As you may have seen recently in McGill’s What’s New, McGill Libraries has launched a new search tool called SciFree that can help you efficiently find which journals offer waivers and discounts to McGill researchers on Article Processing Charges (APCs) for publishing open access. You’ll find information about the tool and can search it here: Announcing SciFree . Unlike the information that the McGill Libraries was previously providing on the webpage on Article Processing Charge Support that only supplied details on APCs at the publisher level (table at the bottom of the page), the new search tool simplifies the process of finding journals that offer waivers and discounts. This new tool can help you make informed decisions about what journals will allow you to publish open-access in as cost-effective a manner as possible. Simply search the journal name in SciFree to determine if there are waivers or discounts available to you. If you have any questions, please feel free to contact schulich.library@mcgill.ca and we will be happy to help!
Welcome back to campus! We hope you enjoyed your summer and are ready for another great semester! How was our summer? So great, thanks for asking! We got some reading done and want to share our favourites with you! All these books are available to borrow through our catalog. While you’re on campus, stop by the Schulich Library and take a look at some of our other picks!
Suggested by Andrea Quaiattini, Health Sciences Librarian, Liaison for Medicine, Postgraduate Medical Education and Indigenous Health
“There is grandeur in this view of life… if you can’t see, shame on you.”
“David Starr Jordan was a taxonomist, a man possessed with bringing order to the natural world. In time, he would be credited with discovering nearly a fifth of the fish known to humans in his day. But the more of the hidden blueprint of life he uncovered, the harder the universe seemed to try to thwart him. His specimen collections were demolished by lightning, by fire, and eventually by the 1906 San Francisco earthquake—which sent more than a thousand of his discoveries, housed in fragile glass jars, plummeting to the floor. In an instant, his life’s work was shattered. Many might have given up, given in to despair. But Jordan? He surveyed the wreckage at his feet, found the first fish he recognized, and confidently began to rebuild his collection. And this time, he introduced one clever innovation that he believed would at last protect his work against the chaos of the world.”
Suggested by Tara Mawhinney, Physical Sciences Librarian, Liaison for Atmospheric & Oceanic Sciences, and Civil and Mechanical Engineering
“In her acclaimed novels, Susan Vreeland has given us portraits of painting and life that are as dazzling as their artistic subjects. Now, in The Forest Lover she traces the courageous life and career of Emily Carr, who, more than Georgia O’Keeffe or Frida Kahlo, blazed a path for modern women artists. Overcoming the confines of Victorian culture, Carr became a major force in modern art by capturing an untamed British Columbia and its indigenous peoples just before industrialization changed them forever. From illegal potlatches in tribal communities to artists studios in pre World War I Paris, Vreeland tells her story with gusto and suspense, giving us a glorious novel that will appeal to lovers of art, native cultures, and lush historical fiction.”
“Maybe that’s what love was — walking willingly into the unknown for the sake of the other.”
Suggest by Sabine Calleja, Health Sciences Librarian, Liaison for Nursing and Palliative Care
“The Sackler name adorns the walls of many storied institutions: Harvard, the Metropolitan Museum of Art, Oxford, the Louvre. They are one of the richest families in the world, known for their lavish donations to the arts and sciences. The source of the family fortune was vague, however, until it emerged that the Sacklers were responsible for making and marketing OxyContin, a blockbuster painkiller that was a catalyst for the opioid crisis.”
“The opioid crisis is, among other things, a parable about the awesome capability of private industry to subvert public institutions.”
Suggested by Maryam DeyhimiHaghighi, Senior Library Clerk
“Sethe, its protagonist, was born a slave and escaped to Ohio, but eighteen years later she is still not free. She has too many memories of Sweet Home, the beautiful farm where so many hideous things happened. And Sethe’s new home is haunted by the ghost of her baby, who died nameless and whose tombstone is engraved with a single word: Beloved. Filled with bitter poetry and suspense as taut as a rope, Beloved is a towering achievement by Nobel Prize laureate Toni Morrison.”
“Freeing yourself was one thing, claiming ownership of that freed self was another.”
Suggested by Andrea Miller-Nesbitt, Life Sciences Librarian, Liaison for Anatomy & Cell Biology, Biochemistry, Biology, Environment and Genetics
My home is full of hope and ghosts.
