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How to interpret PubMed queries and why it matters

Lana Yeganova, Donald C. Comeau, Won Kim, W. John Wilbur
2009 Journal of the American Society for Information Science and Technology  
And, if it does, what is the optimal way of searching with such queries.  ...  Generally, search engines interpret such queries as collections of terms, and handle them as a Boolean conjunction of these terms.  ...  Search results may vary depending on how the query is interpreted by the search engine.  ... 
doi:10.1002/asi.20979 pmid:29456459 pmcid:PMC5815840 fatcat:su7fvph7ibggjikg4nohdmt4tu

How predatory journals leak into PubMed

Andrea Manca, David Moher, Lucia Cugusi, Zeevi Dvir, Franca Deriu
2018 CMAJ - Canadian Medical Association Journal  
What is a predatory journal and why does predatory publishing matter? There is no clear consensus definition for predatory publishers and journals.  ...  PubMed handles millions of queries daily and represents a key source of knowledge for health researchers worldwide.  ...  Lucia Cugusi co-conceived the study, and contributed to the analysis and interpretation of the data.  ... 
doi:10.1503/cmaj.180154 pmid:30181150 pmcid:PMC6148641 fatcat:3zu5svhwt5ei7aqxuw3hygus24

Using Noun Phrases for Navigating Biomedical Literature on Pubmed: How Many Updates Are We Losing Track of?

Devabhaktuni Srikrishna, Marc A. Coram, Andrey Rzhetsky
2011 PLoS ONE  
The "related citations" on PubMed is typically dozens or hundreds of results long, and does not offer hints why these results are related.  ...  Using noun phrases derived from the sentences of the paper, we show it is possible to more transparently navigate to PubMed updates through search terms that can associate a paper with its citations.  ...  and why its search results may be related to the paper.  ... 
doi:10.1371/journal.pone.0024920 pmid:21935487 pmcid:PMC3173492 fatcat:6qn6go6dzra7zknpzwygk7j5eu

Structure-function similarities in deep brain stimulation targets cross-species

Max C. Keuken, Anneke Alkemade, Niek Stevenson, Reilly J. Innes, Birte U. Forstmann
2021 Neuroscience and Biobehavioral Reviews  
Due to its potential, DBS usage is rapidly expanding to target a large number of brain regions to treat a wide range of diseases and neuropsychiatric disorders.  ...  This can potentially be attributed to shared brain networks and might explain why multiple brain areas are targeted for the same disease or neuropsychiatric disorder.  ...  Acknowledgments Funding: This work was supported by an ERC Consolidator (BUF), NWO-Vici (BUF) and STW/NWO (AA, BUF) grant.  ... 
doi:10.1016/j.neubiorev.2021.10.029 pmid:34715147 fatcat:cshn5yveizak3nyyzrkd4imarm

Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data

Chao Zhang, Jochem Bijlard, Christine Staiger, Serena Scollen, David van Enckevort, Youri Hoogstrate, Alexander Senf, Saskia Hiltemann, Susanna Repo, Wibo Pipping, Mariska Bierkens, Stefan Payralbe (+14 others)
2017 F1000Research  
Woolf SH: The meaning of translational research and why it matters. JAMA. 2008; 299(2): 211-213. PubMed Abstract | Publisher Full Text 3.  ...  Nevertheless, complex computational workflows are required to interpret these data. PubMed Abstract | Publisher Full Text | Free Full Text 2.  ...  For example, it may be unclear to the user why there is no access to a certain file, and who should be approached if access is needed.  ... 
doi:10.12688/f1000research.12168.1 pmid:29123641 pmcid:PMC5657030 fatcat:pmccjyaoffbmfd4rdcreqnx7je

Biomedical Informatics [chapter]

C David Page, Sriraam Natarajan
2017 Encyclopedia of Machine Learning and Data Mining  
It provides a simple Google-like interface for easy usage and interpretation.  ...  MiSearch [42] is a web application that queries PubMed to retrieve publications. Its unique feature is the ability to adapt its ranking algorithm to the previous queries built by a user.  ... 
doi:10.1007/978-1-4899-7687-1_30 fatcat:45z6hsbczvaj3ajx3c3xf3bfpm

An Introduction and Applications of DOI [article]

Nader Ale Ebrahim
2017 Figshare  
The DOI is like a digital fingerprint: Each article receives a unique one at birth, and it can be used to identify the article throughout its lifespan, no matter where it goes.  ...  In this workshop you will learn how to define a DOI, prepare Meta Data, and assign a DOI for a journal paper.  ...  For more information on how to query for DOIs to include in your references please refer to the Queries and Retrieving Metadata section of our help documentation. • One tip for simplifying the implementation  ... 
doi:10.6084/m9.figshare.4509044.v1 fatcat:mz4zyryu7ffv3kbrfyvgkylr5a

Hypothesis, analysis and synthesis: it's all Greek to me! [article]

Ioannis Iliopoulos, Sophia Ananiadou, Antoine Danchin, John PA Ioannidis, Peter D Katsikis, Christos A Ouzounis, Vasilis J Promponas
2019 bioRxiv   pre-print
Finally, we invite commentary by both the science community and the humanities, for possible adoption of suggested terms, not least to avoid inaccurate usage or inappropriate notions that may compromise  ...  We argue that the etymology of those critical terms needs to be fully grasped to ensure correct use, in conjunction with other concepts.  ...  'to', 'in') and short verb forms (e.g. 'is', 'was'), and retain mostly nouns and a few adjectives, to examine how many commonly used words deriving from Greek can cover (how much of) PubMed ® .  ... 
doi:10.1101/561175 fatcat:3rghdfz7d5go7e4dvlcnophtim

