This section describes how to manage samples in caNanoLab with the Samples function. Topics in this chapter include:
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 the appropriate security permissions for a sample, you can annotate the 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.
Annotating a sample in caNanoLab involves
Entering sample characterizations (physico-chemical, in vitro and in vivo), including 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.
To enter general information about a sample
Click the Samples menu.
The Manage Samples page displays.
Click Create a New Sample.
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. |
Click Save.
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. |
Once you save the sample, the Update Sample page opens. With the appropriate security permissions you can
Update the sample information.
Generate a data availability metrics for the sample.
Annotate the sample from the Navigation Tree.
The Update Sample page enables you to update sample information, update access to the sample, and generate data availability access.
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. |
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. |
Data Availability Metrics | For more information see 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.
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 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.
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.
A sample search looks for a sample based on added annotations or uploaded characterization or data files.
To launch a basic search for a sample
Click the Samples menu.
The Manage Samples page displays.
Click Search Existing Samples.
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 | 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. |
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
Click the Samples menu.
The Manage Samples page displays.
Click Advanced Sample Search.
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. |
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 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.
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 copies all of the annotation and/or publications, making it easier to create and submit similar samples.
To copy an existing sample
Publications can be associated with a sample using two caNanoLab features.
Delete removes the sample from the caNanoLab database, executed behind the scenes at a scheduled time. |
To delete a sample
My Favorites displays samples, protocols, and publications that you bookmark for quick access.
To add a sample to My Favorites