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

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ManageSamples ManageSamples

Samples Overview

When a a sample is  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 the Samples menu menu, and from Manage Samples you can

• Create a new sample

• Copy an existing sample 

• Search existing samples

You can also perform the following functions with a sample.

•  Update a sample

• Share a sample and  and make it public
• Generate data availability metrics

• Bookmark a sample in My Favorites

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Annotating a a sample is 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 workflow shows how the annotations are organized in caNanoLab.

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To enter general information about a a sample

1. Click the the Samples menu menu.

   The Manage Samples page displays.

2. Click Click Create a New Sample.

3. On the Create Sample page, fill in the following information as needed.

   Name	Definition
   Anchor Sample Page Sample Page Sample Name*	Enter a sample name of your choice (required).
   Point of Contact*	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.

4. Click Save Save.

   Tip
   title My Workspace
   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.

5. Once you save the sample, the Update Sample page opens. With the appropriate security permissions you can

• • Update Update the sample information.

  • Share a sample.
  • Make it public

  • Generate a a data availability metrics for  for the sample.

  • Annotate the sample from the Navigation Tree.

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1. Fill in the following information as needed.

   Info
   To export sample information, see Exporting Sample Information to JSON or XML.

   General Information Characterization Fields	Definition
   Sample Name*	The name assigned to the sample (required).
   Point of Contact*	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.
   Keywords	Keyword(s) the submitter selected to associate with the selected sample.
   Access to the Sample	For more information, see Sharing a Sample with a User or Group or Making the Sample Public. Include Page Adding access include Adding access include
   Data Availability Metrics	For more information see Generating Data Availability Metrics.

2. Click Click Update when  when you are done editing the sample.
   

   Info
   You can also Copy and Delete the sample from the Update Sample page.

   
   

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SharingSample SharingSample

Sharing a Sample with a User or Group

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Metrics Metrics

Generating Data Availability Metrics

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1. Perform a sample search.

2. From the sample search results, if a data availability metrics is generated for a sample, click the link in the Data Availability column

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You can review the entire metrics, and click click Close when  when you are done.

Re/Generating a Metrics for an Individual Sample

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1. Perform a sample search.
2. From the sample search results, click click Edit in  in the Actions column.
3. Update Sample opens and the Data Availability Metrics section is at the bottom.
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   1. If there is no metrics generated for the sample, click click Generate.
   2. If a metrics was previously generated, click click Edit as  as shown in the screen above.
   The metrics table displays high-level medidata for minimal care. 
   

4. Using examples, the following table describes the percentages at the top of the metrics.

   Percentages at the Top of the Metrics	Description
   caNanoLab Availability Score: 23.0% (7 out of 30)	Indicates that the sample has 23% of the total possible number of caNanoLab attributes filled in or 7 out of 30.
   MINChar Availability Score: 11.0% (1 out of 9)	Indicates that the sample has 11% ofthe total possible number of MinChar attributes filled in or 1 out of 9.

5. The following table describes each column on the metrics.

   Columns in the Metrics	Description
   caNanoLab	Lists all data elements that can be added to the sample in caNanoLab.
   MinChar	Lists the minimum nanoparticle characterization standards as established by MinChar Initiatives.
   [Name of sample]	includes check marks where data element annotations are added to the sample.

6. The following buttons are at the bottom of the metrics.
   
   
   1. Click Click Delete to  to delete the metrics for this sample.
   2. Click Click Close to  to return to Update Sample without changing the metrics.

   3. Click Click Regenerate to  to regenerate the metrics.

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SearchSample SearchSample

Searching Existing Samples

A sample A sample search looks for a sample based on added annotations or uploaded characterization or data files.

1. To continue with a basic search, see Performing  Performing a Basic Search.
2. To launch an advanced search, see see Performing an Advanced Search.

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To launch a basic search for a sample

1. Click the the Samples menu menu.
   The Manage Samples page displays.

2. Click Click Search Existing Samples.

   Include Page
   Search Criteria Blank include Search Criteria Blank include

3. From the Sample Search page, fill in the following search criteria as needed. 

   Sample Search Options	Description
   Keywords	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.
   Sample Name	Enter text for the name of a sample. Select Contains (for search using partial text) or Equals (for exact text search).
   Sample Point of Contact	Enter text for the name or organization point of contact. Select Contains (for search using partial text) or Equals (for exact text search).
   Composition	Nanomaterial Entity 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.
   Characterization Type/Characterization	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.

4. Click Click Search.

   For information about the search results, see see Sample Search Results.

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To launch an advanced search

1. Click the the Samples menu menu.
   The Manage Samples page displays.

2. Click Click Advanced Sample Search.

   Include Page
   Search Criteria Blank include Search Criteria Blank include

3. From the Sample Search page, fill in the search criteria as needed.

   Advanced Search Category	Description
   Sample Criteria	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.
   Composition Criteria	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.
   Characterization Criteria	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).

4. Click Click Add to  to each set of criteria you define. As you add criteria, they display in a table above the criteria fields on the page.
5. Select the the And or  or Or operand  operand at the bottom of each set of criteria when you enter more than one criteria in a set. And or  or Or determines  determines whether, for the set, the search finds samples that meet all of the criteria or that meet any one of the criteria.
6. Select the the And or  or Or operand  operand at the bottom of the page that determines whether the search finds samples that meet only all of the criteria or that meet any one of the criteria.
7. Click Click Search.
   

   For information about the search results, see see Sample Search Results.

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A 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.

For information about configuring a sample search, see see Searching Existing Samples.

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