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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 Home 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.
The Sample Links panel on the Manage Sample Home page provides the following options:
Search Existing Samples – This takes you to a form for launching a search for an existing sample. For more information, see 3 - Managing Samples in caNanoLab 2.1 DRAFT.
From the Search Results table, you can add a sample to the My Favorites page. This is like bookmarking a sample that you want to which you want to have 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 Permissions and Visibility. 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.
This help topic opens from the Update Sample page, as well as from the Submit Sample page. For more information about the Update Sample page, see 3 - Managing Samples in caNanoLab 2.1 DRAFT. |
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.
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 3 - Managing Samples in caNanoLab 2.1 DRAFT. |
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.
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 3 - Managing Samples in caNanoLab 2.1 DRAFT.
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 3 - Managing Samples in caNanoLab 2.1 DRAFT 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. An asterisk indicates a required field.
General Information Characterization Fields | Definition |
---|---|
Sample Name* | The name assigned to the sample. |
Point of Contact* | The site that is 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 3 - Managing Samples in caNanoLab 2.1 DRAFT. |
Data Availability Metrics | Click Generate to create the Data Availability Metrics table, as described in . |
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 Pane for which there are no annotations appear in italics. |
Publications can be associated with a sample using two caNanoLab features:
Is this option limited to curator's only?
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 3 - Managing Samples in caNanoLab 2.1 DRAFT 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 has already been 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 annotations that have been added or characterization or data files that have been uploaded. This search feature is accessible even to users for whom other search features are restricted.
You can launch either a basic or an advanced sample search. |
To begin either a basic search or an advanced search for a specific sample:
To launch a basic search for a sample:
Continue from step 2 described in 3 - Managing Samples in caNanoLab 2.1 DRAFT.
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 from the drop-down list on the left, 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. 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 search results, see 3 - Managing Samples in caNanoLab 2.1 DRAFT.
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:
On the Basic Sample Search page, opened as described in 3 - Managing Samples in caNanoLab 2.1 DRAFT, click the Advanced Search link in the upper right corner of the page.
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. Note: 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). |
The samples that fulfill the search criteria are listed as sample name hyperlinks. Click the hyperlink to view the sample. For more information, see Viewing a Sample.
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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 Edit in the first column to display the sample on the 3 - Managing Samples in caNanoLab 2.1 DRAFT.
Click the Add to Favorites link to add a bookmark for the sample on your My Favorites tab. Success appears in the column when the sample is successfully added.
| ||
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 that have been entered for the corresponding sample ID. Example: targeting | ||
Characterizations | A list displaying characterization annotations that have been entered for the corresponding sample ID. Example: oxidative stress | ||
Data Availability | Indicates data availability has been generated for the sample. Click the availability summary to view an availability details page. If N/A is in the column, See also 3 - Managing Samples in caNanoLab 2.1 DRAFT. | ||
Created Date | Indicates the date on which the sample was added. |
For information about configuring a sample search, see 3 - Managing Samples in caNanoLab 2.1 DRAFT.
My Favorites displays samples, protocols, and publications that you bookmark for quick access.
To add a sample to My Favorites
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