agents, such as antibodies, drugs, imaging agents, and reporters or the nanoparticles themselves to which they are attached at the surface.
Click the Samples menu, and from Manage Samples you can
You can also perform the following functions with a sample.
Annotating a Sample
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If you are a curator with the appropriate security permissions for a sample, you can annotate the sample. |
Annotating a sample is the process of adding biological or related data to nanoparticle entities. A single sample can have multiple annotations, either coming from different sources, or the same data source being tested under different conditions (for example, temperature, solvents, instruments). When you search for and edit a sample, the Navigation Tree displays the annotation options.
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The following workflow shows how the annotations are organized in caNanoLab.
- Nanomaterial Sample
- Composition
- Nanomaterial Entity
- Functionalizing Entity
- Chemical Associations
- Characterization
- Protocol
- Physico-Chemical Characterization
- In Vitro Characterization
- In Vivo Characterization
- Publication
- Composition
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To enter general information about a sample
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Click the Samples menu.
The Manage Samples page displays.
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Click Create a New Sample.
On the Create Sample page, fill in the following information as needed.
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Enter a sample name of your choice (required).
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Point of Contact*
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The Point of Contact Add button is not available unless you entered a Sample Name (required).
To add a point of contact, click Add.
- Select an Organization Name from the list or select Other and add one.
- Select a Role in the same manner.
- Fill in the address, name, phone number, and email. Click Cancel or click Save to return and the POC is added.
- To edit a point of contact, click Edit next to the POC, update the information, and click Save.
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Click Save.
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| After saving, the sample is listed on the My Workspace where you can manage all of your submitted samples, and view any samples that a user has shared with you. |
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Once you save the sample, the Update Sample page opens. With the appropriate security permissions you can
Update the sample information.
- Share a sample.
- Make it public
Generate a data availability metrics for the sample.
Annotate the sample from the Navigation Tree.
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The Update Sample page enables you to update sample information, update access to the sample, and generate data availability access.
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Once data is made Public, you can update the data, but it will be retracted from Public, and you will need to resubmit it to the curator again for review. |
Fill in the following information as needed.
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| To export sample information, see Exporting Sample Information to JSON or XML. |
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Sample Name*
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The name assigned to the sample (required).
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Point of Contact*
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The site that is the source of the sample (required).
Click View Details for more information. Click Edit to edit current information. Click Add to add another point of contact.
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Keywords
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Keyword(s) the submitter selected to associate with the selected sample.
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Access to the Sample
For more information, see Sharing a Sample with a User or Group or Making the Sample Public.
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Data Availability Metrics
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For more information see Generating Data Availability Metrics.
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Click Update when you are done editing the sample.
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You can also Copy and Delete the sample from the Update Sample page. |
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Once you successfully save a sample to the database, you or the data curator can generate a data availability metrics table for the sample. The metrics identify the percentage of data available for the sample and displays a metrics of submitted data against caNanoLab-supported data and data supported in the MinChar standard.
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A data curator can generate data availablility metrics in batch mode for samples as well. |
Reviewing the Metrics for an Individual Sample
To review a data availability metrics for an individual sample
- Perform a sample search.
From the sample search results, if a data availability metrics is generated for a sample, click the link in the Data Availability column
You can review the entire metrics, and click Close when you are done.
Re/Generating a Metrics for an Individual Sample
To delete or regenerate availability metrics for a sample
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| If you generate data availability metrics after a sample is made public, the updated metrics will not be included in the public version. You will have to submit the sample for review again. |
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- If there is no metrics generated for the sample, click Generate.
- If a metrics was previously generated, click Edit as shown in the screen above.
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Using examples, the following table describes the percentages at the top of the metrics.
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The following table describes each column on the metrics.
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MinChar
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Lists the minimum nanoparticle characterization standards as established by MinChar Initiatives.
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- Click Delete to delete the metrics for this sample.
- Click Close to return to Update Sample without changing the metrics.
Click Regenerate to regenerate the metrics.
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A sample search looks for a sample based on added annotations or uploaded characterization or data files.
- To continue with a basic search, see Performing a Basic Search.
- To launch an advanced search, see Performing an Advanced Search.
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To launch a basic search for a sample
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Click the Samples menu.
The Manage Samples page displays.
Click Search Existing Samples.
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From the Sample Search page, fill in the following search criteria as needed.
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Keywords
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Enter one or more keywords by which samples could be identified in this search. caNanoLab can search for characterization or publication keywords, as well as text describing characterizations.
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Sample Name
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Enter text for the name of a sample. Select Contains (for search using partial text) or Equals (for exact text search).
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Sample Point of Contact
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Enter text for the name or organization point of contact. Select Contains (for search using partial text) or Equals (for exact text search).
