Managing Publications in caNanoLab

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

Publications Overview

When you click the Publications option on the caNanoLab menu bar, the Manage Publications home page appears. The panel on the page provides the following options:

• Submit a New Publication: This takes you to a form for submitting a new caNanoLab publication. For more information, see Submitting a Publication.

• Search Existing Publications: This takes you to a form to launch a search for an existing publication of interest. For more information, see Searching Publications.

  Search Tips

  From Publications Search Results tables, you can add a sample to the My Favorites page. This is like bookmarking a sample for quick access.

  There is a protocol search option discussed in this chapter. You can also 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 Performing a caNanoLab Keyword Search.

Once a publication is submitted and associated with one or more specific samples, when the sample is opened in caNanoLab, the associated publications are listed on the Publication All tab. Where appropriate, the publication list includes hypertext links so you can open the publication(s).

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Submitting a Publication

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

To define a sample publication:

When no sample is selected:

1. Click the Publications caNanoLab menu option. On the Manage Publication home page, click the Submit a New Publication link. This opens the Submit Publication page. Continue with step #2 below.

From within an open sample:

1. Click Publication from the Navigation Tree when a sample is open. Click the Add button that corresponds to the publication type you plan to add.
   From this point on, the process is very similar. Variations in the steps are noted in the following table.

   1. The following table lists and describes each field. Select or enter the appropriate information in the text fields and drop-down lists.

      Other options

      By default, all fields are blank.

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

      Fields may change, depending upon your launching point and your selection of Publication Type. Asterisks indicate required fields.

      Sample 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.
      Publication Status*	If appropriate, from the drop-down list, select the appropriate status. Or if appropriate, simply review the status. In Preparation In Press Published Submitted
      Title*	Enter the title. (See PubMed ID description for how to auto-populate this field)
      Year of Publication	Enter 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 the Submit Publication page, 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 the Browse button 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 Publication	For more information, see Sharing and Changing Access to a Publication.

      To clear the fields and start again, click Reset.

2. Once you enter the appropriate information on the form, click Submit.

   My Workspace

   Once you submit a publication, it is listed on the My Workspace page where you can manage all your submitted publication, and view any publications that a user has shared with you. For more information, see Using My Workspace.

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Editing a Publication

You can edit a publication using the following techniques:

• Updating a Publication
• Sharing and Changing Access to a Publication
• Downloading a Publication
• Deleting a Publication
• Copying a Publication to a Sample
• Deleting a Publication from a Sample

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Updating a Publication

The Publication Update page opens when you click the Edit link corresponding to a publication listed in Publication Search Results. The page displays all of the information for a Publication that was entered when the Publication was created in caNanoLab (Submitting a Protocol). With appropriate permissions, you can edit information.

The following table lists and describes the fields. An asterisk indicates a required field. Click Update when you are done editing the Protocol. To disregard the changes, click Reset.

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Sharing and Changing Access to a Publication

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Deleting a Publication

To delete a publication, perform a publication search, find the publication that you want to delete, and click the Edit link in the first column of the the Publication Search Results page. The Update Publication page opens. From the Update Publication page, click the Delete button in the lower-left corner of the window. Confirm the deletion.

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Copying a Publication to Samples

When you are in the process of adding a publication to a sample, on the Publication page you can copy that publication to other caNanoLab samples that have the same point of contact.

1. From within an open sample, click the Publication link in the Navigation Tree.
2. In the Copy text box, select one or more additional samples with which you want the publication associated.
3. Click Submit. The publication is copied to other samples you selected.

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Deleting a Publication from a Sample

To delete a publication for a selected sample, follow these steps:

1. Open the sample of your choice.
2. In the Navigation Tree on the left sidebar, click the Publication button. The All tab displays the summary of any publications that have been associated with the sample.
3. Click the Edit hypertext link at the right of the section you want to delete. This opens the corresponding Publication page.
4. Click the Delete button at the bottom left of the page. Deleting the publication is removes its association with the open sample. The publication remains in the database so that it can be available for other samples.

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Searching Publications

The Search Publications feature looks for submitted existing publications or Publications can be associated with one or more samples.

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Search Existing Publications

To launch a search for a specific publication, follow these steps:

1. Click the Publications caNanoLab menu option. On the Manage Publication home page, click the Search Existing Publications link. This opens the Search Publications form.

   When defining search criteria, there are no "required" fields. You can add only those parameters that you consider essential to the search. Add an asterisk for searching wildcards. If you do not define any search criteria, caNanoLab will list all publications in the search results. 

2. The following table lists and describes the fields. Select or enter the appropriate information in the text fields and drop-down lists. Asterisks indicate required fields.

   Publication Search Options	Description
   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 name(s) of the authors. Enter one author 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 from the drop-down list the nanoparticle category to which the sample targeted by the search belongs. Example: Dendrimer Functionalizing Entity Select from the drop-down list the functionalizing category to which the sample targeted by the search belongs. Antibody Biopolymer Small molecule Function Select the function type category which best fits the nanomaterial entity. If you select imaging function, you must specify an Imaging Modality Type.

3. To clear the form and start again, click Reset.
4. To launch the search, click Search.
   For information about search results, see Publications Search Results.

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Publications Search Results

Publications Search Results display in the browser window in table format, sorted by creation date. Column headings are appropriate for the publication(s) for which you searched; cell entries were defined when the report was submitted. Columns are sortable by Creation Date. Column headings are described in the following table.

The following fields are listed in the search results. To return to the Search page, click the Back (  ) button not the Browser button.

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

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Searching for Samples by Publication

To launch a search for samples by publication, follow these steps:

1. Click the Publications caNanoLab menu option. On the Manage Publication home page, click the Search for Samples by Publication link. This opens the Sample Search by Publications form.

2. Specify the Type of sample ID, PubMed or DOI.

3. Enter the ID number.

   To clear the fields, click Reset.

4. Click Search.

   If you click the Search button having defined no parameters, all of the caNanoLab publications will be listed in the Search Results.

5. Sample Information by Publication Search Results

   Access to this page

   You can access this page after logging into caNanoLab or you can access publicly-available sample publication results from the Login page.

   The following fields are listed in the search results. To return to the Search page, click the Back (  ) button not the Browser button.

   Publications Search Results Columns	Description
   Publication REF	Click the hypertext link to open the PubMed.gov page 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 hypertext link in the Title column (first) to open the associated file.

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Adding 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. Find the publication that you want to bookmark and click the + Add to Favorites link in the first column of the Sample Search Results row.
   The <publication name> has already been added to your favorites message appears in the results row.
3. Click the My Favorites option in the menu bar, and the bookmarked publication will be listed under My Publications.

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