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A New PubMed: Highlights for Information Professionals: Questions and Answers

Below are common questions asked during the sessions of "A New PubMed: Highlights for Information Professionals."
Please be sure to view the webinar recording and review the Key Points.

Don't see your question? Please contact us. More questions and answers may be added after the final webinar session.

Want to give feedback on the new PubMed? Please use the green Feedback button on the bottom of PubMed Labs pages.

Access and Links

Q: Where will pubmed.gov lead when the changeover happens? 

A: PubMed.gov and all links to PubMed will automatically direct you to the new PubMed once the new PubMed becomes the default.

Q: If we have canned searches on a website, will they forward to the new PubMed?

A: Yes. All PubMed URLs (including those that run searches) will automatically forward to and run in the new PubMed.

Q: Will Single Citation Matcher be supported in the new PubMed?

A: Yes. The Single Citation Matcher will automatically be redirected to the new system when the new PubMed is the default.

Note that you can also simply put your citation elements into the PubMed search box and the improved PubMed citation sensor will find your article in most cases. Try it out!

Q: How can I look up MeSH terms in the new system? Will I be able to run searches from MeSH?

A: The Medical Subject Heading (MeSH) Database is now and will continue to be the place to look up MeSH terminology and find term explosions from the MeSH hierarchy. Any links or searches run from the PubMed Search Builder in the MeSH Database will be redirected to the new system when the new system is the default.  

Remember that searches that limit to MeSH (e.g., pediculus[mh]) will not include the most recent PubMed records, as they are not yet indexed.

Searching:

Q: What is “best practice” in PubMed searching?

A: For most common informational queries, PubMed gives the best results if you enter your search terms as simple, specific phrases that describe what you’re looking for. For example, for articles on preventing head lice in schools, type preventing head lice in schools into the PubMed search box. Don’t worry about syntax or Boolean operators and avoid using quotation marks – focus on fully describing your research question. Let PubMed find the relevant Medical Subject Headings (MeSH) and other synonyms for you using its automatic term mapping (ATM) process; and let PubMed’s Best Match algorithm bring the most relevant records to the top of your results. You can check the term mapping by viewing your search details from the Advanced screen. If PubMed fails to find a map from your medical search terms to MeSH, try synonyms for your concepts for better results.

Comprehensive searching, as is done in a systematic review, requires a deeper investigation into the MeSH terminology for your concepts as well as a thorough exploration of synonyms used by authors in non-indexed records. Consult a health sciences librarian for assistance.

Q: Why am I getting slightly different results in the new system, compared to the legacy system?

A: There may be variations in your search results due to enhanced synonymy, addition of plural forms, better British/American translations, unlimited truncation, and slight differences in how the new system indexes words and phrases.  Test your searches in the new system, now, and view your search details on the Advanced page to compare.

Q: Is the enhanced synonymy available for tagged searching?

A: Tagging turns off the added synonymy as well as the automatic term mapping (ATM) process. By tagging, you are telling PubMed that you know what you're doing, and don't need its help. If you prefer having maximum control of your search, consider using the untagged search first, viewing the Search Details to see the mapping and enhanced synonymy, then using the results to build a tagged search.

Q: Where are the search details? Can you modify the search details?

A: You can find your search details (including mapping to MeSH and additional synonyms) from the Advanced search page. To modify the details, copy and paste the text to the search box and edit.

Search details on Advanced page

Q: Do the limits (filters) still restrict results to MEDLINE?

A: Age, sex and species filters are based on the MeSH terms applied at indexing, and therefore will include only indexed records. Filtering by article type may exclude non-indexed records. This has not changed from the legacy system.

Q: Will the field tags change in the new PubMed?

A: The field tags are the same as the old system, with two minor exceptions: the author and full author indexes have been combined, and Entrez Date has been renamed to Entry Date. The mechanics of searching PubMed remain the same. You can find a complete list of tags used in the new PubMed in the appendices of the new PubMed FAQ & User Guide.

Q: Will the usual indexing hiatus happen in November and December?

A: Yes, we still need to cease indexing for a period at the end of the year in order to apply the annual update to the Medical Subject Headings (MeSH). However, we are hopeful that the time needed to perform this update will continue to decrease. Monitor the NLM Technical Bulletin for news and announcements about Year-End Processing.

