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. This section includes the following topics:

Samples Overview

When you click the Samples option on the caNanoLab menu bar, the Manage Samples page appears. 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.

On the Manage Samples page, the Sample Links panel lists the following options:

•  Submit a New Sample displays the Submit Sample page to create a sample in the caNanoLab database.

  My Workspace

  Once you submit a sample, the sample is added to My Workspace for quick access.

• Copy an Existing Sample  displays the Copy Sample page to copy a sample with all its annotation and/or publications, making it easier to create and submit similar samples.

• Search Existing Samples displays the Sample Search page to launch a search for existing samples.

• Advanced Sample Search displays the Advanced Sample Search page to build search criteria based on data values or ranges.  

  Search Tips

  There is a basic and advanced sample search option discussed in this chapter. You can also perform a keyword search using the Search box in the upper-right corner of the caNanoLab window. This option searches across protocols, samples, and publications. For more information, see Performing a caNanoLab Keyword Search.

  From Sample Search Results tables, you can add a sample to the My Favorites page. This is like bookmarking a sample for quick access.

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Submitting Data

These are important items to consider when submitting and making data Public:

• Any user who logs into the system can submit data; however, only the Curator can make the data public.
• The user can also assign different accesses to the data but can NOT assign the data to Public unless the user is a curator. The user can submit the data to the curator for review (clicking on the Submit for Review button), and the curator decides whether to assign the data to Public.
• Once the data is assigned to Public by the curator, if the user decides to update the data later, the data would be retracted from Public and need to be resubmitted to the Curator again for review.

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Annotating a Sample

Annotating a sample is the process of adding biological or related data to nanoparticle entities. In caNanoLab, it involves selecting the sample to annotate, submitting the sample composition and function(s), and entering the sample characterizations (physico-chemical, in vitro and in vivo) via the Navigation Tree. Note that annotating a sample with characterizations includes submitting the source of the characterization, the instrument used to perform the characterization, where appropriate, an relevant protocol, the characterization information itself, and applicable information in the form of uploaded files. 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).

Once you open a sample, you can use links in the Navigation Tree in the left sidebar to ascertain if the sample has annotations.

• When logged in as a Curator, click the Composition, Characterization, and Publication links to view associated data, if it has been added.
• If you are not logged in or do have curator visibility, links in the Navigation Pane for which there are no annotations appear in italics.

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Submitting a Sample

To enter general information about a sample

1. Click the Samples caNanoLab menu option. On the Manage Samples page, click the Submit a New Sample link. This opens the Submit a New Sample form.

   Tip

   Some fields may contain the [Other] option. Click Other to enter an alternative to the selections listed. At that point, your entry is enclosed in [new entry] brackets, indicating that your entry is temporary. Once you click Submit (or Update), your entry is persisted and the brackets disappear.

2. The following table lists and describes the fields on the Submit Sample page. Select or enter the appropriate information. Asterisks indicate required fields.

   Name	Definition
   Sample Name*	Enter a sample name of your choice.
   Point of Contact*	The Point of Contact Add button is not available unless you entered a Sample Name. To add a point of contact, click Add. The Point of Contact Information dialog box opens. 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.

   To clear the entries and start again, click Reset.

3. When you finish defining the sample, click Submit. A message appears verifying the submission.

   Availability metrics

   Once you successfully submit a sample to the database, you or the data curator can generate a data availability matrix for the sample. For more information, see Data Availability Metrics.

   The Navigation Tree opens in the left-hand panel of the browser, where you can initiate adding composition, characterization, and publication data for the sample you submitted.

   

   My Workspace

   Once you submit a sample, it is listed on the My Workspace page where you can manage all your submitted samples, and view any samples that a user has shared with you. For more information, see Using My Workspace.

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Editing a Sample

You can edit a sample using the following techniques:

• Copying an Existing Sample
• Updating a Sample
• Sharing and Changing Access to a Sample
• Adding Publications to a Sample
• Deleting a Sample

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Copying an Existing Sample

Copying an existing sample enables you to use an existing sample and its features and annotations to facilitate creating a new sample.

To copy an existing sample

1. Click the Samples menu option. On the Manage Samples page, click the Copy an Existing Sample link.
2. In the Copy Sample page, enter the name (complete for an exact search or partial to search for sample names that contain the entered text) of the sample to be copied. Both fields on this page are required.
   
   • Click the Search icon ( ) to search the caNanoLab database for the sample. If you entered partial text, you must complete this search before you can execute the copy request. Select from the search results the sample you want to copy.
   • If you skip the Search icon (having entered exact text), the system searches the database anyway for the sample whose name you entered.
3. Enter a name for the copied sample and click Submit. Click Reset to clear all fields and begin again.

caNanoLab opens the Update Sample page for the copied sample, entitled with the new name you assigned. You can edit the copied sample as appropriate. For more information, see Updating a Sample.

