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Managing Sample Characterizations | caNanoLab User's GuideManaging Collaboration Groups

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 caNanoLab features associated with caNanoLab's publication features. Topics discussed in this section include:

Publications Overview

When you click the Publications menu, from Manage Publications you can

You can also perform the following functions with a protocol.

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Creating a Publication

Create Publication allows you to identify a publication and associate it with one or more samples.

To create a sample publication

  1. Click Publications.
  2. Manage Publications displays.
  3. Click Create a New Publication.
    1. To add a publication to an open sample, search for a sample, click Edit in the search results,  Publication in the Navigation Tree, and continue to step 2.

      NAVIGATION TREE
      GENERAL INFO
      COMPOSITION
      CHARACTERIZATION
      PUBLICATION
  4. Click Add which corresponds to the appropriate publication type.
  5. Fill in the following information. Fields may change, depending upon your launching point and your selection of Publication Type. 

    To enter an alternative to an option, select other if available and enter a value. The value is added to the list of options.

    Sample Publication CriteriaDescription

    Publication Type*

    Select (or review) the type of publication from the drop-down list. Pre-selected if starting from within a sample.

    Publication Status*
    If appropriate, from the drop-down list, select the appropriate status. Or if appropriate, simply review the status.

    Title*

    Enter the title. (See PubMed ID description for how to auto-populate this field)

    Year of PublicationEnter the year that the publication was published.

    Authors

    To add an author to the publication, click Add. On the pop-up, enter a First Name, Last Name, and Initials of the author. Click Cancel or click Save to save the author to the Publication. 

    To edit an author, click Edit, make changes to the name, and click Save. The changes are saved.

    To remove an author, from Submit Publication, click Edit next to the author's name, and click Remove on the pop-up. 

    Keywords

    Enter a term that can be used in a search query to find the publication. Enter one keyword on each line.

    Description

    Enter the description for the publication.

    Research Category
    Check (or review) the Research Category relevant to the publication.

    Upload
    or
    Enter File URL

    Click Browse to navigate to the publication to be associated with the sample, or enter the URL where the publication is located.

    Sample Name

    There are two options to add samples to a publication:

    Enter one sample name per line in the Sample Name box.

    OR

    Click Search Samples and a list of samples appears in a list box. Click a sample name or Ctrl-click or Shift-click to select more than one. Click Select, and the selected samples are added to the Sample Name box.

    Access to the PublicationFor more information, see Sharing a Publication with a User or Group or Making the Publication Public.
  6. Once you enter the appropriate information on the form, click Save.

    My Workspace

    After saving, the publication is listed on My Workspace where you can manage all of your saved publications, and view any publications that a user has shared with you.

  7. Once you save the publication, Update Publication opens. With the appropriate security permissions you can

    1. Update the publication information.

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Updating a Publication

To update a publication

  1. Perform a publication search.
  2. From the search results, click Edit in the Actions column.
  3. From Update Publication edit the following information as needed.

    Publication Criteria

    Description

    Publication Type*

    Select (or review) the type of publication from the drop-down list. Pre-selected if starting from within a sample.

    The criteria displayed varies depending on the Publication Type that you select.

    Publication Status*

    If appropriate, from the drop-down list, select the appropriate status. Or if appropriate, simply review the status.

    PubMed ID

    PubMed ID (can be a hyperlink). Once you enter the ID, the other appropriate data fields on this form, such as Title, Journal, Authors, etc., are automatically populated. You can enter keywords and description, however, to override the text from PubMed.

    If you remove the PubMed ID, the related data fields are cleared.

    Digital Object ID

    Appropriate DOI.

    Title*

    Enter text for the title of a publication. Select Contains (for search using partial text) or Equals (for exact text search).

    Journal

    Journal in which publication occurs.

    Year of Publication

    Year of the publication.

    Volume

    Volume of the publication

    Start/End Page

    Page range for the publication

    Authors

    To add an author to the publication, click Add. On the pop-up, enter a First Name, Last Name, and Initials of the author. Click Cancel or click Save to save the author to the Publication. 

    To edit an author, click Edit, make changes to the name, and click Save. The changes are saved.

    To remove an author, from Submit Publication, click Edit next to the author's name, and click Remove on the pop-up.

    Keywords

    Enter a logical term that can be used to find the publication. Enter one term per line.

    Description

    Enter a description for the publication.

    Research Category

    Check (or review) the Research Category relevant to the publication.

    Upload
    or
    Enter File URL

    Click Browse to navigate to the publication to be associated with the sample, or enter the URL where the publication is located.

    Sample Name

    There are two options to add samples to a publication.

    Enter one sample name per line in the Sample Name box.

    OR

    Click Search Samples and a list of samples appears in a list box. Click a sample name or Ctrl-click or Shift-click to select more than one. Click Select, and the selected samples are added to the Sample Name box.

    Access to the Publication

    For more information, see Sharing a Publication with a User or Group or Making the Publication Public.
  4. Click Update when you are done editing the publication.

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Sharing a Publication 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 Publication 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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Searching for Existing Publications

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.

To search for existing saved publications

  1. Click Publications.

  2. Manage Publications displays.
  3. Click Search Existing Publications.

    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.

  4. From Search Publications, fill in the following information as needed.

    Publication Search OptionsDescription

    Publication Type

    Select (or review) the type of publication from the drop-down list. Pre-selected if starting from within a sample.

    Research Category

    Check (or review) the Research Category relevant to the publication.

    PubMed ID

    Enter the PubMed ID, if known. Once you enter the ID, the other appropriate data fields on this form, such as Title, Journal, Authors, etc., are automatically populated. You can enter keywords and description, however, to override the text from PubMed.

    If you remove the PubMed ID, the related data fields are cleared.