“Off the reserve and trying to find ways to live and love in the big city, Jonny becomes a cybersex worker who fetishizes himself in order to make a living. Self-ordained as an NDN glitter princess, Jonny has one week before he must return to the “rez,” and his former life, to attend the funeral of his stepfather. The next seven days are like a fevered dream: stories of love, trauma, sex, kinship, ambition, and the heartbreaking recollection of his beloved kokum (grandmother). Jonny’s world is a series of breakages, appendages, and linkages–and as he goes through the motions of preparing to return home, he learns how to put together the pieces of his life.”
“A young woman moves from the place of her birth to the remote northern country of her forebears to be housekeeper to her brother, whose wife has recently left him. Soon after her arrival, a series of inexplicable events occurs – collective bovine hysteria; the demise of a ewe and her nearly born lamb; a local dog’s phantom pregnancy; a potato blight. She notices that the local suspicion about incomers in general seems to be directed with some intensity at her and she senses a mounting threat that lies ‘just beyond the garden gate.’ And as she feels the hostility growing, pressing at the edges of her brother’s property, she fears that, should the rumblings in the town gather themselves into a more defined shape, who knows what might happen, what one might be capable of doing.”
It’s not the meek who inherit the earth. The meek get kicked in the teeth.
Suggested by April Colosimo, Physical Sciences Librarian, Liaison for Math, Chemistry, Physics and Astronomy
The world is changing, you know. A pity you aren’t ready to live in it.
“Shizuka Satomi made a deal with the to escape damnation, she must entice seven other violin prodigies to trade their souls for success. She has already delivered six. When Katrina Nguyen, a young transgender runaway, catches Shizuka’s ear with her wild talent, Shizuka can almost feel the curse lifting. She’s found her final candidate. But in a donut shop off a bustling highway in the San Gabriel Valley, Shizuka meets Lan Tran, retired starship captain, interstellar refugee, and mother of four. Shizuka doesn’t have time for crushes or coffee dates, what with her very soul on the line, but Lan’s kind smile and eyes like stars might just redefine a soul’s worth. And maybe something as small as a warm donut is powerful enough to break a curse as vast as the California coastline. As the lives of these three women become entangled by chance and fate, a story of magic, identity, curses, and hope begins, and a family worth crossing the universe for is found.”
Suggested by Eleni Philippopoulos, Health Sciences Librarian, Liaison for Undergraduate Medicine and LGBTQ+ Health
You’re gonna let the world happen to you, and you’re gonna love it.
“In the male-dominated field of animation, Mel Vaught and Sharon Kisses are a dynamic duo, the friction of their differences driving them: Sharon, quietly ambitious but self-doubting; Mel, brash and unapologetic, always the life of the party. Best friends and artistic partners since the first week of college, where they bonded over their working-class roots and obvious talent, they spent their twenties ensconced in a gritty Brooklyn studio. Working, drinking, laughing. Drawing: Mel, to understand her tumultuous past, and Sharon, to lose herself altogether.
Now, after a decade of striving, the two are finally celebrating the release of their first full-length feature, which transforms Mel’s difficult childhood into a provocative and visually daring work of art. The toast of the indie film scene, they stand at the cusp of making it big. But with their success come doubt and destruction, cracks in their relationship threatening the delicate balance of their partnership. Sharon begins to feel expendable, suspecting that the ever-more raucous Mel is the real artist. During a trip to Sharon’s home state of Kentucky, the only other partner she has ever truly known—her troubled, charismatic childhood best friend, Teddy—reenters her life, and long-buried resentments rise to the surface, hastening a reckoning no one sees coming.”
Suggested by Jill Boruff, Health Sciences Librarian, Liaison for Physical Therapy, Occupational Therapy, Psychiatry and Communication Sciences & Disorders
“France, 1714: in a moment of desperation, a young woman makes a Faustian bargain to live forever and is cursed to be forgotten by everyone she meets. Thus begins the extraordinary life of Addie LaRue, and a dazzling adventure that will play out across centuries and continents, across history and art, as a young woman learns how far she will go to leave her mark on the world. But everything changes when, after nearly 300 years, Addie stumbles across a young man in a hidden bookstore and he remembers her name.”
What is a person, if not the marks they leave behind?
