Managing Sample Characterizations | caNanoLab User's Guide| Managing Collaboration Groups
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, the Manage Publications page appears. The panel on the page provides the following options.
You can also perform the following functions with a protocol.
Creating a Publication
Making an item public
Working from the Publications menu or an open sample
If you add a publication from the Publications menu option, you can associate multiple samples with a publication. If you work from an open sample in the Navigation Tree, you can copy a characterization to associate the publication with other samples.
The Create Publication function allows you to identify a publication and associate it with one or more samples. To define a sample publication
When no sample is selected
- Click the Publications and click Create a New Publication. Continue to step 2.
From within an open sample
- Search for a sample, click Edit in the search results, and click Publication in the Navigation Tree. Continue to step 2.
- Click the Add button corresponds to the appropriate publication type.
The following table lists and describes each field.
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.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 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. 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. To clear the fields and start again, click Reset.
Once you enter the appropriate information on the form, click Save.
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.
Sharing a Publication with a User or Group
Making a Publication Public
Searching for Existing Publications
To search for existing saved publications
Keyword Search
Click the Publications.
Click Search Existing Publications. This opens the Search Publications form.
When defining search criteria, there are no required fields. Add an asterisk for searching wildcards. If you do not define any search criteria, caNanoLab returns all publications in the search results.
From the Search Publications page, fill in the following information as needed.
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.
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.
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.
If you click Search without defining any parameters, all of the caNanoLab sample publications are returned in the search results.
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.
Return to the Search page
To return to the Search page, click the Back ( ) button not the Browser button.
Publications Search Results Columns | Description |
---|---|
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 page. 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 |
Description | Click 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.
Searching for Samples by Publication
To search for publications associated with one or more samples
- Click Publications.
- Click Search for Samples by Publication.
From the Sample Search by Publications form, specify the Type of sample ID, PubMed or DOI.
Enter the ID number.
Click Search.
If you do not specify search criteria, all of the caNanoLab publications are returned in the search results.
Sample by Publication Search Results
The following table lists and describes the Sample Information by Publication Search Results columns.
Return to the Search page
To return to the Search page, click the Back ( ) button not the Browser button.
Publications Search Results Columns | Description |
---|---|
Publication REF | Click the hyperlink 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 hyperlink in the Title column (first) to open the associated file.
Editing a Publication
You can edit a publication using 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.
- Updating a Publication
- Deleting a Publication
- Copying a Publication to Samples
- Deleting a Publication from a Sample
Updating a Publication
To update a publication
- Perform a publication search.
- Click Edit in the search results.
From Public Update edit the following information as needed. An asterisk indicates a required field. Click Update when you are done editing the Publication.
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.
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 the Submit Publication page, 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 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. 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.
Deleting a Publication
Deleting a publication removes the publication from the caNanoLab database, which is executed behind the scenes at a scheduled time.
The button is missing
If you do not see the option described here, you do not have appropriate security permissions.
To delete a publication
- Perform a publication search.
- Click Edit in the search results.
- From the Update Publication page, click Delete in the lower-left corner of the window.
- Confirm the deletion.
Copying a Publication to Samples
The button is missing
If you do not see the option described here, you do not have appropriate security permissions.
To copy a publication to a sample with the same point of contact
- Perform a publication search.
- Click Edit in the search results.
- Click Publication in the Navigation Tree.
- In the Copy text box, select one or more additional samples to associate with the publication.
- Click Submit.
The publication is copied to the sample(s) you selected.
Deleting a Publication from a Sample
The button is missing
If you do not see the option described here, you do not have appropriate security permissions.
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
- Click Sample and Search Existing Samples.
- Click Edit in the search results.
- In the Navigation Tree, click Publication. The All tab displays the summary of any publications associated with the sample.
- Click Edit at the right of the section you want to delete.
- From the Publication page, click Delete at the bottom left of the page.
- 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
- Perform a publication search.
- Find the publication that you want to bookmark and click + Add to Favorites in the first column of the Publication Search Results row.
The <publication name> has already been added to your favorites message appears in the results row. - Click the My Favorites option in the menu bar, and the bookmarked publication will be listed under My Publications.
Managing Publications From an Open Sample
Once a publication is saved 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 hyperlinks so you can open the publication(s).
Click the Publications button on the Navigation Tree. A Publication[s] summary page displays those publications associated with the sample, and the publication identifier, title, authors and year, where appropriate. Additionally, each publication category tab displays its corresponding publications.
From the Publications All tab or the subcategory tabs, you can perform the same tasks.
- 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. The Submit Publication page opens which is identical one accessed Publications menu option with one exception:
If you work from the Publications menu option, you can associate multiple samples with a publication. Alternatively, if you add publications to an open sample using the Navigation Tree option, you can use the copy feature to associate the publication with other samples in the same way you copy characterizations to multiple samples. See Copying Characterizations.