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Managing Protocols in caNanoLab | caNanoLab User's GuideManaging Sample Composition Annotations

Making an item public

Once you log into caNanoLab, you can create and save samples, publications, and protocols to caNanoLab and modify access to an item. If you are a curator, you can also make the saved item publicly-accessible. If you are not a curator, you must submit the item to a curator for review and approval for public release.

This section describes how to manage samples in caNanoLab with the Samples function. Topics in this chapter include:

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.

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Annotating a Sample

Access to annotate 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.

Italic Links

If you are not logged in or do not have curator visibility, the Navigation Tree links appear in italics if no annotations are associated with the open sample.

NAVIGATION TREE
GENERAL INFO
COMPOSITION
CHARACTERIZATION
PUBLICATION
  • General Info displays after you click the sample name and shows the Update Sample page.
  • Composition defines Nanomaterial Entity, Functionalizing Entity, and Chemical Associations.
  • Characterization defines essential physical characteristics that identify the material and structural properties via the Protocol and Physico-Chemical, In Vivo, and In Vitro Characterization.
  • Publication displays articles, books chapters, reviews and reports already added to a sample.

The following workflow shows how the annotations are organized in caNanoLab.

  • Nanomaterial Sample
    • Composition
      • Nanomaterial Entity
      • Functionalizing Entity
      • Chemical Associations
    • Characterization
      • Protocol
      • Physico-Chemical Characterization
      • In Vitro Characterization
      • In Vivo Characterization
    • Publication

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Creating a Sample

To enter general information about a sample

  1. Click the Samples menu.

    The Manage Samples page displays.

  2. Click Create a New Sample.

  3. On the Create Sample page, fill in the following information as needed.

    NameDefinition

    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.

    1. Select an Organization Name from the list or select Other and add one.
    2. Select a Role in the same manner.
    3. Fill in the address, name, phone number, and email. Click Cancel or click Save to return and the POC is added.
    4. To edit a point of contact, click Edit next to the POC, update the information, and click Save.
  4. Click Save.

    My Workspace

    After saving, the sample is listed on the My Workspace where you can manage all of your submitted samples, and view any samples that a user has shared with you.
  5. Once you save the sample, the Update Sample page opens. With the appropriate security permissions you can

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Updating a Sample

The Update Sample page enables you to update sample information, update access to the sample, and generate data availability access.

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.

  1. Fill in the following information as needed.

    To export sample information, see Exporting Sample Information to JSON or XML.
    General Information Characterization FieldsDefinition

    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.

    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.

  2. Click Update when you are done editing the sample.

    You can also Copy and Delete the sample from the Update Sample page.


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Sharing a Sample with a User or Group

The following sections describe how to share an item with a user or collaboration group. To make it available to the public, you must be a curator OR submit it for review first.

Specifying User or Group Access

To share with a user or collaboration group

  1. From a Create or Update page, the Access to the panel lists who initially has access to the item based on your user role.
    1. As a Public user, you have access, along with any Researcher or Curator.
    2. As a Researcher, you have access, along with any Curator.
    3. As a Curator, you and any Curator has access.
  2. To modify the default access, click Add next to Access to the..., and the Access Information panel opens.
    Access to the panel user role access
  3. Click Collaboration Group and enter part or all of the Collaboration Group Name.
    or
    Click User and enter part or all of the User Login Name.
  4. Click Search.
  5. Select an item from the drop-down list to populate the name.
    Access by dialog box
  6. From the Access to the... list, specify READ (only) or READ WRITE DELETE access.

    Public Access to

    If you are a curator and select Public, Access to is pre-populated with READ (only) and cannot be changed.

     

  7. Click Save in the green panel.
    The Access panel is updated, and the item is added to My Workspace with the status, In Draft until the information is completely entered.

Editing and Removing Access

To edit the access, from a Create or Update page, in the Access to panel, click Edit next to the access entry, make changes to the access, and click Save. The Access panel is updated.

Access to Panel click Edit

To delete a listing, from the Create or Update page, click Edit next to the access entry. From the Access Information dialog box, click Remove and confirm the deletion. The Access panel is updated.

Remove Access

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Making a Sample Public

Submitting a Database Item for Review

If you are not a curator and want to make your sample, publication, or protocol, publicly-accessible, you must submit it for review once it is saved to the caNanoLab database.

  1. At the bottom of the Create or Update page, click Submit for Review.

    Submit for Review button

    The status of the database item on your My Workspace page changes to Pending.

    Once a curator reviews the item and is satisfied, the curator will change the access to Public. 

  2. The status of the database item on your My Workspace page will then change to Public.

    Updating a Public item

    If you update an item after it is Public, you must submit the item for review again for the changes to be reflected in the Public version.

Making a Database Item Publicly-Accessible (Curator Only)

To make an item public, you must be a curator and access the Curation menu. For more information, see  Review Data Pending Release.