Happy Pride, all! Did you know that members of the 2SLGBTQIA+ community are more likely to experience health disparities than their heterosexual and cisgender counterparts?1 Many members of this community say they feel uncomfortable accessing healthcare and report facing discrimination because of who they are.2 Not on our watch!
The Wendy Patrick Consumer Health Collection has books to help members of the 2SLGBTQIA+ community take their health into their own hands. Here is a sample of some the books in our collection:
“As a gay man living in London and working as a nutritionist, Daniel O’Shaughnessy knows that the LGBTQ+ community has specific dietary and health needs. Yet while there is huge demand for this kind of information in his private practice, there is very little reliable public information out there for the community to access. Naked Nutrition seeks to change that: it is the first LGBTQ+ focused guide to diet and lifestyle, taking an honest, inclusive and non-judgemental approach to the questions Daniel is asked most frequently. It covers a wide range of subjects, giving detailed, practical advice on matters including: weight loss and muscle gain, digestive health issues, addiction, sex, fertility, nutrition for balancing hormones while transitioning, how to eat if you have a chronic condition, and how to mitigate against the party lifestyle.”
“Like a Boy but Not a Boy explores author andrea bennett’s experiences with gender expectations, being a non-binary parent, and the sometimes funny and sometimes difficult task of living in a body. The book’s fourteen essays also delve incisively into the interconnected themes of mental illness, mortality, creative work, class, and bike mechanics (apparently you can learn a lot about yourself through truing a wheel).”
“Have you ever questioned your gender identity? Do you know somebody who is transgender or who identifies as non-binary? Do you ever feel confused when people talk about gender diversity? This down-to-earth guide is for anybody who wants to know more about gender, from its biology, history, and sociology to the role it plays in our relationships and interactions with family, friends, partners, and strangers. Activities throughout the book will engage people of all genders in a thoughtful, practical way, and help you understand people whose gender might be different from your own.”
“How do I know if I’m actually asexual? How do i come out as asexual? What kinds of relationships can I have as an ace person? If you are looking for answers to these questions, Cody is here to help. Within these pages lie all the advice you need as a questioning ace teen. Tackling everything from what asexuality is, the asexual spectrum, and tips on coming out, to intimacy, relationships, aphobia, and finding joy, this guide will help you better understand your asexual identity alongside deeply relatable anecdotes drawn from Cody’s personal experience. Whether you are ace, demi, gray-ace, or not sure yet, this book will give you the courage and confidence to embrace your unique self.”
“With personal stories and illustrations throughout, this comprehensive resource will help you understand the full range of surgical options available. Information and advice about each procedure is offered, including planning and recovery, sexual health and fertility, and insight into what to expect in the years following an operation. This is essential reading for any trans or non-binary person considering gender confirmation surgery and will help you make the decision that’s right for you”
“Alo Johnston has been where you are. From watching every transition story on YouTube and navigating online message boards for answers to finally starting testosterone and transitioning himself, he now walks alongside you every step of the way to guide you towards acceptance of who you truly are. Born out of thousands of hours of research and conversations with hundreds of trans people, Am I Trans Enough? digs deep into internalized transphobia and the historical narratives that fuel it. It unveils what happens after you come out, or begin questioning living as a trans person, in a world that works against you. Use this book as a space to engage with your fears and explore your doubts without the pressure of needing to be a perfect trans representative. If you are just beginning your trans journey, are twenty years into transition or have no idea if you are even trans at all, this book will help you to become your most authentic self”
You can check out these books and many others on the main floor of the library. You can also visit our catalog to browse more titles in the Wendy Patrick Consumer Health Collection.
Alliance for Healthier Communities. 2SLGBTQ+. (n.d.). Retrieved June 7, 2024, from https://www.allianceon.org/2SLGBTQ#:~:text=Two%20Spirit%2C%20Lesbian%2C%20Gay %2C,to%20stigma%2C%20discrimination%20and%20social ↩︎
Mills, S., Dion, M., Thompson-Blum, D., Borst, C., & Diemert, J. (2019). Mapping the Void: Two-Spirit and LGBTIQ+ Experiences in Hamilton. ↩︎
Sometimes, the search process happens backwards. What I mean by that is that you may find yourself with a stack of articles that you know you want to include in your review, but are then tasked with coming up with the search that will generate these articles and articles like them. The Yale MeSH Analyzer is here to facilitate the task and help you come up with a great list of search terms.
