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Collections

Created: ; Last Revision: March 10, 2015.

Search results from many NCBI databases can be saved in My NCBI using the Collections feature. Collections includes a reference tool called “Other Citations” that helps you create a bibliography of publications authored by other researchers. There is no limit to the number of collections you may store in My NCBI. In addition, collections can be made public to share with

Section Contents

Creating Collections and Adding to an Existing Collection

To save search results to a new collection:

1.

Make sure you are signed into My NCBI. Run a search.

2.

From the search results page, click the check box next to items you want to save. If you do not select any items all results up to 1,000 items will be sent to collections. An automated message will confirm “Add 1,000 items.”

3.

After selecting the items you wish to save, select Collections from the Send to pull-down menu (as shown in the image below). Click Add to Collections.

Image collections-Image002.jpg

4. The My NCBI- Collections page will display. Select Create new collection (A in the image below).

5. My NCBI will create a default collection name using the number of items you are saving in a collection (B). Rename your collection using a short, yet meaningful, title. Identical names for different Collections are allowed and may cause confusion. Collection names have a limit of 100 alphanumeric characters. Click Save to finish.

Image collections-Image003.jpg

As you continue to build data collections, you may want to add new items to an existing collection. To add search results to an existing collection:

1.

Follow steps 1 – 3 under Creating Collections

2.

The My NCBI- Collections page will display. Append to an existing collection will be selected by default (A in the image below).

3.

Choose the collection into which you want to save your new items (B). Click Save to finish.

Image collections-Image004.jpg

In addition, you may add data items from multiple NCBI databases to an existing collection. This type of collection is called “Mixed” because it has data items from multiple NCBI databases.

Image collections-Image005.jpg

Storing PubMed Records in Other Citations

Other Citations is a reference tool that helps you create a bibliography of publications authored by other researchers directly from PubMed or, if not found there, to manually enter citations using templates. PubMed records stored in Other Citations can be easily accessed, exported as a file, and made public to share with others. In addition, eRA Commons and HRA grantees have the option to associate publications which they did not author but shared grant support.

Adding Citations from PubMed

1.

Make sure you are signed in to My NCBI.

2.

Run an author search.

3.

Select the citations you want to add to your Other Citations collection and click the “Send to” link to expand the drop-down menu. Select the destination “My Bibliography” (a message indicates the number of citations selected to be copied to your bibliography) and click “Add to My Bibliography.”

Image collections-Image006.jpg

4. In the resulting page, select “Other Citations” to store the selected citations in your Other Citations collection. Use “My Bibliography” to store citations of publications that you authored (see, My Bibliography).

Image collections-Image007.jpg

Adding Citations Manually

1.

Sign in to My NCBI and go to the Collections window.

2.

Click the “Other Citations” link.

Image collections-Image008.jpg

3. Click the Image collections-Image009.jpg button.

4. Select the type of publication to be entered manually: journal articles, books/chapters, meeting abstracts, presentations, patents, dataset/database, software, and non-standard citations. Enter the publication information in the fields provided. All required fields are denoted with a red asterisk. Click “Add Citation” to save a record in Other Citations.

Image collections-Image010.jpg

Other Citations has multiple templates with fields pertinent to each type of publication (see list in the image above). For example, for patents, inventor and patent number are required fields.

Viewing and Sorting Citations

Sign in to My NCBI and go to the Collections window. The Collections window lists the number of PubMed records stored in your Other Citations bibliography, and its privacy status.

1.

Click the “Other Citations” link.

Image collections-Image008.jpg

The default display in Other Citations is List view, which has all citations that are included in PubMed hyperlinked. Click on each article title to view all information related to a citation in PubMed. Each citation also displays a link to Related Citations, and when available in PubMed Central, a link to Free full text and/or a link to Cited in PMC. In addition, the List view displays a Related PubMed Citations portlet, which presents a brief list of citations recently added to PubMed. Citation retrieval for this portlet is based on the research topics found in the citations stored in Other Citations. This portlet is updated on a weekly basis.

Image collections-Image011.jpg

Click on “Display Settings” to view all sorting options. The default setting for the Sort option is to group by citation type (journal articles, books/chapters, etc.). You may change this default option to “none,” in which case all citations will be listed together in one list.

Image collections-Image012.jpg

When sorting by date: citations are sorted by newest to oldest. Citations are not sorted by Entrez date but the date the citation was published.

When sorting by author: citations are sorted by the first listed authors in alphabetical order.

