Managing Samples in caNanoLab

Managing Protocols in caNanoLab

| caNanoLab User's Guide| Managing Sample Composition Annotations

This section describes how to manage samples in caNanoLab with the Samples function. Topics in this chapter include:

Samples Overview

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

• 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 make it public
• Generate data availability metrics

• Bookmark a sample in My Favorites

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Annotating a 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.

The workflow shows how the annotations are organized in caNanoLab.

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Creating a Sample

To enter general information about a sample

1. Click the Samples menu.

   The Manage Samples page displays.

2. Click Create a New Sample.

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

   Name	Definition
   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 drop-down 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.

   My Workspace

   After saving, the sample is listed on the My Workspace page 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

   1. Update the sample information.

   2. Share a sample.
   3. Make it public

   4. Generate a data availability metrics for the sample.

   5. Annotate the sample from the Navigation Tree.

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Updating a Sample

The Update Sample page enables you to update sample information, update access to the sample, and generate data availability access.

1. Fill in the following information as needed.

   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. If you do not add access If you do not add access, this item remains private and only you, the owner, can view and/or modify it.
   Data Availability Metrics	For more information see Generating Data Availability Metrics.

2. Click Update when you are done editing the sample.
   
3. If you want to submit it to a curator to make it public, see Making a Protocol Public.

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Sharing a Sample with a User or Group

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Making a Sample Public

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Generating Data Availability Metrics

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.

Reviewing the Metrics for an Individual Sample

To review a data availability metrics for an individual sample

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.

   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

1. Perform a sample search.
2. From the sample search results, click Edit in the Actions column.
3. Update Sample opens and the Data Availability Metrics section is at the bottom.
   
   
   1. If there is no metrics generated for the sample, click Generate.
   2. If a metrics was previously generated, click Edit 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% of the 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 Delete to delete the metrics for this sample.
   2. Click Close to return to Update Sample without changing the metrics.

   3. Click Regenerate to regenerate the metrics.

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Searching Existing Samples

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 a Basic Search.
2. To launch an advanced search, see Performing an Advanced Search.

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Performing a Basic Sample Search

To launch a basic search for a sample

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

2. Click Search Existing Samples.

   Leaving all search criteria blank

   There are no required fields when you specify search criteria. If you leave all the fields blank, all items are returned.

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 scroll list the nanoparticle category to which the nanomaterial entity targeted by the search belongs. Example: Dendrimer Functionalizing Entity Select from the scroll list the functionalizing category to which the sample targeted by the search belongs.* Monomer Polymer Quantum Dot Antibody Biopolymer Small Molecule Function Select from the drop-down list the function type category which best fits the sample targeted by the search: Imaging Function [Other]  To enter an alternative to an option, select other if available and enter a value. The value is added to the list of options. Targeting Function Therapeutic Function Transfection *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 drop-down list on the left and select the characterization type that applies to the sample to be searched: Physico-Chemical, In Vitro or In Vivo. 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.) Physico-Chemical Characterizations: Molecular Weight Physical State Purity Relaxivity Shape Size Solubility Surface In Vitro Characterizations: Blood Contact Cytotoxicity Enzyme Induction Immune Cell Function Oxidative Stress Sterility  Targeting Transfection In Vivo Characterizations: Pharmacokinetics Toxicology *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 Search.

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

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Performing an Advanced Sample Search

An advanced search allows you to build search criteria based on data values or ranges.

To launch an advanced search

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

2. Click Advanced Sample Search.

   Leaving all search criteria blank

   There are no required fields when you specify search criteria. If you leave all the fields blank, all items are returned.

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 drop-down list. Select from the second drop-down, 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 drop-down list. Your selection drives the options that display in the second drop-down, as well as the options or text box that displays for the rest of the category. Select from the second drop-down, 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. Available terms are defined in the caNanoLab Glossary.
   Characterization Criteria	Select a Characterization Type in the first drop-down list. Your selection drives the options that display in the second drop-down 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 drop-down list. An optional drop-down box for units displays only if the data has a unit. Select your options or enter appropriate text in the text box(es). Available terms are defined in the caNanoLab Glossary.

4. Click Add 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 And or Or operand at the bottom of each set of criteria when you enter more than one criteria in a set. And or Or 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 And or Or 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 Search.
   

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

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Sample Search Results

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.

The following table lists and describes the Search Results columns.

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

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Additional Sample Tasks

You can edit a sample using the following techniques.

• Copying an Existing Sample
• Adding Publications to a Sample
• Deleting a Sample

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Copying an Existing Sample

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

1. Click the Samples menu.
   The Manage Samples page displays.
2. Click Copy an Existing Sample.
   On the Copy Sample page, both fields are required.
3. In Existing Sample, fill in a complete or partial sample to search for and click the Search icon.
4. Select a sample from the returned list to be copied.
5. Fill in the New Sample Name.
6. Click Submit.
   A filled in Update Sample page appears with the new sample name.
7. Edit the copied sample as needed.
8. Click Update.

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Adding Publications to a Sample

Publications can be associated with a sample using two caNanoLab features.

1. If you work from the Publications menu, you can associate multiple samples with a publication. See Creating a Publication for more information. 
2. 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

To delete a sample

1. Perform a sample search.
2. On the search results page, click Edit in the Actions column.
3. From the Update Sample page, click Delete.
4. Confirm the deletion.

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Bookmarking a Sample to My Favorites

My Favorites displays samples, protocols, and publications that you bookmark for quick access.

To add a sample to My Favorites

1. Perform a sample search.
2. On the search results page, click + Add to Favorites in the Actions column.
   The Added to Favorites message appears in the results row.
3. Click the My Favorites, and the bookmarked sample is listed under My Samples.

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