Information Retrieval in Health-Related Natural Sciences Applied physics, biomedicine, environmental sciences, medical engineering and computing, nutrition, pharmacy, toxicology University of Eastern Finland Library Heikki Laitinen heikki.laitinen@uef.fi 2017 UEF // University of Eastern Finland
Critical success factors in information retrieval Understanding your topic to be searched Ability to transform the topic into keywords and search queries Understanding the process nature of searching Preparation, execution, evaluation of results Part of your research process Continuous process Knowing relevant information sources and how to use them Getting access to primary information Electronic and printed journals Electronic and printed books UEF // University of Eastern Finland Heikki Laitinen 2017 2
The information retrieval problem How can you find all needed information, maximizing the number of relevant search results and minimizing the number of irrelevant ones? UEF // University of Eastern Finland Heikki Laitinen 2017 3
Search recall and precision Recall (sensitivity): Precision (specificity): Recall and precision are inversely proportional In a comprehensive search (high recall), you get also irrelevant results (low precision), and vice versa UEF // University of Eastern Finland Heikki Laitinen 2017 4
Search recall and precision What are the reasons for this phenomenon? But: Search query can be seen as a model of search topic, consisting of keywords and defined relationships between keywords. This model represents topic incompletely. Even scientific language is not exact. The keywords may be inaccurate and have multiple meanings. Information retrieval system finds character strings only, not meanings which are essential to searcher. If all search keywords are exact and have only one meaning, then both recall and precision may be 100%. E.g.: find ADI (acceptable daily intake) for benzoic acid. UEF // University of Eastern Finland Heikki Laitinen 2017 5
How to do a literature search Select suitable literature reference database(s) UEF-Finna -> English -> Browsing views -> Databases Search UEF-Finna by database name UEF library home page -> Information retrieval support -> Quick Reference Define search strategy and formulate search queries Search database(s) Iterative process: review initial search results and modify your search, if necessary Save search results to reference management program, such as RefWorks Select relevant references and obtain complete articles UEF // University of Eastern Finland Heikki Laitinen 2017 6
How to obtain complete articles Use "Full text availability at UEF" links in RefWorks Use SFX links in database search results Try UEF-Finna (printed and e-journals) Try Unpaywall Free plug-in for Firefox and Chrome, available from unpaywall.org Finds legal open access versions from thousands of repositories worldwide How to use see the video: https://www.youtube.com/watch?v=fxjmkwql_dc Try Google Check Finnish National Repository Library (Varastokirjasto) Especially older articles You can request free PDF copies via UEF-Finna, see the video: https://www.youtube.com/watch?v=trjrporoq60 Request via UEF Library Interlibrary Service (subject to charges) UEF // University of Eastern Finland Heikki Laitinen 2017 7
Search strategies Quick search (called also "quick and dirty") Think up some words about your topic and search as if you were using Google Useful, when: you want to find just something quickly, need only few publications, want to familiarize yourself with your topic, etc. Unfortunately too many people use this strategy only in all their searches ("Google effect") How can you be sure that you found all relevant publications? Block search Analyze your topic carefully (main concepts and sub-concepts) Find out keywords which describe your concepts as precisely as possible Create search queries by combining keywords with Boolean operators Useful in situations where your topic is well-defined and you want comprehensive search results UEF // University of Eastern Finland Heikki Laitinen 2017 8
Search strategies Citation pearl growing Useful when your topic is ambiguous and it is difficult to find keywords Start with one known relevant article Search a database to find the article reference Examine the reference to find suitable keywords, and do the actual search with these keywords Some databases display "related articles" links in search results to make pearl growing easy Citation searching Based on the assumption that there is a relationship between publication s content and citations in the publication E.g. you have older "classic" journal article and would like to find newer ones, which have cited the classic UEF // University of Eastern Finland Heikki Laitinen 2017 9
How to formulate a search query Search query is search topic (natural language) interpreted into database search language Define your topic Write a short description about the topic Define concepts and their relationships Mind map or tabular form Dependence: "Effect of A on B" (Boolean AND in search) Parallelism: "C and D are included in B" (Boolean OR in search) Exclusion: "M, but without N" (Boolean NOT in search) Find keywords corresponding to concepts Free-text keywords or thesaurus-based keywords Combine keywords to create search query or queries Usually, several queries are needed even if there is only one search topic UEF // University of Eastern Finland Heikki Laitinen 2017 10