Developed by the team at the Yale University Cushing/Whitney Medical Library, this tool allows you to analyze those perfect articles and extract the Medical Subject Headings (MeSH) and keywords. This is definitely quicker than scanning each article manually.
Here’s how it works! You’ll be asked to enter the PubMed Identification Numbers (PMIDs) for your articles. You can find these on the individual article pages on PubMed:
You can enter up to 20 PMIDs at once for the tool to analyze. Once you’ve entered all your articles, the Yale MeSH analyzer will spit out a handy table, either online or in an downloadable Excel sheet, that allows you to see what MeSH terms the articles have been tagged with. And, despite what the name suggests, it isn’t limited to MeSH terms. The tool will also give you a list of keywords that the authors have used to describe their own articles.
Let’s take a look at an example: A student is interested in looking at experiences of young menstruating individuals in low-income countries and rural areas. She has managed to find four articles through her limited Google search, but would like to build a more comprehensive search in a few medical databases.
Want to follow along? Access the Yale MeSH Analyzer here. The PMIDs of the articles are as follows:
30611223
24244435
29485336
26436841
This is what the MeSH Analyzer produces for her (click on the image to enlarge it):
All four of the articles are tagged with the MeSH term Menstruation, so that’s a pretty good indication that our student should include it in her search! But one of the articles is also tagged with Menarche and that’s something that our student hadn’t thought to include. Other MeSH terms to think about are Rural Populations, Sanitation and Health Knowledge, Attitudes, Practice.
The author keywords are also telling:
One article mentions Menstrual hygiene management and the other Menstrual hygieneproducts. This gives you insight into the various ways different researchers are referring to the same concept. In addition, it allows you to parse your search. Instead of writing every iteration, you can choose to just add menstrual hygiene as a term to ensure that you’re picking up all the varieties.
Congratulations! You now have a great foundation on which to build your search!
Something to look out for in the academic science literature is the ability to read documents that are part of the peer review associated with a published article. These can include reviewer reports, author responses, and editor decision letters. Getting the full story around a paper of interest, from the author’s submission to the final published version, is really exciting. It can also be beneficial to any new researchers or new peer reviewers that would like to learn what to expect from the system.
Clativate has made it easy to identify articles that have peer review documents associated with them by adding “Open publisher-invited reviews” as a quick filter in their multidisciplinary Web of Science database. There may only be a small number of these papers in your search results, but this number will likely grow.
Here is what the option looks like after you run a search in Web of Science:
Let us know if you have any questions about this option, and if you find it useful!
Thanks very much to Antoine Bissonnette & Faiza Ambreen Chowdhury for submitting their FACC 400 assignment to post on The Turret. This guest post looks at the use of cryptocurrency for philanthropy and economic management.
Cryptocurrency: Defying the Norms of Financial Institutions
by Antoine Bissonnette & Faiza Ambreen Chowdhury
In the landscape of global finance, a significant transformation is underway, particularly certain markets where the relevancy of traditional banking institutions is being challenged. Cryptocurrency, once regarded as a niche or speculative asset, is steadily becoming a cornerstone in many industries where traditional banking systems have either failed or cannot adequately meet the needs of the industry. This blog post delves into the pivotal role of cryptocurrency in such industries and emerging markets.
The Rise of Crypto Philanthropy
A growing number of charitable organizations are starting to embrace cryptocurrency donations. While there are organizations dedicated to accepting only crypto-donations like The Giving Block, nowadays even major charity funds such as UNICEF, Greenpeace and the Human Rights Foundation, all offer it as an option to potential donors [4].
There are multiple advantages this offers to both donors and recipients. Firstly, the use of cryptocurrency ensures transparency between donors and organizations, facilitated by the public logging of transactions inherent to cryptocurrency. So donors, recipients and the public can track where the money is going and witness the real-time impact of donations [1]. Digital currency also offers significant tax advantages for donors, the amount donated would not be subject to capital gains taxes, therefore deducted from the donor’s overall gross income [2].
For organizations, providing the choice for crypto donations helps broaden their funding sources. With the rise in popularity of bitcoin, there are more and more people who want to donate, but only have access to cryptocurrency. Another feature that can work in organizations’ favor is the price volatility of the digital currency market. Some organizations have been known to hold donations for some amount of time, to increase the value of donations with time [3].
