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Managing Protocols in caNanoLab | caNanoLab User's Guide| Managing Sample Composition Annotations
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This section describes how to manage samples in caNanoLab with the Samples function. This section includes the following topics:
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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.
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Click the Samples caNanoLab menu option. On the Manage Samples page, click the Submit a New Sample link. This opens the Submit a New Sample form.
Info title Tip 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.
Info title Availability metrics 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.
Info title My Workspace 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.
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The following table lists and describes each field. Asterisks indicate a required information.
| General Information Characterization Fields | Definition | |||||
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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.
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- Perform a search for an existing sample that you submitted. If you are a curator, you do not have to submit the sample to generate the metrics. See Searching Existing Samples.
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.
Info 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.
- To generate an editable availability metrics for a sample, on the search results page, click Edit corresponding to the sample.
- At the bottom of the sample details page that opens, click Generate corresponding to Data Availability Metrics.
- The metrics table displays high-level medidata for minimal care. Three columns are shown:
- 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
.Multiexcerpt include MultiExcerptName ExitDisclaimer nopanel true MultiExcerptName ExitDisclaimer PageWithExcerpt wikicontent:Exit Disclaimer to Include - [Name of sample] – Check marks indicate the data element annotations added to the sample.
- The top of the table displays two percentages based on the total and actual number of attributes available for the sample:
- The total possible number of caNanoLab characteristics is 30. The sample may have 23 out of 30 filled in. A percentage is calculated from 23 out of 30.
- The total possible number of MinChar characteristics is 9. The sample may have 4 out of 9 filled in. A percentage is calculated from 4 out of 9.
Click Cancel to close the data availability section of the Update Sample page. - Click Update to regenerate the metrics.
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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.
Info title "Other" option 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 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:
*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.
Info title No parameters? Include Page No parameter search No parameter search For information about the search results, see Sample Search Results.
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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. Click Reset to clear the fields.
- 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 clear all fields and start again, click the Reset button.
- To execute the search, click the Search button.
For information about the search results, see Sample Search Results.
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The following table lists and describes the Search Results columns.
| Sample Search Results Columns | Description | ||||||||||
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| 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.
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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.
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- 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.
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