Mind map example UEF // University of Eastern Finland Heikki Laitinen 2017 11
Tabular form example Topic: Workers exposure to organophosphates and carbamates through skin UEF // University of Eastern Finland Heikki Laitinen 2017 12
Free-text keywords Words which appear in titles and abstracts of publications Think up by yourself, look from dictionaries, use Google, etc. Must be in language used in the database (mostly English) Use truncation to retrieve different wordings, singular, plural, etc. pollut* -> pollution, polluted, pollutant, pollutants, etc. Use synonyms if you want to do comprehensive search Dust OR "fine particles" OR "particulate matter" (place phrases in quotes) UK English / US English (sulphur, sulfur, "coeliac disease", "celiac disease", etc.) Homonyms (words with multiple meanings) produce false search results E.g there are 8 different meanings for "administration" in MOT dictionary Use complete phrase instead of abbreviation, if it is ambiguous NLP: "neuro-linguistic programming" or "natural language processing"? Use free-text keywords when: Your topic is specific / precisely defined Terminology of the topic is well established and unambiguous UEF // University of Eastern Finland Heikki Laitinen 2017 13
Thesaurus-based keywords Also known as descriptors or subject headings Thesaurus is a structured, subject-specific list of descriptors Descriptors are standardized words (controlled vocabulary) used in information storage and retrieval Subjects of publications are described with descriptors in the database The same descriptors may be used in searching Link to thesaurus is often on database search page Descriptors highlight the essential content of a publication, regardless of words in title and abstract Use of descriptors increases search recall and precision Most recent concepts may not be found in descriptors You can combine descriptors and free-text keywords Medical Subject Headings (MeSH) is the most important thesaurus in health sciences and related natural sciences Use MeSH in PubMed search queries UEF // University of Eastern Finland Heikki Laitinen 2017 14
Combining keywords Boolean operators OR, AND, NOT Keywords and Boolean operators may be typed either in lower or UPPER case (type operators always in upper case when searching PubMed database) Use OR to combine synonyms: eye OR ocular Use AND to join dependent concepts: soil AND pollution Use NOT to exclude concepts: solvents NOT (ethanol OR methanol) It is possible to use several operators in one query AND s are executed first by default, then OR s If there are both AND and OR operators in a query, use parentheses to override default execution and retain correct search syntax Operators in parentheses are executed first (dust OR particle* OR particulate*) AND atmospher* UEF // University of Eastern Finland Heikki Laitinen 2017 15
Boolean logic UEF // University of Eastern Finland Heikki Laitinen 2017 16
Tabular form example Topic: Workers exposure to organophosphates and carbamates through skin UEF // University of Eastern Finland Heikki Laitinen 2017 17
Search query example 1 Thesaurus-based search in PubMed database Topic: workers exposure to pesticides Concepts Workers Exposure Pesticides Medical Subject Headings Occupational Exposure Pesticides Search query "Occupational Exposure"[mesh] AND Pesticides[mesh] UEF // University of Eastern Finland Heikki Laitinen 2017 18
Search query example 2 Free-text keyword search in Scopus database Topic: health effects of molds in indoor air Concepts and free-text keywords indoor (air) mold, mould health effects (also: effects on health, etc.) Search query indoor AND (mold* OR mould*) AND (health* W/2 effect*) Note parentheses, keyword truncation and proximity operator W/2 Keywords may be in either order but no more than specified number of words apart Number may be chosen freely, usually 1-4 is appropriate UEF // University of Eastern Finland Heikki Laitinen 2017 19
Search query example 3 Boolean AND is not the same as "and" in natural language Topic is expressed as: "big data and data mining in nutrigenetics, in nutrigenomics, in pharmacogenetics and in pharmacogenomics" Information is actually needed: Either about big data or about data mining, or about both topics together Related to nutrition or to pharmacy, or to both Thus the search query is: ("big data" OR "data mining") AND (nutrigen* OR pharmacogen*) UEF // University of Eastern Finland Heikki Laitinen 2017 20
What to do, if you get Too few search results or no results at all Increase search recall (sensitivity) and decrease precision (specificity) Check spelling of keywords (e.g. naphthalene instead of naphtalene) Use broader (more general) keywords Use fewer AND operators Find synonymous keywords and combine them with OR operators Truncate keywords Too many search results Increase search precision (specificity) and decrease recall (sensitivity) Use narrower (more precise) keywords Add more keywords with AND operators Use fewer synonyms (fewer OR operators) Limit your search: keywords in titles only; the most recent references only; english only; review articles only UEF // University of Eastern Finland Heikki Laitinen 2017 21
