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 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.
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, 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.
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Creating a Sample
Making an item public
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.
Click Save.
My Workspace
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, the Update Sample page opens. With the appropriate security permissions you can
Update the sample information.
- Share a sample and make it public
Generate a data availability metrics for the sample.
Annotate the sample from the Navigation Tree.
Updating a Sample
The Update Sample page enables you to update sample information, update access to the sample, and generate data availability access.
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. If you do not add access If you do not add access, this item remains private and only you, the owner, can view and/or modify it. |
Data Availability Metrics | For more information see Generating Data Availability Metrics. |
Click Update at the bottom of the page when you are done. To disregard the changes, click Reset.
Sharing a Sample with a User or Group
Making a Sample Public
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.
Curators and batch metrics
A data curator can generate data availablility metrics in batch mode for samples as well.
Reviewing the Metrics for an Individual Sample
To review a data availability metrics for an individual sample
- Perform a sample search.
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.
Re/Generating a Metrics for an Individual Sample
To delete or regenerate availability metrics for a sample
Updating a public sample
- From the sample search results, click Edit in the Actions column.
- Update Sample opens and the Data Availability Metrics section is at the bottom.
- If there is no metrics generated for the sample, click Generate.
- If a metrics was previously generated, click Edit as shown in the screen above.
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. - The following buttons are at the bottom of the metrics.
- Click Delete to delete the metrics for this sample.
- Click Close to return to Update Sample without changing the metrics.
Click Regenerate to regenerate the metrics.
Searching Existing Samples
If you are not logged in or are browsing caNanoLab
If you are not logged into caNanoLab and perform a search or you are browsing caNanoLab from the public home page, only publicly-accessible items will be returned in the search results. This also applies to Performing a caNanoLab Keyword Search.
A sample search looks for a sample based on added annotations or uploaded characterization or data files.
- To continue with a basic search, see Performing a Basic Search.
- To launch an advanced search, see Performing an Advanced Search.
Performing a Basic Sample 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.
Leaving all search criteria blank
There are no required fields when you specify search criteria. If you leave all the fields blank, all items are returned.
The following table lists and describes each field. Enter text or select options as appropriate.
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 scroll list the functionalizing category to which the sample targeted by the search belongs.*Select from the drop-down list the function type category which best fits the sample targeted by the search:
- Imaging Function
- [Other]
To enter an alternative to an option, select other if available and enter a value. The value is added to the list of options.
- 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:
In Vitro Characterizations:
- Blood Contact
- Cytotoxicity
- Enzyme Induction
- Immune Cell Function
- Oxidative Stress
- Sterility
- Targeting
- Transfection
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.
Performing an Advanced Sample 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
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.- 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.
- 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.
- 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.
- To execute the search, click Search.
For information about the search results, see Sample Search Results.
Sample Search Results
No parameters?
A sample search looks for a sample based on annotations that added or characterization or data files uploaded. 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.
Note
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 the 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. Note: Edit is only available for people that have an account and are logged into the system and are associated with the 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. Note If the Sample is already added as a Favorite, clicking + Add to Favorites displays the <sample name> has already been added to your favorites message. |
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.
Additional Sample Tasks
You can edit a sample using the following techniques.
Updating data after it is Public
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
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
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
- Click the Samples menu option. On the Manage Samples page, click the Copy an Existing Sample link.
- 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.
- 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.
Adding Publications to a Sample
Publications can be associated with a sample using two caNanoLab features:
- If you work from the Publications menu, you can associate multiple samples with a publication. See Creating a Publication for more information.
- If you add documents from within an open sample, you can use the copy feature to associate the publication with other samples. See Managing Publications from an Open Sample for more information.
Deleting a Sample
Note
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.
Bookmarking 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
- Perform a sample search.
- 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. - Click the +Add to Favorites option in the menu bar, and the bookmarked sample will be listed under My Samples.