Posts

Tip #49 Command Line Syntax and Quotations in Embase on Ovid

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The Crux: when including the terms use, root, scope, or ptx (a protein) in a search query, you may need to apply quotation marks either around the term or around the phrase in which it appears. Many databases ignore or remove frequently occurring terms from search queries to expedite processing time. So called stopwords in Embase are and, as, for, from, is, of, that, the, this, to, was, and were . The stopword and is also a Boolean operator. If you use and in an advanced search, it will not be ignored but will act as an operator unless you enclose it in quotation marks, which will render it a stopword. Either way, your search should not result in a database error or baffling results. A notable exception in Embase (Ovid) are controlled vocabularies. A search for aerosolized particles and droplets/ [forward slash signifies a subject heading], will return zero results. However, if you enclose it in quotation marks, "aerosolized particles and droplets"/ , you'll correctly

Tip #48: Searching the Topic Fields in Web of Science Core Collection

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Many thanks to Zahra Premji, Health Research Librarian from the University of Victoria Libraries ( @ZapTheLibrarian ), for this week's post! We frequently use the Web of Science Core Collection (WoSCC) Topic field for systematic searching in evidence synthesis, because it is a multi-field option that includes relevant fields such as title, abstract, and author-keywords. What is the Topic field searching? According to the Web of Science interface, the Topic field in WoSCC searches "title, abstract and author keywords" (January 10th, 2024).  This is a change from the description that was provided In the past (as recently as November 2023), where the Topic field description specifically mentioned title, abstract, author keywords, and keywords plus . So the removal of Keywords Plus from the Topic field description is a recent change. But you will see below that despite the field description (on the database) not mentioning Keywords plus, the TS field still includes Keywords p

Tip #47: Beta PubMed translation tool in Embase

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 I grabbed the following announcement from Embase.com. It appears to be available in Beta now! "The tool streamlines the process, saving time and reducing potential errors in query translation, making it a valuable resource for researchers and medical professionals looking to access the extensive and focused content available in Embase. Key Features: Seamless Transition: It offers a seamless and intuitive platform to effortlessly translate your PubMed queries into Embase queries. No need for manually reformatting your search strings; our tool does it for you. MeSH to Emtree Mapping: Take advantage of our unique mapping feature that automatically converts MeSH terms to Emtree terms. This ensures that your search is as precise as possible, capturing a more extensive range of relevant literature in the Embase database. Time-Saving: Save valuable time with our tool, which streamlines the search process. Quickly and accurately adapt your PubMed queries to the Embase database, allowing

Tip #46: Exporting Records from Clinicaltrials.gov into EndNote

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Many thanks to Ben Harnke, MLIS from the Strauss Health Sciences Library, University of Colorado (ben.harnke@cuanschutz.edu) for this week's tip!   Overview The following are instructions to export records from clincicaltrials.gov (Trials) to EndNote, with the ultimate goal of sending the records to a screening software, namely Covidence. The new Trials website ( https://www.clinicaltrials.gov /) will only export in JSON (Java Script format) and Comma Separated Values (CSV) formats. We will be using the CSV export format, the format for spreadsheets. These instructions are simply slight modifications to the Clarivate instructions for importing tab-delimited files (spreadsheets) into EndNote. Before proceeding with the following instructions, first decide whether it is necessary to export directly from clinicaltrials.gov to begin with. Cochrane CENTRAL contains records from Trials and is more user friendly. CENTRAL is limited to "randomized and quasi-randomized controlled tri

Tip #45: Exploding Subject Terms in EBSCO APA PsycInfo vs. EBSCO MEDLINE

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On the EBSCO platform (or EBSCOhost, if you prefer), MEDLINE and APA PsycInfo both have searchable thesauri. However, while these two thesauri are both hierarchical, EBSCO does not index them in the same way, which leads to inconsistent explosion behavior. This post addresses just those two databases, but the issue itself is relevant across the EBSCO platform. According to EBSCO's documentation,   only MEDLINE, CINAHL, Environmental Policy Index and ERIC support traditional explosion . Those of us who search PubMed are accustomed to how the use of the search tag MeSH (i.e., [mesh] or [mh]) defaults to "explode." In PubMed, exploding begins at the selected term (e.g., Sleep), and retrieves results for that term and everything narrower, all the way to the bottom of the tree. There is no need to manually explode on any narrower terms, even if those terms, (e.g., Sleep Hygiene), have their own narrower terms.  The MEDLINE thesaurus works the same way on EBSCO. In the image be