PubMed The essential journal article reference database in health sciences and related areas, produced by the U.S. National Library of Medicine Freely accessible on the Internet Contains more than 27 million references from about 5600 journals, starting in 1950 s Search techniques: Enter complete query in Search box Use Advanced search to find individual concepts first, then combine these search sets to produce the final result Search results (references) are linked to full texts SFX link on top right corner of the abstract page You can set alerts (automatic e-mail notification of new articles) UEF // University of Eastern Finland Heikki Laitinen 2017 22
Scopus Multidisciplinary literature reference database, produced by Elsevier, the Netherlands About 22800 peer reviewed journals, of which 3600 are open access journals Articles In press from more than 5000 journals More than 67 million journal article references 8 million references to conference papers 28 million references to patents from 5 patent authorities Analysis of search results To find out e.g. research institutions, authors, or journals in certain subject area Do a broad (high recall) search to get statistically significant analysis Click "Analyze search results" on top of the search results screen Citation counts and author h index available UEF // University of Eastern Finland Heikki Laitinen 2017 23
Scopus Search results are SFX-linked to full text articles Search results may be exported directly to RefWorks Stemming You may enter keyword in singular form, Scopus finds plural and possessive forms automatically Use asterisk to truncate and replace 0-n characters inside keyword metabol* *tocopherol sul*ur You may also use question mark or marks to replace characters wom?n Number of question marks equals number of characters replaced UEF // University of Eastern Finland Heikki Laitinen 2017 24
Scopus Use braces to search for exact phrases {or not to be?} Use quotes to search for broader phrases "heart attack*" (phrase truncation is possible) If braces of quotes are missing, keywords are combined automatically with AND orange juice -> orange AND juice UEF // University of Eastern Finland Heikki Laitinen 2017 25
Scopus Boolean operators (AND, OR, AND NOT) may be either selected from menus or written directly to query (sweeten* AND NOT (sugar* OR sucrose)) AND diabet* Proximity operators W/n (n=0-255) : There may be at most n other words between keywords, keywords may be in either order PRE/n (n=0-255) : There may be at most n other words between keywords, keywords must be in given order (indoor* PRE/2 pollut*) AND (health* W/2 effect*) Use of proximity operators increases search precision UEF // University of Eastern Finland Heikki Laitinen 2017 26
Web of Science Multidisciplinary journal article reference database, produced by Clarivate Analytics, USA Citation counts and author h index available Web of Science in the University of Eastern Finland: Science Citation Index Expanded 1975- Fully covers 8300 journals (150 disciplines) Social Sciences Citation Index 1975- Fully covers 2900 journals (50 disciplines) Arts & Humanities Citation Index 1975- Fully covers 1600 journals UEF // University of Eastern Finland Heikki Laitinen 2017 27
Web of Science Ordinary searching is possible by: topic, author, journal name, publication year, author address Topic = title words, abstract words, free-text keywords There is no thesaurus in Web of Science Search results are SFX-linked to full text articles Search results may be exported directly to RefWorks Analysis of search results To find e.g. research institutions, authors, or journals in certain subject area Do a broad (high recall) search to get statistically significant analysis Click "Analyze Results" on top of the search results screen Select analyzing parameters UEF // University of Eastern Finland Heikki Laitinen 2017 28
Web of Science Use asterisk to truncate and replace 0-n characters metabol* *tocopherol sul*ur Use question mark to replace exactly one character wom?n Use dollar sign to replace 0-1 characters colo$r You may include several truncation characters in a keyword organi?ation* UEF // University of Eastern Finland Heikki Laitinen 2017 29
Web of Science Use quotes to search for phrases "heart attack*" (phrase truncation is possible) If quotes are missing, keywords are combined automatically with AND orange juice -> orange AND juice UEF // University of Eastern Finland Heikki Laitinen 2017 30
Web of Science Boolean operators (AND, OR, NOT) may be either selected from menus or written directly to query (sweeten* NOT (sugar* OR sucrose)) AND diabet* Proximity operator NEAR/n : There may be at most n other words between keywords, keywords may be in either order NEAR (without a number) : There may be at most 15 other words between keywords (equivalent to NEAR/15) (indoor* NEAR/2 pollut*) AND (voc OR volatile) Use of proximity operators increases search precision UEF // University of Eastern Finland Heikki Laitinen 2017 31
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