When sorting by title: citations are sorted alphabetically.

Note:

  • Meeting abstracts have two different dates: conference date and publication date. When listed in Other Citations with sorting by Date and No Grouping, the publication date will be used to determine the sort date
  • When a publication has both a print date and Epub date, the print date will be used for sorting dates
  • Citations to your published works are stored in My Bibliography where Award view is available through “Display Settings” for eRA Commons users. The Award view feature is explained in detail in Managing Compliance with the NIH Public Access Policy
  • When adding citations manually, there will be no hyperlink for the citation title unless the citation exists in PubMed. These manually entered citations will continue to be displayed with a pencil icon Image collections-Image013.jpg for you to edit if necessary

Downloading, Deleting and Sharing Citations

Sign in to My NCBI and go to the Collections window. Click the “Other Citations” link.

To view multiple citations at once click the “View” button (A in the image below). To view your citations without hyperlinks, go to “Display Settings” (B) and select Print.

Image collections-Image014.jpg

In the image above there are five buttons which facilitate moving, deleting, copying, downloading and suggesting citations.

To move a citation from Other Citations to “My Bibliography” (a separate bibliography where you can store citations of your published works), select the citations you wish to move and click “Move” (C in the image above).

To delete citations from Other Citations, select the citations you wish to remove and click “Delete” (D in the image above).

To copy citations to a new collection or add them to an existing collection, click “Copy” (E).

To suggest individual citations to others, select the citation(s), click “Suggest” (F) and then enter the recipient’s name and e-mail address. Multiple recipients can be added to receive citations using the “Suggest” feature.

To share your entire Other Citations bibliography, click the “make it public” link (G).

To download selected citations in MEDLINE (text) format, click “Download as text” (H).

To download all your citations in MEDLINE (text) format, click “text file MEDLINE format” link (I).

Note:

  • When using the “Suggest” feature to send citations to others, the article titles are hyperlinked to lead to the corresponding records in PubMed

Award View in Other Citations

Assign Awards is a feature that is used to associate or disassociate grants to citations. It consists of three tabs: NIH Awards, HRA Awards (Health Research Alliance) and Search/Add other Awards.

To associate multiple citations with awards at once, select the citations you wish to associate to awards and click the Image collections-Image015.jpg button. Select the appropriate tab and choose the pertinent award(s) id (s) from the list presented to you under “My awards” and click “Save.”

Image collections-Image016.jpg

To associate individual citations to awards, click the “Add award” link and select the pertinent award(s) id (s) from the list presented to you, and click “Save & Close.”

The NIH and HRA Awards tabs

The “My awards” section (see Assign Awards window above) provides a list of awards associated to your personal profile. The “Other awards” section displays those awards that are not associated with your personal profile, but have been linked to citations in your My Bibliography collection.

To add or delete award associations from either list to your citations, check or uncheck the checkbox next to an award and click the “Save” button. In some cases, it is not possible to deselect awards through the Assign Awards window. For example, if a grant association was created in the NIH Manuscript Submission (NIHMS) system or if a grant was linked to one of your citations by the grant owner, in both cases the award checkboxes will be disabled. Contact the eRA Commons or NIHMS help desks for assistance in removing disabled award associations.

The Search/Add other Awards tab

In the “Search/Add other awards” tab, you can search for awards using a grant number, award title or grantee name. The search box includes an auto-complete feature, which provides a list of possible grant number or name matches that are displayed as hyperlinks.

Image collections-Image017.jpg

Select an award from the list provided and click the “Search” button. A list of grantee names affiliated with the award will be provided. Check the award you wish to associate to a citation in your Other Citations collection and click the “Save” button. The award will be listed under the citation selected, and it will be listed in the “Other Awards” section of the Assign Awards window.

Image collections-Image018.jpg

Adding Records to Favorites

The Favorites collection is a feature of My NCBI which helps you keep a list of your preferred NCBI database records. This feature is active only while signed into My NCBI and is currently available with the PubMed database.

1.

Make sure you are signed into My NCBI. Run a search

2.

From the search results page, click on the citation you want to save in Favorites. In the single Abstract display you will see the Favorite button Image collections-Image019.jpg

3.

Click on the Favorite button and the star next to it will turn blue. A blue star signals that the record has been saved in My NCBI Favorites

Image collections-Image020.jpg

The Favorite button also includes a drop-down menu, which displays a list of all the collections available in your My NCBI account. Clicking the star next to a collection name will automatically add the citation to the collection. You may also choose to create a new collection from the drop-down menu.