Tip #44 : Using LitSense for Sentence Retrieval from PubMed and PMC

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Many thanks to Erica Lake (Outreach Coordinator, NNLM Region 6 ) for this week's tip! LitSense is a free, web-based tool from NLM that enables simultaneous semantic searching of PubMed and PMC content. LitSense searches at the sentence-level rather than the article-level, allowing for direct retrieval of specific statements. And it searches by best-match and by meaning, retrieving articles containing sentences with an exact match of keywords as well as those with semantic similarity. Popular uses of this product Discover similar findings across different studies to compare and contrast. Locate and validate publications for evidence attribution. Identify MeSH terms and keyword variations for a PubMed search by reviewing the semantically similar results. Retrieve citations containing a phrase used by requestors when discussing their search topic or completing a search request form. Non-experts can type in a question as a sentence and retrieve relevant information without having to

Tip #43: EMBASE (Ovid) Candidate Terms

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The Gist: Candidate terms can uncover relevant articles not retrieved using title, abstract, or keywords. The difference between word indexed and phrase indexed fields is really important, not just with candidate term fields, but with ALL fields.  In EMBASE, on Ovid, my favored fields are TI (title) , AB (abstract), KF (keyword heading word) and DQ (candidate term word). If you are curious about the KF field, Kate wrote about why you might use it rather than KW in Tip #4 . That keystroke heard around the world on the day Kate's blog dropped was the sound of searchers changing KW to KF.  Today's post, however, is about candidate terms, which Ovid defines as new concepts proposed during indexing and judged to be useful additions to Emtree (EMBASE's thesaurus). Over 100,000 candidate terms are proposed each year!  In addition to having their own fields (DJ & DQ), candidate terms are indexed in SH (EMBASE subject headings) and HW (heading word) fields. Since HW is one of th

Tip #42: PubMed Subheadings and Explosion

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Many thanks to Molly K. Maloney, Pharmacy Liaison Librarian, University at Buffalo, mkm9@buffalo.edu, and Marijane White, Data and Research Engagement Librarian, Oregon Health & Science University, whimar@ohsu.edu for this week’s tip. Molly and Marijane would like to acknowledge and thank Barbara S. Reich, Director, Medical Library, Hackensack University Medical Center, barbara.reich@hmhn.org, Paije Wilson, Health Sciences Librarian, University of Wisconsin-Madison, paije.wilson@wisc.edu, and Michelle L. Zafron, Associate Librarian, University at Buffalo, mlzafron@buffalo.edu for their contributions to this conversation. In a recent post on the Expert Searching mailing list, Molly asked, "In helping a student craft a search that includes a MeSH term with subheading, I realized I was assuming the subheading carry over to the child terms when exploded. As an example, if searching for "Mental Disorders/pathology"[Mesh] will you also get "Anxiety Disorders/pathology

Tip #41: Hyphens in Ovid EMBASE: the Long and Short of it.

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When is a hyphen not a hyphen? When it is a longer hyphen. Dashes range in size from the most narrow, known as a hyphen , to the the slightly wider en dash , to the widest em dash . The en dash is used to represent a span or range of numbers, dates, or time. The em dash can take the place of commas, parentheses, and colons. Unfortunately, neither is meant to appear in your search query in Ovid EMBASE .  Two-part or "hyphenated"  used-for terms in Emtree (EMBASE's thesaurus) on the Ovid platform appear to have either en or em dashes instead of hyphens. I discovered that if you paste one of these "hyphenated" terms into the search box, it returns an unsupported characters error .   For example, if you copy/paste  harmal−d , a used-for term for the medication  tamsulosin ,   into the search box, it will return an unsupported characters error. However, if you replace the long hyphen by typing the hyphen key, your search will work. I contacted Ovid Support bac

Tip #40: Proquest change to set searching syntax

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Proquest has recently changed the query syntax for combining "set" searching from the search history. To reference a previous query in the session, you now need to enclose the set reference in square brackets .  To combine my previous queries in the example below, I must use [S1] AND [S2] AND [S3] .