While cryptocurrency philanthropy showcases the transformative potential of digital assets, its influence extends far beyond charitable donations. In emerging markets, cryptocurrencies are reshaping entire economies, offering financial inclusion and economic empowerment to those who have been left behind by traditional banking systems.
Countries like Venezuela and Argentina, facing hyperinflation and economic instability, have turned to cryptocurrencies not just as an investment but as a means to preserve wealth, transact, and participate in the global economy. In fact, cryptocurrency has become a beacon of hope in emerging markets, offering financial inclusion and economic empowerment to those who have been left behind by traditional banking systems.
Case Study: Cryptocurrency Adoption in Venezuela
In Venezuela, cryptocurrencies serve as a crucial tool against hyperinflation and government control. The country ranks high in global crypto adoption, driven by the necessity to preserve savings in a stable asset and the ease of conducting transactions even during power and internet outages [5] [6]. Moreover, Venezuela’s engagement with cryptocurrencies extends beyond just transactions; it has a significant presence in the crypto mining world, thanks to the country’s low electricity costs. This has led to the creation of a legal framework to support and regulate the mining industry, further solidifying the role of digital currencies in its economy [7].
Influence on Economic Stability in Argentina
Argentina presents another compelling case of crypto’s impact, where the devaluation of the local currency has pushed individuals and businesses towards cryptocurrencies. Stablecoins, in particular, have become popular for preserving the value of earnings and savings, acting as a digital stand-in for the much-sought-after US dollar. The adaptability of cryptocurrencies has allowed for innovative solutions like crypto debit cards, enabling Argentinians to make everyday purchases directly from their crypto wallets, thus circumventing the volatile local currency [8].
These case studies shed light on a broader trend within the financial system, where cryptocurrencies are not just speculative assets but vital financial tools. They offer a way to mitigate the impacts of economic volatility, and enable businesses to operate smoothly despite fluctuating local currencies. As new markets continue to evolve, the role of cryptocurrencies is likely to expand, potentially transforming the global financial landscape and making financial inclusion a tangible reality for millions.
In summary, cryptocurrency is revolutionizing global finance by challenging traditional banking norms. From transforming philanthropy to providing economic stability in emerging markets, its impact is undeniable. Cryptocurrency’s journey is just beginning, promising a dynamic future for finance worldwide.
Over the past few years, the most significant trend in academic publishing has arguably been in the introduction of so-called Transformative Agreements. These agreements aim to repurpose the funds paid out by libraries for subscription fees, instead redirecting them to cover the publishing fees required to make articles open-access and freely available to the public.
Earlier this month a new transformative agreement was signed between Elsevier and the Canadian Knowledge Resource Network (CRKN), a partnership of 85 libraries and research institutions across Canada. This means that corresponding authors at McGill will benefit from unlimited open access publishing at no cost in more than 1,800 Elsevier hybrid journals in this list; for these journals the article processing charge (APC) will be completely waived. For Gold Access journals there is a 20% reduction in the APC. The agreement will last three years, from January 1, 2024, to December 31, 2026 inclusive. When submitting an article, make sure that you use your McGill email in order to be eligible, and be sure to check out the detailed instructions before submitting.
We at the Library are very excited about this new agreement and we hope that it leads to many more McGill authors being able to publish their work without worrying about publishing fees, while also being able to more easily satisfy the Tri-Council Open Access Funding Policy.
We may want to believe that citation practices in STEM are unbiased, but the evidence out there says otherwise. It speaks to the politics and privilege that have pervaded peer review and the published literature.
Kahalon, R., Klein, V., Ksenofontov, I., Ullrich, J., & Wright, S. C. (2022). Mentioning the Sample’s Country in the Article’s Title Leads to Bias in Research Evaluation. Social Psychological and Personality Science, 13(2), 352-361. https://doi.org/10.1177/19485506211024
Ross, M. B., Glennon, B. M., Murciano-Goroff, R., Berkes, E. G., Weinberg, B. A., & Lane, J. I. (2022). Women are credited less in science than men. Nature, 608(7921), 135-145. https://doi.org/10.1038/s41586-022-04966-w
Teixeira da Silva, J. A. (2021). The Matthew effect impacts science and academic publishing by preferentially amplifying citations, metrics and status. Scientometrics, 126(6), 5373-5377. https://doi.org/10.1007/s11192-021-03967-2
There are a few things that we can do in our citation practices to make a difference. First, if we recognize that citations are power, then we can exercise that power in our own reference lists. When we write articles or otherwise disseminate our research outputs, we can choose to break away from citing the usual suspects and cite responsibly. One easy to remember rule of thumb is the Gray test. Our works pass the Gray test if they cite and discuss the scholarship of at least two women and two non-white people. We can also consider including citation diversity statements.