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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

  1. Perform a sample search.
  2. From the sample search results, if a data availability metrics is generated for a sample, click the link in the Data Availability column

    Data Availability Metrics link in Sample Search Results

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

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.
  1. Perform a sample search.
  2. From the sample search results, click Edit in the Actions column.
  3. Update Sample opens and the Data Availability Metrics section is at the bottom.
    Data Metrics Availability section of Update Sample
    1. If there is no metrics generated for the sample, click Generate.
    2. If a metrics was previously generated, click Edit as shown in the screen above.
    The metrics table displays high-level medidata for minimal care. 
    Data Metrics Availability section of Update Sample
  4. Using examples, the following table describes the percentages at the top of the metrics.

    Percentages at the Top of the MetricsDescription
    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.
  5. The following table describes each column on the metrics.

    Columns in the MetricsDescription
    caNanoLabLists 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.
  6. The following buttons are at the bottom of the metrics.
    caNanoLab Data Metrics Buttons
    1. Click Delete to delete the metrics for this sample.
    2. Click Close to return to Update Sample without changing the metrics.
    3. Click Regenerate to regenerate the metrics.

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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 a keyword search as well.

sample search looks for a sample based on added annotations or uploaded characterization or data files.

  1. To continue with a basic search, see Performing a Basic Search.
  2. To launch an advanced search, see Performing an Advanced Search.

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Performing a Basic Sample Search

To launch a basic search for a sample

  1. Click the Samples menu.
    The Manage Samples page displays.

  2. 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.

  3. From the Sample Search page, fill in the following search criteria as needed. 

    Sample Search OptionsDescription

    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

    Nanomaterial Entity

    Select from the list the nanoparticle category to which the nanomaterial entity targeted by the search belongs. Example: Dendrimer

    Functionalizing Entity
    Select the functionalizing category to which the sample targeted by the search belongs.*Select 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 list on the left and select the characterization type that applies to the sample to be searched: Physico-Chemical, In Vitro, In Vivo, Ex Vivo, or Other Ex VV.

    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.)*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.

  4. Click Search.

    For information about the search results, see Sample Search Results.

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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

  1. Click the Samples menu.
    The Manage Samples page displays.

  2. Click Advanced Sample Search.

    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.

  3. From the Sample Search page, fill in the search criteria as needed.

    Advanced Search CategoryDescription

    Sample Criteria

    Select an option in the first list. Select from the second list, 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 list. Your selection drives the options that display in the second list, as well as the options or text box that displays for the rest of the category. Select from the second list, 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 list. Your selection drives the options that display in the second list 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 list. An optional list for units displays only if the data has a unit. Select your options or enter appropriate text in the text box(es).

  4. 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.
  5. 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.
  6. 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.
  7. Click Search.

    For information about the search results, see Sample Search Results.

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Sample Search Results

No parameters?

If you click the Search button having defined no parameters, all of the caNanoLab samples will display in the search results.

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.

Do not use your browser button

Click Back ( caNanoLab Back button ) to return to the previous page. Do not use the browser's back button.

The following table lists and describes the Search Results columns.

To export sample information, see Exporting Sample Information to JSON or XML.
Sample Search Results ColumnsDescription
Action

Click View in the first column to display the sample on the Updating a Sample page.

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 DateIndicates the date on which the sample was added.

For information about configuring a sample search, see Searching Existing Samples.

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Additional Sample Tasks

The following table lists how to edit a sample with 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.

TaskHow to

Copying an Existing Sample

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

  1. Click the Samples menu.
    The Manage Samples page displays.
  2. Click Copy an Existing Sample.
    On the Copy Sample page, both fields are required.
  3. In Existing Sample, fill in a complete or partial sample to search for and click the Search icon.
  4. Select a sample from the returned list to be copied.
  5. Fill in the New Sample Name.
  6. Click Submit.
    A filled in Update Sample page appears with the new sample name.
  7. Edit the copied sample as needed.
  8. Click Update.

Adding Publications to a Sample

Publications can be associated with a sample using two caNanoLab features.

  1. If you work from the Publications menu, you can associate multiple samples with a publication. See Creating a Publication for more information. 
  2. 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

Delete removes the sample from the caNanoLab database, executed behind the scenes at a scheduled time.

To delete a sample

  1. Perform a sample search.
  2. On the search results page, click Edit in the Actions column.
  3. From the Update Sample page, click Delete.
  4. Confirm the deletion.

Exporting Sample Information to JSON or XML

To export an individual sample's information or all the samples listed in the search results to JSON or XML, click Export (JSON) or Export (XML).

Export to JSON or HTML

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

  1. Perform a sample search.
  2. On the search results page, click + Add to Favorites in the Actions column.
    The Added to Favorites message appears in the results row.
  3. Click the My Favorites, and the bookmarked sample is listed under My Samples.

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Managing Protocols in caNanoLab | caNanoLab User's GuideManaging Sample Composition Annotations
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