Have it your way with My NCBI!

Would you like email alerts when new sequences or literature references for your favorite organism appear in Entrez? Would you like to archive your Entrez search strategies? Would you like to automatically partition your nucleotide search results by source database, species of origin, or sequence type? Would you like Entrez links displayed right on the web page rather than as a menu? My NCBI and a few simple configuration panels are all it takes to have it your way.

Getting Started

To try My NCBI, click on the “My NCBI” link under “Hot Spots” on the NCBI home page. Cubby users can log into their My NCBI accounts immediately, using their Cubby user names and passwords. New users can click on the “register for an account” link to open an account. In order for My NCBI to remember your preferences and apply them whenever you log on, your web browser must be configured to accept cookies.

Archiving Search Strategies

Searches are archived by performing an Entrez search and clicking on the “Save search” link that appears to the right of the query box when the results are returned. To see a table of your saved searches, click on the “Saved searches” link in the My NCBI sidebar. Searches that are no longer needed can be selected using checkboxes in the table and deleted. Saved search strategies remain within My NCBI indefinitely, until changed or deleted by you.

Requesting Email Alerts

Search results are emailed on a regular schedule to users who specify ‘Schedule’ options in the “Saved searches” table. A flexible scheduler accommodates email intervals of days to months and allows the specification of particular days of the week so that results always arrive when you expect them. Report styles include full text, summary, and several other Entrez formats and may be emailed in HTML or plain text. A Document Delivery service to which PubMed will send your orders when you use the “Send to Order” option may be specified by clicking on the “Document delivery” link in the My NCBI sidebar and choosing a service from the list. By default, PubMed sends document delivery orders to Loansome Doc, NLM’s document delivery service.

Configuring Filter Tabs

Each of the Entrez databases in My NCBI offers a rich selection of filters from which you can select up to five that automatically partition your search results. To configure filters, click on the “Filters” link on the My NCBI page and select the desired Entrez database. A default set of filters is used for each database in new My NCBI accounts and these can be seen under the “My Selections” tab. To delete a filter, simply uncheck it. The full selection of filters can be examined using the “Browse” tab where they are organized as three hierarchical groups, “Linkouts,” “Links,” and “Properties”. The “Linkouts” group offers tabs for records with links to resources provided by outside organizations. The “Links” group provides filters for records that link to other Entrez databases. Use the “properties” group to create tabs for records that fall into various categories, such as PubMed publication type, Nucleotide molecule type, or database source.

Figure 1 shows filter tabs in use during a search of the Entrez Protein database for “superoxide dismutase.” Of the 4410 records returned, accessible via the “All” tab, 626 are RefSeqs, 3075 have links to the Entrez Nucleotide database, 229 have links to the Map Viewer, 456 have links to the Protein Data Bank, and 113 have linkouts to an external organism-specific database, Saccharomyces Genome Database. The latter set is shown in the active tab; the inset shows the result of clicking on the “linkout” link for the first record. To add a filter to your original Entrez query, click on the push-pin shown on the active tab.

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Figure 1: Document summaries returned by a query of "superoxide dismutase" in the Entrez Protein database. The records returned are partitioned into 5 tabbed sets; those with linkouts to organism-specific databases, those derived from the Protein Data Bank, those linked to the Map Viewer, those linked to records in Entrez Nucleotide, and those that are RefSeqs. The linkout target of the first record is Saccharomyces Genome Database. Note that the Entrez links are displayed as "Plain links" rather than as components of a pulldown "links" menu. This configuration option is available under "User preferences" on the My NCBI page.

Configuring Entrez Link Formats

To configure the Entrez link display format, click on “User Preferences” in the blue side bar and choose the format you prefer from the “Links Display” menu. Choices are “javascript menu,” the default, “plain links,” “standard pull-down,” and “pop-up menu.” Figure 1 shows an Entrez display in which links have been configured as “Plain Links” using My NCBI, and are therefore visible for each record without the need to first click on a “Links” link.

—MR