Second, we can be representative in the works that we recommend to others. For example, here is a Gender Balance Assessment Tool that is available to check that our reading lists are not mostly works written by male authors.
Third, when we find ourselves in a position to judge the work of others we can let go of our reliance on citation metrics. We can commit to evaluating works on their scientific merit and consider alternative metrics not based on citation counts.
Of course, we can also talk about citation politics with our colleagues. There is lots to think about and discuss!
In a previous blog post, we discussed the use of ChatGPT for PubMed searches. Now that Gemini, previously Bard from Google, has become available in Canada, it’s worth taking a look at how the technology interprets requests for PubMed searches and how it differs from ChatGPT.
We’ll be using the exact same example that we used previously:
In former smokers with chronic obstructive pulmonary diseases, is pulmonary rehabilitation an effective treatment method?
When asked to generate a MeSH only search string, this is what the program comes up with:
("Chronic Obstructive Pulmonary Disease"[Mesh] AND "Pulmonary Rehabilitation"[Mesh]) AND ("Exp-Smokers"[Mesh] AND "Smoking Cessation"[Mesh]) [Optional: AND "Treatment Outcome"[Mesh]]
It seems like all AI programs share a brain cell when it comes to MeSH. Like ChatGPT, Gemini is making up its own MeSH terms – Pulmonary Rehabilitation and Chronic ObstructivePulmonary Disease are not MeSH terms! It has also included Exp-Smokers, when the correct MeSH term is Ex-Smokers. Yikes.
Another obvious issue is the use of AND to combine “Exp-Smokers”[Mesh] and “Smoking Cessation”[Mesh]. In the context of this question, these are synonyms, part of the same concept, and would therefore be combined using OR.
Let’s take a look at Gemini’s response as a whole:
While ChatGPT just spits out MeSH terms, Gemini seems to take it one step further and offer advice. The use of Required and Optional is presumptuous, but I can appreciate that the program tries to explain what kind of articles your query will return.
The biggest problem, and the one I take the most issue with, is the program’s declaration that adding the MeSH term Treatment Outcome will broaden your search. While Treatment Outcome might be a broad term, including this MeSH term will severely narrow your search and potentially eliminate relevant articles. The more concepts you combine using the Boolean operator AND, the less results you will end up with.
When asked to generate a list of keywords, Gemini provided one or two synonyms for each concept, even though we know from the complete search we generated in the last post that there are way more out there:
If you’re going to be using any AI program to generate synonyms, it’s best to enter your terms one at a time, and only after you’ve combed through other sources, like relevant journal articles or a thesaurus.
Gemini is also struggling with the concept of Booleans. The search string it generates is riddled with Boolean errors:
(COPD OR ex-smoker) AND pulmonary rehabilitation AND (exercise training OR dyspnea OR quality of life)
My head hurts just looking at this… I’ve used different colours to group together keywords of the same concept. COPD and ex-smoker are two entirely different concepts and should not be grouped together. If exercise training is often used in conjunction with pulmonary rehabilitation like Gemini says, then why is it not being combined using OR? Presumably, Gemini thinks that dyspnea and quality of life are important outcomes, so the use of OR to combine them is not false, but it shouldn’t have grouped exercise training with them. Overall, it’s a mess.
One thing that I think Gemini does better than ChatGPT is the explanation for searching both MeSH terms and keywords, and I trust it more as a learning tool than as a search string generator:
If you’re still not sure why you should complement your MeSH terms with appropriate keywords, take a look at our Health Sciences FAQ.