Q: What about my systematic review searches? Will they still work?

A: Your searches will work in the new system. There may be variations in your search results due to enhanced synonymy, addition of plural forms, better British/American translations, unlimited truncation, and slight differences in how the new system indexes words and phrases. Test your systematic review searches in the new system now.

Display and Navigation

Q: The spacing and punctuation in the citation is different on the summary display. Can we get this into a standard format?

A: We have some display errors in the current summary display. We are reviewing it now. Send your suggestions using the Feedback button on the PubMed Labs pages. In the meantime, you can use the new Cite button to access the citation for an article, formatted according to your choice of NLM, AMA, MLA, or APA rules.

Q: I don’t see the Publication Date sort in PubMed Labs. Will this not be an option in the new PubMed?

A: A publication date sort is not currently available in the new system. You can use the Results by Year graph to view and access records by publication date.

Q: Where is the MEDLINE display?

A: PubMed is now using the RIS format for tagged output to reference management systems. RIS is a standardized tag format which allows citation programs to exchange data. On the search results page, click the Save button and select RIS as your format.

Q: Will the new PubMed have an XML display?

A: PubMed XML is available via the E-utilities (our API). Use the Feedback button to tell us how you are using the XML format so we can best meet your needs.

Q: Will the new PubMed support RSS Feeds?

A: RSS feeds are not currently supported in the new system. Send your suggestions using the Feedback button on the PubMed Labs pages.

My NCBI and LinkOut

Q: Will My NCBI saved searches, collections and preferences be saved?

A: Your My NCBI account will be available in the new PubMed system. All NCBI searches, collections and the preferences which are relevant to the new system will be available.

Q: Will we have to do anything for LinkOut to prepare for new version?

A: A consolidation of LinkOut services in preparation for the new PubMed system was announced in the Spring of 2019. Libraries can provide a link to their holdings and institutional information via Outside Tool. If you have set up Outside Tool for your institution, you can activate it and test it now in the new PubMed via PubMed Labs.

Q: Will I be able to use Library LinkOut filters in the new system?

A: As announced in March, LinkOut for Libraries is being consolidated into a single service: Outside Tool.  The new service will not have the capability to create a filter for library holdings. However, it will allow you to link from every PubMed citation to holdings and interlibrary loan information from your institution. Learn more about Outside Tool.

Help, Training, etc.

Q: Will you be distributing informational materials that I can share with my users?

A: If you teach others about PubMed, please use and adapt our slide presentations:

  • A New PubMed (full version) Slides introducing the new PubMed to an audience of experienced users (such as health sciences librarians). We encourage you to copy and adapt these slides to your outreach and training needs and style appropriate to your audience. These slides are free of copyright restriction, but we appreciate attribution to the U.S. National Library of Medicine. This is a 25-30 minute presentation without abridgment.
  • A New PubMed (brief version) Slides introducing the new PubMed to an audience of experienced users (such as health sciences librarians). We encourage you to abridge, expand, adapt and/or redistribute these slides to better meet the needs of your audience. These slides are free of copyright restriction, but we appreciate attribution to the U.S. National Library of Medicine. This short version would be appropriate for a 5-10 minute presentation.
  • Introduction to PubMed These slides were designed to introduce PubMed to new users who have no prior experience with PubMed, and can be presented in about 45 minutes, as-is. However, we encourage you to abridge, expand, adapt and/or redistribute these slides to better meet the needs of your audience. Additionally, five slides (numbers 1, 2, 6, 13, and 38) should be either removed or modified, depending on your specific needs. These slides are free of copyright restriction, but we appreciate attribution to the U.S. National Library of Medicine.

Q: Will the PubMed tutorials be updated?

A: We will be providing new training materials as our resources allow. We would love your suggestions for what types of online tutorials would be most useful to you and your users so that we can prioritize this work. Use the green Feedback icon in the bottom corner of PubMed Labs to send us suggestions.

Q: I’m having a problem specific to my institution in the new system. What should I do?

A: To ask about an issue specific to your institution, use the Feedback icon in the bottom corner of every new PubMed page, or you can use the Support Center link (at the bottom of each page) to contact the Help Desk. Give us as much specific information as you can so that we can help you.

 

Last Reviewed: November 7, 2019