Image collections-Image021.jpg

To remove a record, click the Favorite button or the star next to a collection name a second time, as the star turns gray, the record will be removed from your Favorites or other collections. In addition, records in My NCBI Favorites can be deleted in the same manner as records in any other collection - see Deleting Collections.

Viewing and Sorting Collections

Sign into My NCBI and go to Collections. The Collections window lists all of your saved collections, the number of items stored per collection, the collection privacy status and the collection database record type. Click “Manage Collections” to sort your collections, view collections details, merge collections or delete collections.

Image collections-Image022.jpg

To view items stored in a collection:

1.

Click the “Edit” link next to the Collection Name you would like to view. The resulting page displays all the items found in that collection.

2.

To view the items in their source database, click the checkbox next to items you want to view and click the “View” button. Alternatively, to select all records to view use the link “All.”

Image collections-Image023.jpg

In the example above, collection items are sorted by Date, however, they can also be sorted by Author or Title using the “Display Settings” drop-down menu.

Image collections-Image024.jpg

To sort Collections in your My NCBI account, click the link “Manage Collections” and then click on the descending or ascending arrow next to the column headings. A black arrow indicates the currently selected sort option.

Image collections-Image025.jpg

Collections can be sorted:

  • alphabetically by name
  • by number of items in the collection
  • by privacy status
  • by date last modified
  • by database

Editing Collections

Collections can be renamed, made public to share with others, saved to a plain text or CSV file (to download to MS Excel or other programs), and individual items in a collection can be deleted. To delete entire collections, see Deleting Collections.

To change the name of a collection and/or to make a collection public:

1.

Sign into My NCBI and go to Collections. Click the gear icon Image collections-Image026.jpgnext to the Collection Name you would like to rename.

2.

On the resulting screen, you may also click on the link “Edit Settings for this collection” (A in the image below). The option to save a collection to a text file (C) or CSV (D) file is also available on this page.

Image collections-Image027.jpg

3. Enter a new name for the collection in the Collection Name text box. You may also change the collection status from private to public in this page, and obtain a URL to send to others or HTML to create a link to the collection in a Web page or blog. A quick way to change a collection status is to click “Publish” (B in the image above); however a URL/HTML will not be provided. Click Save.

Image collections-Image028.jpg

To view a brief animated tutorial, see Editing Collections.

To delete items from a collection:

1.

Sign into My NCBI and go to Collections. Click the “Edit” link next to the Collection Name you wish to modify.

2.

Click the checkbox next to items you want to delete and click the Delete button. A pop up message will ask you to confirm your action.

Image collections-Image029.jpg

Merging Collections

In the Collections portlet, click the link “Manage Collections.”

1.

Select the collections you wish to merge into a new collection and click “Merge.”

Image collections-Image030.jpg

2. A confirmation message notifies you of the collections to be merged and requires you to provide a name for the merged collection. Click “Merge Collections.”

Image collections-Image031.jpg

3. Back to Collections, you will notice that only the merged collection is listed.

Image collections-Image032.jpg

Sharing Collections

My NCBI collections are set as Private by default. However, a collection can be set as Public to be shared with others. To change a collection from Private to Public:

1.

Sign into My NCBI and go to Collections.

2.

Under the "Privacy" column, click the Private link for the collection you want to share.

3.

Under Collection Sharing, click the radio button for Public (as shown in the image below). Notice that a URL and an HTML code are provided. You can use the URL to share with others and the HTML code to post onto a web page. Click Save.

Image collections-Image033.jpg

To view a brief animated tutorial, see Sharing Collections.

Note:

  • Any time someone uses the public collection URL/HTML to see a collection; the retrieval will include all the items currently in the collection maintained by the user of the My NCBI account. Adding or deleting items in the collection does not require an update to the public collection URL/HTML
  • My NCBI Collection URLs may change, however, all prior public URLs will remain functional and will lead to the most recent version of a collection
  • If a collection is changed back to Private, the collection URL/HTML will no longer work

Deleting Collections

To delete a collection, start by clicking the “Manage Collections” link. The steps below apply to deleting entire collections. To delete specific items within a collection see “Editing Collections.”

1.

Use the check boxes to select collections to delete and then click Delete.

Image collections-Image034.jpg

2. A popup message will confirm the collections to be deleted. Click “Delete Collections.” Once a collection is deleted, this action cannot be undone.

Image collections-Image035.jpg

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