By now you’re probably thinking, “Gee, I don’t think Gemini could possibly get any more wrong.” Well, BUCKLE UP! I asked Gemini how to exclude keywords, wanting to know how it would explain the Boolean operator NOT:
Here, Gemini is telling you that instead of using NOT, you can simply use AND – to exclude a term. That’s not how that works! Booleans are sacred! They’re as old as time itself! You can’t just go around changing them! PubMed’s own User Guide warns that the minus sign (-) is converted to a space. Consequently, if you wanted to retrieve articles that mention COPD but not bronchitis, Gemini would have you type this: (“COPD” AND – “Bronchitis”). But PubMed isn’t interpreting this search the way Gemini thinks it is:
PubMed is ignoring your minus, turning it into a space, and searching instead for articles that mention both COPD and bronchitis. The correct way to exclude bronchitis is by entering: “COPD” NOT “bronchitis”.
I’m not ready to give you my blessing to generate searches using ChatGPT or Gemini. Maybe one day we’ll get there, but for now, I think I’ve demonstrated why you shouldn’t trust either of these tools with the job. The good news is that if you’re struggling with searching in PubMed or other medical databases, your librarians are here to help you! Contact us with any questions relating to searches and databases.
With the advent of new AI technologies geared at making academic life simpler, it can be tempting to try to use these tools to help when in unchartered territory. And while some of these tools like ChatGPT can be helpful starting points, they should not be relied on entirely for your medical research.
PubMed is a freely available biomedical database that has over 36 million records from leading journals in the medical field. It is usually the starting point for most medical research. However, it is not always easy to navigate, and some researchers struggle with building a comprehensive search. Although PubMed is taught to medical students at the undergraduate level and to other students in the health sciences, it can take a while before you feel comfortable searching on your own.
Searching in PubMed requires using a balance of the controlled vocabulary terms, MeSH terms, and keywords. These are meant to complement each other and allow you to find the most complete set of results.
ChatGPT can definitely help you get started, and even make helpful suggestions, but we want to make sure you’re using it properly!
When doing any kind of searching, it is important to break down your research question to its basic searchable components. In the health sciences, we point people to the PICO model, which allows you to identify the patient population (P), the intervention (I), the comparator (C) and the patient outcomes (O). We would then combine these components to come up with a searchable question.
For the purposes of this blog post, we will be using the following research question as an example: In former smokers with chronic obstructive pulmonary diseases, is pulmonary rehabilitation an effective treatment method?
We can start by asking ChatGPT to tell us the MeSH terms that are appropriate for use in this question:
Looks good, right? Wrong!
Let’s talk about what works, first. ChatGPT does a great job of breaking down the question and telling you what concepts should be searched. The way the search is entered into the database is also correct. In PubMed, search terms should always be entered between quotation marks and the search fields should be entered in square brackets.
The most glaring problem is that ChatGPT has made up MeSH terms. Pulmonary Rehabilitation is not a MeSH term! Neither is Former Smokers! If you enter “Pulmonary Rehabilitation”[mesh] or “Former Smokers”[mesh] into PubMed as ChatGPT suggests, you would get zero results. The closest MeSH term for Former Smokers is Ex-Smokers, but there is no close MeSH term for Pulmonary Rehabilitation.
Although ChatGPT’s suggestions are valuable, you always need to check the MeSH database for the accuracy of the terms provided.
Next, let’s take a look at what ChatGPT will generate when asked to build a keyword search:
(“Former Smokers” OR “Smoking Cessation” OR “Tobacco Use Cessation”) AND(“Chronic Obstructive Pulmonary Disease” OR COPD) AND (“Pulmonary Rehabilitation” OR “Respiratory Therapy” OR “Exercise Therapy for Lungs”) AND (“Treatment Effectiveness” OR “Therapeutic Efficacy” OR “Outcome Assessment”)
One of the first things that jumps out at me, and what I’ve written in red, is the acronym COPD. While it is not incorrect to enter the acronym as a keyword, the lack of quotation marks is what worries me. In failing to add quotation marks, PubMed triggers Automatic Term Mapping, a problematic feature that adds unnecessary search terms and results based on what the database thinks you are searching for.
The image below will show you the difference between searching with and without quotation marks:
PubMed has translated the search to include the correct MeSH term, but also include the individual words (disease, pulmonary, obstructive, chronic) as their own, stand-alone keywords. Are you still going to find articles related to chronic obstructive pulmonary disease? Sure. But there are certainly going to be more irrelevant articles for you to sift through. Just look at the difference in the numbers – 109 thousand as compared to 62 thousand!