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Updating a Sample

The Update Sample page appears when you copy an existing sample or perform a search and click the Edit link in the first column of the the Sample Search Results page. This page also opens when you, as a curator, choose to edit a sample while you are reviewing data prior to public release. On this page, only after login and with appropriate permissions, you can edit the sample information.

The following table lists and describes each field. Asterisks indicate a required information. 

Click the Composition and Characterization links to view associated data, if it has been added. You can edit these categories, as described in  Managing Sample Composition Annotations and Managing Sample Characterizations.

Click Update at the bottom of the page when you are done. To disregard the changes, click Reset.

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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 option, you can associate multiple samples with a publication. See  Publications Overview for more information
2. If you add documents from within an open sample, you can use the copy feature to associate the document with other samples. See Submitting a Publication for more information.

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Sharing and Changing Access to a Sample

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Deleting a Sample

To delete a sample, perform a sample search, find the sample to be deleted, and click Edit =in the first column of the the Sample Search Results page. The Update Sample page opens. This page also opens when you, as a curator, choose to edit a sample while you are reviewing data prior to public release. From the Update Sample page, click Delete in the lower-left corner of the window. Confirm the deletion.

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Data Availability Metrics

Once you successfully submit 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 (see step #5 below).

To generate or review a data availability metrics

1. Perform a search for an existing sample that you submitted. If you are a curator, you do not have to submit the sample to generate the metrics. See Searching Existing Samples.

2. If data availability is generated for a sample, you will see its matmetricsrix summary in the Data Availability column of the Search Results list. Click the link for the availability results in the column to view them in their entirety.

   If you open the data availability metrics in this manner, you can only review the metrics. To edit it, proceed with step 3.

   If you open the data availability metrics in this manner, you can only review the metrics. To edit it, proceed with step 3.

3. To generate an editable availability metrics for a sample, on the search results page, click Edit corresponding to the sample.
4. At the bottom of the sample details page that opens, click Generate corresponding to Data Availability Metrics.
5. The metrics table displays high-level medidata for minimal care. Three columns are shown:
   
   • 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] – Check marks indicate the data element annotations added to the sample.
6. The top of the table displays two percentages based on the total and actual number of attributes available for the sample:
   • The total possible number of caNanoLab characteristics is 30. The sample may have 23 out of 30 filled in. A percentage is calculated from 23 out of 30.
   • The total possible number of MinChar characteristics is 9. The sample may have 4 out of 9 filled in. A percentage is calculated from 4 out of 9.
   Click Delete to delete the metrics for this sample.
   Click Cancel to close the data availability section of the Update Sample page.
7. Click Update 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. This search feature is accessible even to users for whom other search features are restricted.

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

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Launching a Basic Search

To launch a basic search for a sample

1. There are three ways to access the basic sample search: From the home page Browse caNanoLab panel, or if you are logged in, click the Workflow menu option and Search Samples icon, or just click the Samples menu option.
   The Manage Samples page displays.

2. Click Search Existing Samples in the Sample Links panel.

   The following table lists and describes each field. Enter text or select options as appropriate.

   "Other" option

   Some fields may contain the [Other] option. Click Other to enter an alternative to the selections listed. At that point, your entry is enclosed in [new entry] brackets, indicating that your entry is temporary. Once you click Submit (or Update), your entry is persisted and the brackets disappear.

   When defining search criteria, there are no required fields. You can add only those parameters that you consider essential to the search.

   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] 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.

    

   To clear all fields and start again, click Reset.

3. To execute the search, click Search.

   No parameters?

   If you click the Search button having defined no parameters, all of the caNanoLab samples appear in the search results.

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

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Launching an Advanced Search

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

To launch an advanced search of the samples in the caNanoLab database

1. There are two ways to access the advanced sample search: Click the Workflow menu option and Search Samples icon, or just click the Samples menu option
   The Manage Samples page displays.

   Click Advanced Sample Search in the Sample Links panel.

   The following table lists and describes each field. Enter text or select options as appropriate.

   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.

2. 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. Click Reset to clear the fields.
3. 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.
4. 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.
5. To clear all fields and start again, click the Reset button.
6. To execute the search, click the Search button.
   

   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 added or characterization or data files uploaded. Sample Search Results display in the browser window in table format. Column headings are appropriate for the sample for which you searched. They are described in the following table. Columns are sortable by clicking the column headings.

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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Adding 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. Find the sample that you want to bookmark and click Add to Favorites in the first column of the Sample Search Results row.
   The Added to Favorites message appears in the results row.
3. Click the +Add to Favorites option in the menu bar, and the bookmarked sample will be listed under My Samples.

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