pubmed / myncbi...created by amurrell last updated july 20, 2015 tsri, 400-s [email protected]...

Created by amurrell Last updated July 20, 2015

TSRI, 400-S [email protected]

858-784-8705

PubMed / MyNCBI My NCBI is a free service available in PubMed (and all other NCBI databases) that allows you to save searches, set up email alerts for search results, create collections of article citations, set customized filters, and other features. This is also the tool NIH funded researches must use to track and report publications on progress reports and Fellowship progress reports.

pubmedmyncbi2015.docx

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1. Registering for MyNCBI

• Click on the My NCBI link in the top right corner of PubMed. • My NCBI now lets you sign in using a Partner login system:

o Sign in with Google o Sign in with NIH Login: use this for eRA Commons log in (for those using

My NCBI to add publications to your grant RPPR reports, SciENcv) o See more 3rd party sign in options

• You can create a new account by clicking the by “Register for an account” link under

“Sign In”

• Enter a Username (3-10 alpha-numeric characters) • Enter a Password (6-8 alpha-numeric characters). • Choose a security question and answer, used to reset your password if you forget it. • You can enter a default e-mail address. Only one e-mail address may be associated

with each MyNCBI account. • A confirmation e-mail message will be sent to the e-mail address to activate

automatic e-mail updates. Recipients must confirm their e-mail account before MyNCBI will automatically send updates.

• You can change this email address by signing in to My NCBI, then click on the Preferences link on the left sidebar.


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2. Saving your search & setting automatic e-mail alerts

• Sign in to MyNCBI if you have not already done so. • Run or preview your search. • Click on Create Alert under the search box.

• The Save Search window appears.

• You can change the search terms and test the new strategy. • If you only want to save the search, and not receive emails, select “No, thanks.” • Otherwise, complete the following items:

• Choose how often you would like email

o once a month o once a week o daily

• Choose the day.

• Select the Report format o Summary o Summary - text o Abstract o Abstract - text o MEDLINE- import into EndNote

• Number of records sent in each alert. • Add text to the email. • Click Save


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3. Manage Searches • Manage searches from the main My NCBI screen:

o To edit E-mail alerts or change the schedule for automatic emails, click on the gear icon next to a search,

o Then edit the settings (just like when originally saving the search).

o To run the search in PubMed and see all results (not just new ones), click on the search name.

o To see the results from the latest alert, or since the last time the search was run, click on the number in the “What’s New” column.

• Manage searches from the Save Searches screen o Click on “Manage Saved Searches” at the bottom of the box.

o To edit the alert settings and frequency, click the gear icon next to a search,

or the word (e.g., daily) in the “Schedule” column. o To see the results from the latest search or since the last time the search was

run, mark the box next to the search and click the “What’s New” button at the top.


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4. Collections After performing a search in PubMed, you can mark and save citations in MyNCBI.

• Mark the records you want to keep. • Click on the “Send to” link and mark Collections. • Click Add to Collections button.

• The citations can be saved in a new collection or added to an existing collection.

• Once a collection is saved, you can add to it or share it.

• Click on the Private link in the “Privacy” column for the collection.


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5. Filters Filters allow you to set up automatic links to sort search results when logged into MyNCBI. Filters can be set up for the different NCBI databases as well as any of the common Filters Set up filters for each NCBI database.

• Sign into MyNCBI • Scroll down to the “Filters” box on the lower right. • Choose the database from the drop down menu (PubMed for example) • If you have no Filters set up, click “Add filters for the selected database.” • Otherwise, click “Manage Filters” at the bottom of the box.

The filters available depend on the Database chosen.

• Set the collection to “Public”

• Click Save.

• Go back to the collection and copy the URL that appears in the Direct URL box.

• MyNCBI will also give you the HTML code that you can paste into a web page or blog.


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Use the “Search with terms” box to locate a specific filter, e.g., ‘review’.

For PubMed, the filters include: • Popular

o Usually includes “Full text”, “Review”, “English”, “Human”, “Published in the last 5 years”

• LinkOut – will show links to outside sources (library website, outside web sites, outside databases):

o Have their collections linked in PubMed (publisher links, PubMed Central links, UCSD Library) but access to the full text may be restricted.

• Properties, including: o Age groups o Publication Types (Clinical Trial, reviews, etc.) o Humans or Animals (includes a “Humans and English” filter) o Languages o Publication date (7 days to 10 years) o Subsets (e.g., Subject collections, “In process” records, OLDMEDLINE)

• Links – when the result has links to other NCBI databases (OMIM, Protein, PMC, etc.) it will group these results in a link on the right, e.g., “Links to OMIM (164)”.


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• Custom Filters These are custom searches that you might want to apply to many searches, for example, you always want to know which papers in your search TSRI authors published.

o Click “Create custom filter”

o Compose a search using field tags, keywords, Boolean. o Click Test This Query. If there are no results, check the search for errors. o Name the filter. o Click Save Filter when there are valid results.

• The filters will apply when you are signed in to My NCBI and searching PubMed.


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6. My NCBI Site Preferences

Common Preferences – apply to any Entrez database while logged into My NCBI.

• Change your password or email address. • Highlighting - select a color and search terms will be highlighted in the result set. • Share Settings – allows you to let others see your highlighting, filters, or Outside

Tool (i.e., SFX@TSRI button) when you share a collection with them.

PubMed Preferences – apply only while searching PubMed and signed in to My NCBI. • Abstract Supplemental Data – choose to have the extra data (e.g., Publication

Types, MeSH Terms) displayed in the Abstract view (You can always expand or collapse the additional information while viewing the record.)

o Choose Open to have it automatically expanded, or Closed to have it collapsed.

• Outside Tool – this allows you to select the SFX@TSRI button to be displayed. This button allows you to see whether TSRI has access to the full text of an article, or provides an easy way to request it through interlibrary loan (i.e., ILLiad).

• Auto Suggest – turns the pop up search suggestion box ON or OFF. • Result Display Settings – customize how results display.


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7. Customize MyNCBI Homepage

Now you can also choose which boxes to display on you’re my NCBI homepage.


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8. SciENcv SciENcv is NLM’s Science expert network. https://www.ncbi.nlm.nih.gov/sciencv/ Currently you can create an NIH Biosketch or NSF biosketch. NLM plans to add functionality to allow CV and other document creation, as well as support for data import from multiple systems.

• Data is pulled from:

• My NCBI My Bibliography • eRA Commons information • ORCID • Manually entered data.

Click “Create New Profile” to create a new profile from an existing profile, from scratch, or from data imported from an external source (eRA Commons at the moment).

pubmed / myncbi...created by amurrell last updated july 20, 2015 tsri, 400-s [email protected]...

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