Another problem with ChatGPT is its inclusion of outcome search terms. We don’t normally build a search with outcomes, especially such generic ones. Instead, outcomes are screened for once we have our set of results. You will certainly find articles about pulmonary rehabilitation in former smokers with COPD that don’t use terms like “treatment effectiveness” and “outcome assessment” in the title and abstract. By putting these terms in the search, you are forcing the database to look for them and consequently eliminating relevant results.
When asked to generate a search with MeSH terms and keywords for our initial question, ChatGPT combines what we’ve seen above and gives you one big search string to enter into the database:
(“Former Smokers”[MeSH] OR “Smoking Cessation”[MeSH] OR “Tobacco Use Cessation”[MeSH] OR “Former Smokers” OR “Smoking Cessation” OR “Tobacco Use Cessation”) AND (“Chronic Obstructive Pulmonary Disease”[MeSH] OR COPD OR “Chronic Obstructive Pulmonary Disease”) AND (“Pulmonary Rehabilitation”[MeSH] OR “Respiratory Therapy”[MeSH] OR “Exercise Therapy for Lungs”[MeSH] OR “Pulmonary Rehabilitation” OR “Respiratory Therapy” OR “Exercise Therapy for Lungs”) AND (“Treatment Effectiveness”[MeSH] OR “Therapeutic Efficacy”[MeSH] OR “Outcome Assessment”[MeSH] OR “Treatment Effectiveness” OR “Therapeutic Efficacy” OR “Outcome Assessment”)
At the time of this writing, this search yields two results. TWO! In fact, PubMed isn’t too happy with our search either, and issues the following warning:
Not only has it kept the two made-up MeSH terms that we already saw, but it’s created a few new ones, too, including, Exercise Therapy for Lungs, Treatment Effectiveness, Therapeutic Efficacy and Outcome Assessment. And Chronic Obstructive Pulmonary Disease is not technically a MeSH term. The correct MeSH term is Pulmonary Diseases, Chronic Obstructive. MeSH terms need to be exact.
Do better, ChatGPT…
Now, let’s take a look at a search that I, a health sciences human librarian made for the same research question:
(“Ex-Smokers”[MeSH] or “Tobacco Use Cessation”[mesh] or “ex smoker*” or “exsmoker*” or “former smoker*” OR ((“history” AND (“smoking” or “cigarette*” or “tobacco”))) AND (“Breathing Exercises”[Mesh] or “breathing exercise*” or “pulmonary rehab*” or “respirat* rehab*” or “respiratory muscle training” or “breath* control*” or “lung rehab*” or “lung exercise*” or “respiratory exercise*”)) AND (“Pulmonary Disease, Chronic Obstructive”[mesh] or “Chronic Obstructive Lung Disease*” or “Chronic Obstructive Pulmonary Disease*” or “COPD” or “COAD” or “Chronic Obstructive Airway Disease*” or “Chronic Airflow Obstruction*” or “Chronic Bronchitis” or “Pulmonary Emphysema*” or “Centrilobular Emphysema*” or “Panlobular Emphysema*” or “Focal Emphysema*”)
This search combines the correct MeSH terms with keywords and synonyms. I brainstormed different terms for all of the key concepts, and included conditions that fall under the umbrella term of chronic obstructive pulmonary diseases. All search terms are nicely encased in quotation marks to avoid automatic term mapping and I used truncation to account for different spellings. This search yielded 157 results.
Eat your heart out, ChatGPT!
While ChatGPT may not be great at making your search strategy, it can be useful. It can help you break down your question into concepts and offer suggestions during the brainstorming process. Try asking the program to generate synonyms for words – it might bring up things that you never thought of before.
For example, I asked ChatGPT to generate a list of synonyms for cancer:
They’re not all winners, and I wouldn’t enter them all into a search engine, but maybe I didn’t think to include malignancy and this was a great reminder. Or maybe I didn’t think to truncate the word cancer as cancer* to include terms such as cancers or cancerous, or to truncate malignan* to account for malignant, malignancy or malignancies. Thanks, ChatGPT! While I don’t recommend using ChatGPT for everything, using it as a thesaurus can be quite fruitful.
Try these tips out the next time you use ChatGPT, or any other AI program, and see the difference in your searches. Don’t forget to contact your librarians for specific questions related to PubMed. You can find a list of librarians by subject matter here.
