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This section describes how to manage samples in caNanoLab with the Samples function. This section includes the following topics:
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 Sample 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.
Once you submit a sample, the sample is added to My Workspace for quick access. |
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.
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 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. |
These are important items to consider when submitting and making data Public:
Only users with Data Curator permissions can annotate a sample. For more information, see What Options You See and Why. You can access this page after logging into caNanoLab, or you can access publicly-available sample information from the Login page. |
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.
To enter general information about a sample
Click the Samples caNanoLab menu option. On the Manage Samples Home page, click the Submit a New Sample link. This opens the Submit a New Sample form.
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. |
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.
When you finish defining the sample, click Submit. A message appears verifying the submission.
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.
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. |
You can edit a sample using the following techniques:
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
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.
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.
General Information Characterization Fields | Definition | |
---|---|---|
Sample Name* | The name assigned to the sample. | |
Point of Contact* | The site that is the source of the sample. 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 and Changing Access to a Sample. | |
Data Availability Metrics | Click Generate to create the Data Availability Metrics table. For more information, see Data Availability Metrics.
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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.
If you are not logged in or do have curator visibility, links in the Navigation Tree for which there are no annotations appear in italics. |
Publications can be associated with a sample using two caNanoLab features:
This action deletes the sample from the caNanoLab database, executed behind the scenes at a scheduled time. |
To delete a sample, perform a sample search, find the sample to be deleted, and click the Edit link 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 the Delete button in the lower-left corner of the window. Confirm the deletion.
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
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.
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.
This section describes the basic and advanced sample search. You can also perform a keyword search using the Search box in the upper-right of the caNanoLab window. This option searches across protocols, samples, and publications. For more information, see Performing a caNanoLab Keyword Search. |
To launch a basic search for a sample
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.
Click Search Existing Samples in the Sample Links panel.
The following table lists and describes each field. Enter text or select options as appropriate.
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 | 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 drop-down list 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 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: In Vitro Characterizations:
In Vivo Characterizations: *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 execute the search, click the Search button.
To clear all fields and start again, click the Reset button.
For information about the search results, see Sample Search Results.
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
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. |
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). |
For information about the search results, see 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 number of items located in the search display appears in the the upper-left of the search results table. The bottom right of the search results table enables you to navigate to pages. To return to the Search page, click the Back ( ) button not the Browser button. |
The following table lists and describes the Search Results columns.
Sample Search Results Columns | Description | ||
---|---|---|---|
Action | Click View in the first column to display the sample on the Updating a Sample.
Click the + Add to Favorites link to add a bookmark for the sample on your My Favorites tab. Added to Favorites appears in the column when the sample is successfully added.
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Sample Name | The fully-qualified name of the sample located in the search. | ||
Primary Point of Contact | The name of the source of the original sample. | ||
Composition | The term for the sample composition. Examples: antibody; dendrimer. | ||
Functions | A list of one or more terms displaying functions entered for the corresponding sample ID. Example: targeting | ||
Characterizations | A list displaying characterization annotations entered for the corresponding sample ID. Example: oxidative stress | ||
Data Availability | 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. | ||
Created Date | Indicates the date on which the sample was added. |
For information about configuring a sample search, see Searching Existing Samples.
My Favorites displays samples, protocols, and publications that you bookmark for quick access.
To add a sample to My Favorites
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