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Composition
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Select from the list the nanoparticle category to which the nanomaterial entity targeted by the search belongs. Example: Dendrimer
Functionalizing Entity
Select the functionalizing category to which the sample targeted by the search belongs.*
Select the function type category which best fits the sample targeted by the search.
*You may see terms in caNanoLab that are not defined in the help glossary. These have been added by curators as [other]; they may be reviewed and defined at a later time.
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Click the list on the left and select the characterization type that applies to the sample to be searched: Physico-Chemical, In Vitro, In Vivo, Ex Vivo, or Other Ex VV.
Your selection determines the sub-categories that display in the Characterization field to the right.
Select one or more of the items in the Characterization list.* (CTRL + click to select more than one.)
*You may see terms in caNanoLab that are not defined in the help glossary. These have been added by curators as [other]; they may be reviewed and defined at a later time.
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Click Search.
For information about the search results, see Sample Search Results.
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An advanced search allows you to build search criteria based on data values or ranges.
To launch an advanced search
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Click the Samples menu.
The Manage Samples page displays.
Click Advanced Sample Search.
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From the Sample Search page, fill in the search criteria as needed.
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Sample Criteria
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Select an option in the first list. Select from the second list, Contains (for search using partial text) or Equals (for exact text search). Enter complete or partial text in the text box.
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Composition Criteria
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Select an option in the first list. Your selection drives the options that display in the second list, as well as the options or text box that displays for the rest of the category. Select from the second list, Contains (for partial text search) or Equals (for exact text search). Select your options or enter appropriate text in the text box. The Chemical name is optional.
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Characterization Criteria
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Select a Characterization Type in the first list. Your selection drives the options that display in the second list as well as the options or text boxes that displays for the rest of the category. The last text box is either a boolean value or number value, depending on the third list. An optional list for units displays only if the data has a unit. Select your options or enter appropriate text in the text box(es).
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For information about the search results, see Sample Search Results.
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A sample search looks for a sample based on annotations that were added or characterization or data files uploaded. Column headings vary based on the sample returned.
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The following table lists and describes the Search Results columns.
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| To export sample information, see Exporting Sample Information to JSON or XML. |
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Click View in the first column to display the sample on the Updating a Sample page.
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Edit is only available for people that have an account and are logged into the system and are associated with the sample. |
Click + Add to Favorites to add a bookmark for the sample on your My Favorites page. Added to Favorites appears in the column when the sample is successfully added.
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If the Sample is already added as a Favorite, clicking + Add to Favorites displays the <sample name> has already been added to your favorites message. |
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Sample Name
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The fully-qualified name of the sample located in the search.
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Primary Point of Contact
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The name of the source of the original sample.
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Composition
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The term for the sample composition. Examples: antibody; dendrimer.
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Functions
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A list of one or more terms displaying functions entered for the corresponding sample ID. Example: targeting
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Characterizations
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A list displaying characterization annotations entered for the corresponding sample ID. Example: oxidative stress
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Data Availability
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Indicates data availability generated for the sample. Click the availability summary to view an availability details page. If N/A is in the column, See also Data Availability Metrics.
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For information about configuring a sample search, see Searching Existing Samples.
Additional Sample Tasks
The following table lists how to edit a sample with the following techniques.
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Once data is made Public, you can update the data, but it will be retracted from Public and you will need to resubmit it to the curator again for review. |
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Copying an existing sample copies all of the annotation and/or publications, making it easier to create and submit similar samples.
To copy an existing sample
- Click the Samples menu.
The Manage Samples page displays. - Click Copy an Existing Sample.
On the Copy Sample page, both fields are required. - In Existing Sample, fill in a complete or partial sample to search for and click the Search icon.
- Select a sample from the returned list to be copied.
- Fill in the New Sample Name.
- Click Submit.
A filled in Update Sample page appears with the new sample name. - Edit the copied sample as needed.
- Click Update.
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Adding Publications to a Sample
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Publications can be associated with a sample using two caNanoLab features.
- If you work from the Publications menu, you can associate multiple samples with a publication. See Creating a Publication for more information.
- If you add documents from within an open sample, you can use the copy feature to associate the publication with other samples. See Managing Publications from an Open Sample for more information.
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Deleting a Sample
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Delete removes the sample from the caNanoLab database, executed behind the scenes at a scheduled time. |
To delete a sample
- Perform a sample search.
- On the search results page, click Edit in the Actions column.
- From the Update Sample page, click Delete.
- Confirm the deletion.
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Exporting Sample Information to JSON or XML
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To export an individual sample's information or all the samples listed in the search results to JSON or XML, click Export (JSON) or Export (XML).
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Bookmarking a Sample to My Favorites
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My Favorites displays samples, protocols, and publications that you bookmark for quick access.
To add a sample to My Favorites
- Perform a sample search.
- On the search results page, click + Add to Favorites in the Actions column.
The Added to Favorites message appears in the results row. - Click the My Favorites, and the bookmarked sample is listed under My Samples.