    Digital Object ID

    Enter the name of the digital object ID, if known.

    Publication Title

    Enter text for the title of a publication. Select Contains (for search using partial text) or Equals (for exact text search).

    Authors

    Enter the last name of an author. For more authors, add one author's last name per line.

    Keywords

    Enter a logical term that can be used to find the publication. Enter one term per line.

    Sample Name

    Enter text for the name of a sample. Select Contains (for search using partial text) or Equals (for exact text search).

    Composition

    Nanomaterial Entity

    Select the nanoparticle category to which the sample targeted by the search belongs. Example: Dendrimer

    Functionalizing Entity

    Function

    Select the function type category which best fits the nanomaterial entity.
    If you select imaging function, you must specify an Imaging Modality Type.

  5. Click Search.

    Publication Search Results opens.

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Publication Results

Publications Search Results display sorted by Creation Date with information appropriate for the publication type.

The following table lists and describes the Publications Search Results columns.

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.

Publications Search Results ColumnsDescription
Action

Click View in the first column to display the publication abstract and information on the PubMed web site.

Note:

Edit is only available for people that have an account and are logged into the system and are associated with the publication.

Click + Add to Favorites to add a bookmark for the publication on your My Favorites. Added to favorites appears in the column when the publication is successfully added.

Note

If the publication is already added as a Favorite, clicking Add to Favorites displays the <publication name> has already been added to your favorites message.

Bibliography Information

Lists bibliography information about the publication and provides a link to the publication abstract at PubMed.gov.

Publication Type

The publication category you selected when you created the report.

Research Category

The research category you selected when you created the document. (Publications only)

Associated Sample Names

Names of sample(s) associated with the publication

DescriptionClick View to display a popup with a complete description of the Publication.

Publication Status

If appropriate, from the drop-down list, select the appropriate status. Or if appropriate, simply review the status.

Created Date

Date the publication was submitted

For any entry, click on the hyperlink in the Title column (first) to open the associated file.

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Searching for Samples by Publication

To search for publications associated with one or more samples

  1. Click Publications.
    Manage Publications displays.
  2. Click Search for Samples by Publication.

    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 Sample Search by Publications, specify the Type of sample ID, PubMed or DOI.

  4. Enter the ID number.

  5. Click Search.
    The Sample by Publication Search Results opens.

Sample by Publication Search Results

The following table lists and describes the Sample Information by Publication Search Results columns.

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.

Publications Search Results Columns

Description

Publication REF

Click the hyperlink to open PubMed.gov for that Publication.

Authors

The author(s) of the publication.

Title

The title of the publication.

Sample Composition

Click the link to open the caNanoLab Sample Composition form.

Sample Characterization

Click the link to the open the caNanoLab Sample Characterization form.

Journal

The journal where the publication was published.

Year

The year that the journal was published.

Vol(lss)Pg

The volume and page number in the journal where the publication was  published.

For any entry, click on the hyperlink in the Title column (first) to open the associated file.

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Additional Publication Tasks

The following table lists how to edit a publication 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.

If you do not see the button

If a button does not display, you have read-only access to the data.
TaskHow to

Printing Publication(s)

To print the publication(s), from the All tab publication summary, click Print at the top right of the page.

Exporting Publication(s) to a Spreadsheet

To export the publication(s) to a spreadsheet, from the All tab publication, click Export at the top right of the page.


To export all publication information to JSON or XML, see Exporting Sample Information to JSON or XML

Deleting a Publication from a Sample

Deleting a publication from a sample removes its association with the open sample. The publication remains in the database and is available for other samples.

To delete a publication from a selected sample

  1. Click Sample and Search Existing Samples.
  2. Click Edit in the search results.
  3. In the Navigation Tree, click Publication. The All tab displays the summary of any publications associated with the sample.
  4. Click Edit at the right of the section you want to delete.
  5. From Publication, click Delete
  6. Confirm the deletion.

Bookmarking a Publication to My Favorites

My Favorites displays samples, protocols, and publications that you bookmark for quick access.

To add a publication to My Favorites

  1. Perform a publication search.
  2. From the search results, click + Add to Favorites in the Actions column. 
    Bookmarking a publication from Publication Search Results
    The <publication name> has already been added to your favorites message appears in the results row.
  3. Click My Favorites, and the bookmarked publication is listed under My Publications.

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Managing Publications From an Open Sample

Once a publication is saved and associated with one or more samples, when you search for and edit the sample, you can view the publication(s) from the Navigation Tree, Publications option.

Publications Menu Versus Publications Navigation Tree

If you use the Publications menu, you can associate multiple samples with one publication. If you open a sample first from the Navigation Tree, you can copy the publication to additional samples the same way you copy characterizations to multiple samples. See Copying Characterizations.

 To access publications function in the Navigation Tree

  1. Click Samples and Search Existing Publications.
  2. Fill in criteria, and click Search.
  3. Click Edit in the search results Action column
  4. The Navigation Tree appears on the left sidebar and comprises functions which you can use to add annotations to the sample.

    NAVIGATION TREE
    GENERAL INFO
    COMPOSITION
    CHARACTERIZATION
    PUBLICATION
  5. Click Publication. 
    The All tab displays publications associated with the sample, and the publication identifier, title, authors and year, where appropriate. Additionally, each publication category tab displays its corresponding publications.

    Access to publications

    Publications Summary

    With read-only access, you can review a summary of the publications added to the sample on the All tab.

  6. To open a publication, click the Abstract/Download hyperlink.
  7. To add a publication to the open sample, click the Add button corresponding to the publication type on the All tab or select a publication type tab and add a publication to the sample.

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Managing Sample Characterizations | caNanoLab User's GuideManaging Collaboration Groups
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