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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 publication.

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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. Choose a method of initiating the process: 
    • To create a publication (and optionally add it to multiple samples): Click Publications. The Manage Publications page appears. Click Create a New Publication. The Create Publication page appears. Select a publication type.
    • To add a publication to one sample: Search for the sample. In the search results, click Edit. In the Navigation Tree, click Publication. Next to the appropriate publication type, click Add. The Edit (sample name) Publication page appears. 

      NAVIGATION TREE
      GENERAL INFO
      COMPOSITION
      CHARACTERIZATION
      PUBLICATION
  2. 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. (Refer to 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. In the panel, enter the Last Name, First Name, and Initials of the author. Confirm that you have read and understood the following message. Click Save

    Enter only public business-related contact information into these fields (such as institutional points of contact used in public publications). Do not add private contact information here, as this information will be made available to the public viewing the system. The system will contact you yearly, via the email address you provide, to ask if you would like to correct, update, or delete this information. If you would like to update it earlier, contact us via caNanoLab-Support@isb-cgc.org.

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

    To remove an author, click Edit next to the author's name, and click Delete in the panel. 

    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.

    To select multiple categories, you can Shift-click or Ctrl-click.

    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. Select one or more samples. To select multiple samples, you can Shift-click or Ctrl-click. Click Select, and the selected samples are added to the Sample Name box.

    Access to the PublicationFor more information, refer to Sharing a Publication with a User or Group or Making the Publication Public.
  3. When you are done entering information, click Submit.

    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.

  4. Once you save the publication, the Edit Publication page opens. With the appropriate security permissions you can

    1. Edit the publication information.

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Editing a Publication

To edit a publication

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

    Publication Criteria

    Description

    Publication Type*

    Review the type of publication in the drop-down list.


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

    Publication Status*

    In the drop-down list, 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. 

    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. In the panel, enter the Last Name, First Name, and Initials of the author. Confirm that you have read and understood the following message. Click Save

    Enter only public business-related contact information into these fields (such as institutional points of contact used in public publications). Do not add private contact information here, as this information will be made available to the public viewing the system. The system will contact you yearly, via the email address you provide, to ask if you would like to correct, update, or delete this information. If you would like to update it earlier, contact us via caNanoLab-Support@isb-cgc.org.

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

    To remove an author, click Edit next to the author's name, and click Delete in the panel. 

    Keywords

    Enter one or more logical terms 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.

    To select multiple categories, you can Shift-click or Ctrl-click.

    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. Select one or more samples. To select multiple samples, you can Shift-click or Ctrl-click. Click Select, and the selected samples are added to the Sample Name box.

    Access to the Publication

    For more information, refer to Sharing a Publication with a User or Group or Making the Publication Public.
  4. When you are done editing the publication, click Submit.

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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 the 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 have access, along with any other Curator.
  2. Next to Access to the..., click Add. The access information panel opens.
    The access information panel, listing groups and users.
  3. Select Collaboration Group or User. Click Search. A list appears next to that button. From the list, select a group or user.
    The Access By panel, for adding group or user.
  4. 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.

     

  5. Click Save. The system updates the access information panel and updates the item in My Workspace.

Editing and Removing Access

To edit the access: From the Update page, in the Access to the ... panel, locate the access entry you want to edit. Next to that entry, click Edit. Make changes to the access and click Save. The system updates the access information panel. 

The access information panel, listing groups.

To delete a listing: From the Update page, click Edit next to the access entry. From the access information panel, click Delete and confirm the deletion. The system updates the access information panel and updates the item in My Workspace.

The Access By panel, for deleting a group or user.

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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 Performing a caNanoLab Keyword Search.

To search for existing saved publications

  1. Click Publications. The Manage Publications page appears.

  2. Click Search Existing 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 Search Publications, fill in the following information as needed.

    Publication Search OptionsDescription

    Publication Type

    Select the type of publication from the drop-down list.

    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 one or more logical terms 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.

  4. Click Search. The Publication Search Results page appears.

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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.

Publications Search Results ColumnsDescription
Actions

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. When the system has successfully added the publication to your favorites, the Added to Favorites message appears in the column.

Bibliography Info

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

Type

The publication category you selected when you created the report.

Research Category

The research category you selected when you created the document. 

Associated Sample Names

Names of sample(s) associated with the publication

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

Status

Review the status.

Created

Date the publication was submitted

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Searching for Samples by Publication

To search for publications associated with one or more samples

  1. Click Publications. The Manage Publications page appears.
  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. Enter the ID number.
  4. From Sample Search by Publications, specify the Type of sample ID, PubMed or DOI.
  5. Click Search. The Sample by Publication Search Results page appears.

Sample by Publication Search Results

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

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 Publication REF 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)

  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 Print at the top right of the page.

Exporting Publication(s) to a Spreadsheet

To export the publication(s) to a spreadsheet

  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 Export at the top right of the page.


To export all publication information to JSON or XML, refer to 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. Click Publication and Search Existing Publication.
  2. From the search results, click Add to Favorites in the Actions column. 
    Bookmarking a publication from Publication Search Results
    When the system has successfully added the publication to your favorites, the Added to Favorites message appears in the column.

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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. For details, refer to Copying a Characterization to Samples in the Same Primary Organization.

  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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