Tag Archives: literature searching

Disability Pride Month: Library Edition

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This month we celebrate Disability Pride Month, marking the anniversary of the Americans with Disabilities Act (ADA) being signed into law by President George HW Bush on July 26, 1990.

Nearly 1 in 4 Americans live with some type of disability, and despite nearly 40 years since the ADA’s passage, many Americans with disabilities still live with significant barriers to living their lives to their fullest. Barriers can be physical, such lack of ramps, elevators, and ADA-compliant spaces. But they can also be less visible, including design and function of technology.

Accessible Library Resources

As library resources shifted to a predominantly digital format, the importance of these resources providing accessible and inclusive information for users of all abilities has become even more vital.

The Rehabilitation Act of 1978 defines and protects the same individuals as the ADA, but covers a different scope. In 1998, it was amended to include Section 508, which focused on the accessibility of electronic and information technology products and services that federal agencies buy, create and use.

Section 508 mandates that individuals with disabilities have access to information and services that is comparable to the access and use available to non-disabled individuals. It also provides guidelines to follow to ensure electronic resources are accessible, including making websites and apps accessible to assistive technologies (screen readers, alternative mouse and keyboard devices like motion trackers, magnification software, etc).

The Library Accessibility Alliance (LAA) is an organization made up of multiple library consortia across the country that advocates for improving library e-resource accessibility and shifting library culture to one that promotes justice and inclusion for people with disabilities. The group provides independent accessibility evaluations of library resources, training and toolkits for libraries and librarians, as well as specific licensing language for libraries to use or adapt to address concerns with electronic resources vendors.

LAA hosts a searchable database of independent evaluations of over 100 electronic resources.

ADA Compliance Tools

Vendors are recommended to provide documentation that shows how their hardware or software is accessible.

An Accessibility Conformance Report (ACR) is a document that explains how information and communication technology (ICT) products such as software, hardware, electronic content, and support documentation meet (conform to) the Revised 508 Standards for IT accessibility. Use the ACR to make specific statements in simple recommended language to demonstrate how the features and functional characteristics of your product meet the Section 508 standards.

There are multiple products and tools available to help create ACRs, including the VPAT.

Voluntary Product Accessibility Template (VPAT™)

Vendors that offer software, hardware or electronic content can voluntarily provide a VPAT™ that discloses how they support accessibility guidelines. The VPAT™ outlines the Revised Section 508 Standards for accessibility, and allows vendors to indicate their conformance with each standard. 

However, even if a vendor provides a VPAT™, it doesn’t guarantee that the vendor’s resource is actually Section 508 or ADA compliant.

W3C Web Content Accessibility Guidelines (WCAG)

WCAG are guidelines and criteria produced by the W3C (World Wide Web Consortium) to ensure that websites and electronic content are accessible to all. They provide quantitative means of evaluating websites for accessibility, and should be used by both developers and content creators.

There are currently two standards in use today: WCAG 2.0 and WCAG 2.1 which added additional criteria to address accessibility for mobile devices, people with low vision, and people with cognitive disabilities. 

Popular Biomedical Resources: ADA Compliance

If you are interested in learning more about different resources and their ADA compliance status, see the lists below which feature some of the MSK Library’s most popular resources.

Literature Databases

Citation Management tools

Clinical Databases

What’s NOT: More About the Boolean Operator “NOT”

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Boolean Operators (AND, OR, NOT) are tools for combining search terms and are inherent part of online database searching. While experienced searchers will use Boolean Operators directly in their search strategies, even novice searchers that just enter a string of terms into a database’s search box will end up indirectly using the Boolean operator AND, as each space between words will be treated by the database as AND, thus combining each term together into a search strategy that would retrieve results that have all terms present.

Image Source: https://sru.libguides.com/english/librarybasics/booleanoperators

Most search strategies will either use just AND or a combination of both AND and OR. The third Boolean operator, NOT, is much more complicated and requires some understanding to use properly in a search.

Using the Boolean Operator NOT

The Boolean operator NOT can be used when a term or terms needs to be excluded from your search strategy.

For example, if you were interested in articles that looked at children with cancer, but you did not want articles that looked specifically at infants, you could create a search strategy like this:

cancer AND child* NOT infant*
— or —
(cancer AND child*) NOT infant*

The Problem with NOT

When using the Boolean operator NOT to exclude terms, it can become problematic when the database excludes records that contain both the term(s) you want to exclude and the term(s) you want in your search.

In the above example, not only articles about cancer in infants will be excluded from the results but it will also exclude any articles about cancer in both children and infants.

Information professionals (librarians and informationists) advise using the Boolean operator NOT with extreme caution when conducting searches. It’s better to reach out to an information professional for assistance with complex search techniques and how to best proceed with a search when there is a term you want to avoid.

Variations Across Databases

Not all databases function the same way, and using the Boolean operator NOT is no different. While most databases allow for using simply NOT to exclude terms, depending on the database or platform, you might need to use the operator AND NOT instead (Scopus), or once the search is performed use the Exclude button found within the Refine Search panel (also in Scopus).

