This section describes how to manage samples in caNanoLab with the Samples function. This section includes the following topics:
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
You can also perform the following functions with a sample.
If you are a curator with appropriate security permissions, you can annotate samples. For more information, see Managing Sample Composition Annotations, Managing Sample Characterizations, and Managing Publications in caNanoLab. |
Annotating a sample is the process of adding biological or related data to nanoparticle entities. In caNanoLab, it involves selecting the sample to annotate, saving 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, a 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 save and open a sample, if you are a curator, you can use links in the Navigation Tree to review and add annotations. The flow chart shows how annotations are organized.
To enter general information about a sample
Click the Samples caNanoLab menu option. On the Manage Samples page, click the Create a New Sample link. This opens the Create Sample form.
The following table lists and describes the fields on the Create 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 Save.
The sample is listed on the My Workspace page where you can manage all of your submitted sample, and view any samples that a user has shared with you. |
Once you save the sample, with the appropriate security permissions you can
Generate a data availability metrics for the sample.
Annotate the sample from the Navigation Tree.
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.
You can also perform a keyword search using the Search box in the upper-right of the caNanoLab window to search across protocols, samples, and publications. |
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 clear all fields and start again, click Reset.
To execute the search, click Search.
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 + Add to Favorites to add a bookmark for the sample on your My Favorites page. Added to Favorites 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 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.
You can edit a sample using the following techniques.
Once data is made Public, you can update the data, but it will be retracted from Public and you will need to resubmit it to the curator again for review. |
Copying an existing sample enables you to use an existing sample and its features and annotations to facilitate creating a new sample.
Copying a sample copies all of the annotation and/or publications, making it easier to create and submit similar samples. |
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.
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 releas
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 a Sample with a User or Group or Making the Sample Public. | |
Data Availability Metrics | Click Generate to create the Data Availability Metrics table.
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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 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.
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.
A data curator can generate data availablility metrics in batch mode for samples as well. |
To review a data availability metrics for an individual sample
From the sample search results, if data availability 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.
To delete or regenerate availability metrics for a sample
If you generate data availability metrics after a sample is made public, the updated metrics will not be included in the public version. You will have to submit the sample for review again. |
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. |
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. |
Click Regenerate to regenerate the metrics.
My Favorites displays samples, protocols, and publications that you bookmark for quick access.
To add a sample to My Favorites