6 - Managing Publications in caNanoLab 2.1 DRAFT

 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 6 - Managing Publications in caNanoLab 2.1 DRAFT.
• Search Existing Publications: This takes you to a form to launch a search for an existing publication of interest. For more information, see 6 - Managing Publications in caNanoLab 2.1 DRAFT.

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).

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, follow these steps:

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.

2. Select or enter the appropriate information in the text fields and drop-down lists. Fields are described in the following table. Fields may change, depending upon your launching point and your selection of Publication Type. Asterisks indicate required fields.

   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.

   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
   Research Category*	Check (or review) the Research Category relevant to the publication.
   PubMed ID	Enter the PubMed ID (click the Click to look up PubMed Identifier hypertext link where you can search for the ID).  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 digital object ID, if you know it.
   Title	Enter the title. (See PubMed ID description for how to auto-populate this field)
   Journal	Enter the journal. (See PubMed ID description for how to auto-populate this field).
   Year of Publication/Volume	Enter the year of the publication and the volume, where available.
   Start Page/End Page	Enter the page range for the publication.
   Authors	Enter the name of one author. (See PubMed ID description for how to auto-populate this field). Click Add Author to add additional authors.
   Keywords	Enter a term that can be used in a search query to find the publication.
   Description	Enter an appropriate description for the publication.
   Upload File 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. Note: This field appears on the page only when opened from the Publication menu option, not the Navigation Tree.
   Sample Name*	Enter the exact or partial name and click the search icon ( ) to find the names of samples in caNanoLab. Select one or more sample sample names to be associated with the publication. Notes: You can submit a publication without identifying a sample ID. If you are submitting a publication from within an open sample, this field is replaced by the Copy section, described below.
   Copy	This section replaces the Sample Name field if you are submitting a publication from within an open sample. If that is the case, you can use this copy feature to associate the publication with other samples to which you have access. Select one or more samples to be associated with this publication.
   Access to the Publication	Access to the Publication can be assigned to either Collaboration Groups or Users. Click the search icon  to select select from collaboration groups to which you have read access. When you submit new data into the system, by default, the person submitting the data and anybody in the Curator group automatically have CURD (create, update, read, delete) access to the data. Other access must be manually assigned through this function.

3. To clear the fields and start again, click Reset.
4. Once you enter the appropriate information on the form, click Submit.

Editing a Publication

You can edit a publication using the following techniques:

• Updating a Publication
• 6 - Managing Publications in caNanoLab 2.1 DRAFT
• Downloading a Publication
• 6 - Managing Publications in caNanoLab 2.1 DRAFT
• 6 - Managing Publications in caNanoLab 2.1 DRAFT
• 6 - Managing Publications in caNanoLab 2.1 DRAFT

Updating a Publication

The Publication Update page opens when you click the Edit link corresponding to a publication listed in 6 - Managing Publications in caNanoLab 2.1 DRAFT. 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.

Details are described in the following table. An asterisk indicates a required field. Click Update when you are done editing the Protocol. To disregard the changes, click Reset.

Changing Group Access to the Publication

To change the group access to the Publication:

1. Perform a search, click the Edit link corresponding to a publication listed in Publication Search Results, and the Update Publication page opens.
2. Scroll down to the Access to the Publication field, and click Add.
   The Access Information dialog box opens.
3. For Access By, you will specify the group or user to which you are specifying access:
   • Collaboration Group: If you click this option, Collaboration Group appears below the selection. You can type in a group name and click Search or select a group from the drop down to the right.
   • User: If you click this option, User Login Name appears below the selection. You can type in a login name and click Search or select a login from the drop down to the right.
   • Public: If you click this option, Public appears in the Collaboration Group box and cannot be edited.
4. For Access to This Publication, specify whether the selected group or user can read, update, and delete the publication or read (only).
5. Click Cancel to remove the entries or click Save to add the access information.
   The Update Publication page appears with the group or user added to the Access to the Publication panel.

Downloading a Publication ???

If a publication is uploaded, with proper permissions you can download the publication. If the Download Publication link is available in the Download Publication field, then that means you can download it.

Deleting a Publication

To delete a publication, perform a search, and click the Edit link in the first column of the the 6 - Managing Publications in caNanoLab 2.1 DRAFT page. The Update Publication page opens. From the Update Publication page, click the Delete button in the lower left of the window. Confirm the deletion.

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.

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.

Searching Publications

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

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..

2. Select or enter the appropriate information in the text fields and drop-down lists. Fields are described in the following table. Asterisks indicate required fields.
   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 click the Search button having defined no parameters, all of the caNanoLab publications will be listed in the Search Results.

   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 you know it.
   Publication Title	Enter the name of the document.
   Authors	Enter the name(s) of the authors
   Keywords	Enter a logical term that can be used to find the publication.
   Sample Name	Enter the name of the sample.
   Composition Nanomaterial Entity	Nanomaterial Entity Select from the drop-down list the nanoparticle category to which the sample targeted by the search belongs. Example: Dendrimer Composition 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  6 - Managing Publications in caNanoLab 2.1 DRAFT.

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.

Search 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.

   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.