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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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Add Faves from Sample pages??
Samples Overview
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.
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- Submit a New Sample – This takes you to a form for creating a sample in the caNanoLab database. For more information, see 3 - Managing Samples in caNanoLab 2.1 DRAFT Submitting a Sample.
- Copy an Existing Sample – This enables you to copy a sample with all its annotation and/or publications, making it easier to create and submit similar samples. For more information, see Copying an Exisiting Sample.
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. Searching Existing Samples.
Info title Tip 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.
Advanced Sample Search – This takes you to a page where you can build search criteria based on data values or ranges. For more information, see 3 - Managing Samples in caNanoLab 2.1 DRAFT. Launching an Advanced Search.
Info title Keyword Search You can perform a keyword search using the Search box in the upper-right of the caNanoLab window. This option searches across protocols, samples, and publications. For more information see, Getting Started.
Submitting Data
These are important items to consider when submitting and making data Public:
- Any user who logs into the system can submit data; however, only the Curator can make the data public.
- The user can also assign different accesses to the data but can NOT assign the data to Public unless the user is a curator. The user can submit the data to the curator for review (clicking on the Submit for Review button), and the curator decides whether to assign the data to Public.
- Once the data is assigned to Public by the curator, if the user decides to update the data later, the data would be retracted from Public and need to be resubmitted to the Curator again for review.
Annotating a Sample
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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. |
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- When logged in as a Curator, click the Composition and Characterization links to view associated data, if it has been added.
- 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.
Submitting a Sample
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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 Updating a Sample. |
To enter general information about a sample:
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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 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.
Editing a Sample
You can edit a sample using the following techniques:
- Copying an Existing Sample
- Updating a Sample
- Changing Group Access to the Sample
- Adding Publications to a Sample
- Deleting a Sample
- 3 - Managing Samples in caNanoLab 2.1 DRAFT
- 3 - Managing Samples in caNanoLab 2.1 DRAFT
- 3 - Managing Samples in caNanoLab 2.1 DRAFT
- 3 - Managing Samples in caNanoLab 2.1 DRAFT
- 3 - Managing Samples in caNanoLab 2.1 DRAFT
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.
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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 Updating a Sample.
Updating a Sample
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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 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 release. On this page, only after login and with appropriate permissions, you can edit the sample information.
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General Information Characterization Fields | Definition |
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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 Changing Group Access to the Sample. |
Data Availability Metrics | Click Generate to create the Data Availability Metrics table, as described in . |
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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. |
Adding Publications to a Sample
Publications can be associated with a sample using two caNanoLab features:
- If you work from the Publications menu option, you can associate multiple samples with a publication. See Publications Overview for more information
- If you add documents from within an open sample, you can use the copy feature to associate the document with other samples. See Submitting a Publication for more information.
Sharing and Changing Access to a Sample
Is this option limited to curator's only?
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Deleting a Sample
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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 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 the Delete button in the lower-left corner of the window. Confirm the deletion.
Data Availability Metrics
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).
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- Perform a search for an existing sample that you submitted. If you are a curator, you needn't have submitted the sample to generate the metrics. See 3 - Managing Samples in caNanoLab 2.1 DRAFT. Searching Existing Samples.
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.
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 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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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.
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- From the Welcome to caNanoLab login page , you can browse publicly available nanotechnology samples before logging in. Click the Search Samples hypertext link,
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Having logged in, on the Welcome to caNanoLab home page, in the workflow diagram, click Search Samples. On the Manage Sample Homepage, click the Search Existing Samples link. This opens the Basic Sample Search form.
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Click the Samples caNanoLab menu option. On the Manage Sample Homepage, click the Search Existing Samples link. This opens the Basic Sample Search form. - To continue with a basic search, see 3 - Managing Samples in caNanoLab 2.1 DRAFT. Launching a Basic Search.
- To launch an advanced search, on the Manage Samples page, click Advanced Sample Search or on a Basic Sample Search form, click the Advanced Search hypertext link in the upper right of the page. For more details, see 3 - Managing Samples in caNanoLab 2.1 DRAFT Launching an Advanced Search.
Launching a Basic Search
To launch a basic search for a sample:
Continue from step 2 described in 3 - Managing Samples in caNanoLab 2.1 DRAFT. Searching Existing Samples.
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 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.
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 execute the search, click the Search button.
Info title No parameters? Include Page No parameter search No parameter search
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. Sample Search Results.
Launching an Advanced Search
An advanced search allows you to build search criteria based on data values or ranges.
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On the Basic Sample Search page, opened as described in 3 - Managing Samples in caNanoLab 2.1 DRAFT Searching Existing Samples, 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.
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.
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.
Sample Search Results
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Sample Search Results Columns | Description | ||||||||||
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Action | Click View in the first column to display the sample on the 3 - Managing Samples in caNanoLab 2.1 DRAFT Updating a Sample.
Click the + Add to Favorites link to add a bookmark for the sample on your My Favorites tab. 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 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. Data Availability Metrics. | ||||||||||
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. Searching Existing Samples.
Adding a Sample to My Favorites
My Favorites displays samples, protocols, and publications that you bookmark for quick access.
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- Perform a sample search.
- Find the sample that you want to bookmark and click the Add to Favorites link in the first column of the 3 - Managing Samples in caNanoLab 2.1 DRAFT 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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