Studying PubMed usages in the field for complex problem solving: Implications for tool design

Barbara Mirel, Jennifer Steiner Tonks, Jean Song, Fan Meng, Weijian Xuan, Rafiqa Ameziane
2013 Journal of the American Society for Information Science and Technology  
Few, if any, studies, however, examine scientists' problem-solving uses of PubMed in actual contexts of work and corresponding needs for better tool support.  ...  Our findings highlight the need to use results from context-rich studies to inform decisions in tool design about when to offer improved features to users.  ...  Acknowledgments This research was funded by two NIH grants: 1 RO1LM009812-01A2 and U54 DA021519.  ... 
doi:10.1002/asi.22796 pmid:24376375 pmcid:PMC3873776 fatcat:rmboc7rwgfbbpjsn3mbnjw3rh4

Think outside the search box: A comparative study of visual and form-based query builders [article]

Tanja Svarre, Tony Russell-Rose
2022 arXiv   pre-print
In this paper, we evaluate a new approach to query building in which users express concepts as objects on a visual canvas and compare this with traditional form-based query building in a lab-based user  ...  In the majority of cases, these query builders are designed using a form-based paradigm that requires the user to enter keywords and ontology terms on a line-by-line basis and then combine them using Boolean  ...  In addition, the tool allows researchers to visualise why the queries they formulate retrieve citations, and to understand how to refine queries into more effective ones.  ... 
arXiv:2205.04212v1 fatcat:anpiydmjjfaj3ic4k3za4pjeti

Lost in PubMed. Factors influencing the success of medical information retrieval

Klaar Vanopstal, Joost Buysschaert, Godelieve Laureys, Robert Vander Stichele
2013 Expert systems with applications  
The queries in this collection are all aimed at finding the same specific information in PubMed, which allowed us to identify what exactly went wrong in the query formulation step.  ...  PubMed/MEDLINE offers an alternative to freetext searching on the web, allowing searchers to do a keyword-based search using Medical Subject Headings.  ...  - provided that the user understands how search terms map to MeSH terms and how PubMed's search engine works in general.  ... 
doi:10.1016/j.eswa.2013.01.036 fatcat:gs23hoxk6bgmlebq3us6qn3k2a

Health services and health literacy: from the rationale to the many facets of a fundamental concept. A literature review

Guglielmo Bonaccorsi, Chiara Lorini, Alberto Baldasseroni, Barbara Rita Porchia, Leonardo Capecchi
2016 Annali dell'Istituto Superiore di Sanità  
A literature search was conducted in PubMed, Embase, PsycINFO, ERIC, Health Evidence, Centre for Reviews and Dissemination and Cochrane Library.  ...  Google and OpenGrey were searched to find additional papers and unpublished works. Among 7000 papers founded, we selected 26 works.  ...  Acknowledgements The authors wish to thank Claudia Dellisanti for the support in the development of the search strategy.  ... 
doi:10.4415/ann_16_01_18 pmid:27033626 fatcat:uun2dkzg2rajrf6qhd244nlaua

Spelling correction in the PubMed search engine

W. John Wilbur, Won Kim, Natalie Xie
2006 Information retrieval (Boston)  
It is known that users of internet search engines often enter queries with misspellings in one or more search terms.  ...  Here we describe the methodology we have developed to perform spelling correction for the PubMed search engine.  ...  Acknowledgments The authors would like to thank David Kenton and Pramod Paranthaman for insightful discussions and for their work evaluating the algorithm and Vladmir Sirotinin and Grisha Starchenko for  ... 
doi:10.1007/s10791-006-9002-8 pmid:18080004 pmcid:PMC2137159 fatcat:vlhpvoleezdjbmto37pfy3mytu

Public access policy support programs at libraries: A roadmap for success

Molly Keener, Cathy Sarli
2010 College & research libraries news  
Smith Reynolds Librar y at Wake Forest University, e-mail:, and Cathy Sarli is scholarly communications specialist at the Becker Medical Library at Washington University School of Medicine  ...  affairs, legal matters, or grants and contracts or sponsored research.  ...  an office that handles grant and contracts or sponsored research, or using databases such as PubMed, Web of Science, or NIH's RePORTER. 2 One caveat to using PubMed and Web of Science is that retrieval  ... 
doi:10.5860/crln.71.10.8457 fatcat:56cfmczaibeyheccxd3jgktjvu

The Why and the How of Evidence-Based Medicine

Eddy Lang
2020 McGill Journal of Medicine  
SHEDDING LIGHT ON RESEARCH LITERATURE: THE WHY OF EBM In thinking about this article I decided that it might be instructive to describe how I became a proponent (some would say zealot) of the EBM approach  ...  The Why and the How of Evidence-Based Medicine Eddy Lang*, MDCM, CCFP(EM), CSPQ The term "Evidence-Based Medicine" (EBM) has become so ubiquitous in the health care literature that many have begun to wonder  ... 
doi:10.26443/mjm.v8i1.552 fatcat:2l3kgvqvxfairfzd4obynqwggu
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