Making an item public
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.
Creating a Publication
Create Publication allows you to identify a publication and associate it with one or more samples.
To create a sample publication
- 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 SYNTHESIS
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 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.Title*
Enter the title. (Refer to 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. 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 URLClick 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. 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.
Once you save the publication, the Edit Publication page opens. With the appropriate security permissions you can
Edit the publication information.
Editing a Publication
To edit a publication
- Perform a publication search.
- From the search results, click Edit in the Actions column.
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.
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 URLClick 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. When you are done editing the publication, click Submit.
Sharing a Publication with a User or Group
Specifying User or Group Access
To share with a user or collaboration group
- From the Update page, the Access to the panel lists who initially has access to the item based on your user role.
- As a Public user, you have access, along with any Researcher or Curator.
- As a Researcher, you have access, along with any Curator.
- As a Curator, you have access, along with any other Curator.
- Next to Access to the..., click Add. The access information panel opens.
- Select Collaboration Group or User. Click Search. A list appears next to that button. From the list, select a group or user.
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.
- 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.
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.
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.
At the bottom of the Create or Update page, click Submit for Review.
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.
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, refer to Reviewing Data Pending Release.
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
Click Publications. The Manage Publications page appears.
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.
From Search Publications, fill in the following information as needed.
Publication Search Options Description 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.
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
Select the functionalizing category to which the sample targeted by the search belongs.
Function
Select the function type category which best fits the nanomaterial entity.If you select imaging function, you must specify an Imaging Modality Type.Click Search. The Publication Search Results page appears.
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 Columns | Description |
|---|---|
| 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 |
| Description | Click View to display a popup with a complete description of the Publication. |
Status | Review the status. |
Created | Date the publication was submitted |
Searching for Samples by Publication
To search for publications associated with one or more samples
- Click Publications. The Manage Publications page appears.
- 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.
- Enter the ID number.
From Sample Search by Publications, specify the Type of sample ID, PubMed or DOI.
- 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.
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
| Task | How to |
|---|---|
Printing Publication(s) | To print the publication(s)
|
Exporting Publication(s) to a Spreadsheet | To export the publication(s) to a spreadsheet
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
|
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
|
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
To access publications function in the Navigation Tree
- Click Samples and Search Existing Samples. The Sample Search page appears.
- Fill in criteria, and click Search. The Sample Search Results page appears.
In the search results, in the row for the sample you want to edit, click Edit. The Update Sample page appears, with the Navigation Tree on the left sidebar. The Navigation Tree comprises functions which you can use to add annotations to the sample.
NAVIGATION TREE GENERAL INFO COMPOSITION CHARACTERIZATION PUBLICATION SYNTHESIS In the Navigation Tree, 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
With read-only access, you can review a summary of the publications added to the sample on the All tab.
- To open a publication, click the Abstract/Download hyperlink.
- 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.
