Author Archives: Johanna

Complying with the NIH Public Access Policy

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The new NIH Public Access Policy has been in effect for a couple of months, requiring that NIH-funded research be made available in PubMed Central immediately upon acceptance for publication.

How can you comply?

Our library guide walks you through some of the key steps you need to do as an author, from strategically selecting where to publish, publisher-specific policies, and when and how to deposit the author-accepted manuscript. In addition, a recent webinar from the University of Nevada, Reno’s Savitt Medical Library highlighted some of the details of this policy change:

  • The new policy applies to “manuscripts accepted for publication in a journal, on or after July 1, 2025.” Compliance will be tracked through My Bibliography based on the earliest publication date in PubMed.

  • If the published work is based on a grant that ended before July 1, 2025, it is not subject to the updated policy.

  • Neither publishing open access nor posting your manuscript to a preprint server counts as compliance.

The webinar and our guide offer useful advice that may help you select a journal to target for publication:

  • The PMC journal list includes key information from journals that currently or previously agreed to deposit the final published version of NIH-funded articles directly to PMC. You can search for journals based on their agreement status and embargo period.

  • The agreement status remains the most up-to-date piece of information listed. If a journal is listed as “no longer participating,” no further articles are being deposited into PMC, regardless of previous agreements.

    Filters available when searching the PubMed Central journal list, at right.

    • After searching the PMC journal list, visiting our frequently updated publisher policy list, or viewing the website of the journal in question, reaching out to the journal to confirm the policy in writing remains a best practice.

    Still have questions? Reach out to the Library and we will do our best to advise you.

    MSK Chatbots Can’t Perform a Literature Search

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    MSK now offers employees access to Open WebUI, a source for several chatbots available for workplace use. But if you think this tool can be used for searching the literature, think again.

    What is Open WebUI and How Do I Access It?

    This portal is “a proprietary, user-friendly, and PHI-secure portal where staff can access a wide array of popular large language models (LLMs) as well as tools for experienced developers behind the MSK firewall.”

    To access:

    1. Log on to the VPN or be onsite
    2. Visit https://chat.aicopilot.aws.mskcc.org/
    3. Select “Continue with MSK PingID” if prompted
    4. You’ll then get the message “Account Activation Pending” followed by “Contact Admin for WebUI Access.”

    No further action is needed and contacting admin isn’t necessary. You will not get confirmation once your account has been activated. But once it has, visiting the URL while onsite or on the VPN will take you to the tools.

    Open WebUI includes the following chatbots:

    Chatbot Description
    Amazon Nova Pro A reasoning model for general analysis and summarization. Knowledge cutoff date: Unknown
    Claude Sonnet 3.5 A general-use model by Anthropic. Effective with code generation. Knowledge cutoff date: April 15th, 2024
    Claude Sonnet 3.7 Improved version of Sonnet 3.5, and also targets code generation as a differentiator. Knowledge cutoff date: October 2024
    Claude Sonnet 4 High intelligence and balanced performance. Good for complex coding/debugging, detailed explanations, and documentation review. Detailed prompts recommended. Knowledge cutoff date: January 2024
    DeepSeek R1 A reasoning model for logical inference, math problem-solving, code generation, or text-based clinical reasoning. Cannot process images. Knowledge cutoff date: October 2023
    OpenAI o1 A reasoning model that thinks before it answers, making it suitable for deep analysis, task breakdown, or image-based clinical analysis. Knowledge cutoff date: October 2023
    OpenAI GPT-4o A general-purpose model that balances quality, speed, and cost-effectiveness. Knowledge cutoff date: October 2023

    You can toggle between tools on the top left of the page and click the “set as default” option under a tool name after you’ve selected it.

    Why Can’t I Use These Tools to Perform a Literature Search?

    When you ask Amazon Nova Pro to perform a literature search, it appears to do so:

    A screenshot of Amazon Nova Pro appearing to summarize the literature in response to a prompt.

    However, a follow-up question reveals that all is not as it seems, and that any citations provided are likely not real:

    Amazon Nova Pro answering a prompt asking if it searched databases to come up with its answer. It says it did not.

    Other tools are clearer about their limitations from the start:

    OpenAI o1 saying it does not have database access and giving advice on how to search.
    Claude Sonnet 3.7 saying it does not have database access and recommending speaking to a librarian.

    What Should I Do Instead?

    There are AI tools that specialize in searching the literature, but even these are typically limited to open-source texts. Use these tools cautiously, perhaps in the brainstorming and planning stages of a project.

    As an alternative, we welcome you to contact us to request a literature search.

    Want to learn more about the use of AI for literature searching? Sign up for our next class on August 19 from 12-1 pm.

    How To Search for a Phrase in PubMed

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    Searching for phrases in PubMed can be an exercise in frustration. To understand why, we need to look at how PubMed interprets your search, a process that is now described in detail in a new training module from the National Library of Medicine.

    When you enter a phrase into PubMed without using quotation marks, the database does several things:

    1. Looks for the phrase as a subject heading, or MeSH, term. Subject headings have been preselected by the database and are assigned to each citation on a topic.
    2. Breaks apart the phrase and looks for each word separately.
    3. Looks for the phrase, if recognized.
    A graphic describing how PubMed Searches for a phrase.

    How PubMed searches for a phrase. From the National Library of Medicine.

    Sometimes, this process brings back the results you need. But it can also lead to search results that do not match your topic.

    What happens when you search using quotation marks?

    • Instead of looking for matching subject headings, PubMed checks for the phrase in its phrase index, a list drawn from the literature included in the database.
    • Not every phrase is included in the phrase index. If your phrase is not found, PubMed may ignore your quotation marks and follow the search steps above, bringing in irrelevant results.
    • You can see how many results include your phrase from the advanced search page. Start typing your term, then click “Show index” to the right of the search box.
    A screenshot showing how to check if a phrase is included in PubMed's phrase index.

    Use the “Check index” button on the advanced search page to see if your phrase is included in PubMed’s Phrase index. From the National Library of Medicine.

    Fortunately, there is a workaround if your phrase is not found. You can recommend the addition of phrases to PubMed. You can try searching for the phrase in different databases,  most of which are much more user-friendly when phrase searching. You can also try searching for the phrase in PubMed using adjacency.

    For example, “Adult Non-Verbal Pain Scale” is not a phrase PubMed recognizes. Have PubMed look for the phrase with all words next to each other, in any order, by telling it to look in the title and abstract fields (tiab) with the words adjacent to each other (:~0):

    The PubMed advanced search page showing the difference in results using quotation marks and proximity searching for a phrase.

    Using proximity searching ([tiab:~0]) when a phrase is not included in PubMed’s phrase index can lead to more focused results compared to using quotation marks alone.

    For more search help, or to request a literature search, contact the Library.