Takeaway

The Boolean operator NOT should be used with extreme caution. It is best to consult a Librarian on its use in your search.

Search Smarter with the Latest Technology

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The amount of published biomedical literature has been growing exponentially for decades, and that trend is not slowing down anytime soon. With this explosion of published content, it can be overwhelming to find exactly what you are looking for.

The 21st Century Digital Age

The start of the 21st century was heralded as the “digital age”, and the growth of content shifted from a linear to an exponential growth model. There were approximately 13 million citations in PubMed at the start of the 21st century. Within the first decade that number rose to 20 million. Today there are over 36 million citations in PubMed. 

Growth of PubMed citations from 1986 to 2010
Source: Lu Z. PubMed and beyond: a survey of web tools for searching biomedical literature. Database (Oxford). 2011;2011:baq036. Published 2011 Jan 18.

Zhiyong Lu, from the National Center for Biotechnology Information (NCBI), wrote about going beyond PubMed back in 2011, and shared an initial overview of web-based tools available that work alongside or on top of PubMed to provide more search functionality to users.

From the Digital Age to the Age of Artificial Intelligence

Today, as we now inch closer to the quarter-century point, digital technology has literally begun taking on a life of its own. With the advent of machine-learning and generative artificial intelligence, suddenly technology itself can create its own content! And while there are plenty of ethical issues surrounding the use and abuse of AI that cover nearly all aspects of life, this technology allows for considerable benefits as well.

New tools have emerged to help us better navigate, digest, and synthesize the overwhelming amount of digital information available, including biomedical literature. Many of these tools are web-based resources that either overlay or work in conjunction with PubMed to provide functionality that goes beyond basic search and retrieval.

Last month, Zhiyong Lu and several of his colleagues from NCBI published an update to his 2011 overview; PubMed and beyond: biomedical literature search in the age of artificial intelligence. This update focused on how user search needs have expanded and AI tools can provide search functionality to address these different needs.

Overview of five specialised search scenarios in biomedicine
Source: Jin Q, Leaman R, Lu Z. PubMed and beyond: biomedical literature search in the age of artificial intelligence. EBioMedicine. 2024;100:104988. 

They looked at five specific types of specialized search needs, and addressed the various tools and resources that can provide necessary functionality to support those search needs: evidence-based medicine, precision medicine, semantic searching, recommendations, and text mining.

Harness Technology with these Search Tools

Using these five identified search needs categories, below are selected resources to assist users in navigating and digesting the ever-expanding field of biomedical research.

Evidence-Based medicine

PubMed Clinical QueriesThis PubMed tool uses predefined filters to help you quickly refine PubMed searches on clinical or disease-specific topics.
Cochrane Clinical AnswersCCA provides readable, digestible, clinically focused actionable point-of-care information directly from Cochrane Reviews.
Joanna Briggs Institute (JBI) EBP DatabaseThe JBI EBP Database provides the latest research and evidence-based guidelines regarding patient care, treatment options, and interventions to empower clinicians and healthcare administrators to make informed, confident decisions. 
TRIP DatabaseTRIP is a clinical search engine designed to allow users to quickly and easily find and use high-quality research evidence to support their practice and/or care.

Precision Medicine & Genomics

OncoSearchOncoSearch is a text mining search engine that searches Medline abstracts for sentences describing gene expression changes in cancers. 
LitVarLitVar normalizes different forms of the same variant into a unique and standardized name so that all matching articles can be returned regardless of the use of a specific name in the query.
DigSeeDigSee is a text mining search engine to provide evidence sentences describing that “genes” are involved in the development of “disease” through “biological events”. With a query of (disease, genes, events), Medline abstracts with highlighted evidence sentences will be retrieved.

Semantic Searching

LitSenseLitSense is a unique search system for making sense of the biomedical literature at the sentence level. Given a query, LitSense finds the best-matching sentences based on overlapping terms as well as semantic similarity via a cutting-edge neural embedding approach.
AskMEDLINESearch PubMed using free-text and natural language
BioMed ExplorerBioMed Explorer applies semantic understanding of the content of the papers to pull out answers and highlight snippets and evidence for the user. 
Semantic ScholarSemantic Scholar provides free, AI-driven search and discovery tools, and open resources for the global research community. 

Literature Recommendations

LitSuggestAdvanced machine learning and information retrieval techniques are utilized for finding and ranking publications pertinent to a topic of interest. 
Connected PapersConnected Papers is a unique, visual tool to help researchers and applied scientists find and explore papers relevant to their field of work.

Text Mining

PubTator PubTator Central (PTC) is a Web-based system providing automatic annotations of biomedical concepts such as genes and mutations in PubMed abstracts and PMC full-text articles. 
PubMedKBPubMedKB combines a multitude of state-of-the-art text-mining tools optimized to automatically identify the complex relationships between biomedical entities in the PubMed abstracts.

As technology evolves, so will the research environment, and it’s imperative that we are able to leverage technology to keep up. It’s also important to understand these new technologies, how they work, and how they can be used to make work more efficient. But it’s also important to understand their limitations and the ethical issues that could arise when using these technologies without further human insight.