Basic reading, writing and informatics skills for biomedical research

1. Basic reading, writing and informatics skills for biomedical research Segment 3. Using the virtual library Ganesha Associates

2. The scientific research process[Greatly simplified!] More experiments Experiments Problem definition Seminar Conference proceedings Writing-up Publication Grant proposal Key: Experiments Reading and writing Verbal communication Ganesha Associates

3. Finding a place to start • Finding the frontier • Scientific weeklies, Nature, Science • Top international journals in your field • Conference reports • Talk with a leader in the field • Understanding the background • Review journals • Trends in…, Current Opinions in…, Annual Reviews in…, Nature Reviews in… • Use ‘cited by’ functionality in Scopus and WoS • Use ‘related article’ functionality in PubMed Ganesha Associates

4. “Little is known about…” • Means either the area is of little interest, or you haven’t done your literature search effectively! • Ask an expert for guidance • Use a comparative or inductive approach and look for examples in similar systems - this technique is particularly useful in any field with a molecular component Ganesha Associates

5. What is a literature review ? • A literature review is a survey of what has been published in peer-reviewed scientific journals about a particular research question at this moment in time. • The aim is to provide the reader with an overview of the knowledge theories and main areas of discourse within a particular subject. • It will include descriptions and summaries of key ideas, plus critical evaluation of the ideas being presented, comparison between commentators etc. • As a piece of writing, the literature review must be defined by a guiding concept - your research objective. • So it is not just a descriptive list of the material available, or a set of summaries – it is a proposal, a plan of action, based on a solid foundation of evidence. Ganesha Associates

6. How to write a literature review • Start from a general perspective to orient the reader to the importance of field to are working in • But bring them quickly to the areas that of particular importance today • Provide a logical framework for selecting one of these problems • And then explain how the problem can be solved, giving the reasons for the approach you have selected Ganesha Associates

7. Search not just document retrieval • Get me the abstract/full text for this specific citation • What is the latest research on subject x ? • What is the latest review on subject y ? • Who has cited this article recently • What labs are working on this problem ? Ganesha Associates

8. How many piano tuners live in Chicago ? • What genes are involved in the melanogenesis of human lung cancers? • What proteins in rats perform functions different from those of their human homologs? • What is the drug of choice for condition x ? • Can drug x cause (adverse) finding y ? • Find safety-related information associated with GSK product x, competitor product y and drug class z Ganesha Associates

9. Can drug x cause (adverse) finding y ? • Drug x synonyms, spelling ? • Finding y synonyms • “Adverse”, “side effect”, etc • Query finds all documents containing these words, regardless of causal relationship Ganesha Associates

10. How do search engines find things ? • All documents are indexed by building a list of key words, often called an index • The index algorithm will make an entry for each term or word found in a document • Stop words, such as "the", “by”, “within” which are both too common and carry too little meaning to be useful for searching are ignored Ganesha Associates

11. The structure of an A&I database record • Journal name, ISSN, date of publication, volume, page numbers • Authors names • Address, affiliation, contact details • Titles • Keywords • Abstract • Metadata Ganesha Associates

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13. How do search engines find things ? • Some indexers also use ‘stemming’, for example any of the words “enzyme", “enzymatically", or “enzymatic" will be recorded in the index under “enzyme" • At the retrieval stage only the index is searched rather than the text of the original documents • Documents containing the search terms can be ranked in a variety of very different ways Ganesha Associates

14. How do search engines find things ? • Google uses PageRank • PubMed ranks by data of acquisition • Scopus and Web of Science rank either by data of publication or relevance • Relevance is calculated by a formula which takes into account of where and how often the search terms appear in the document • Even if the search engines searched the same content (they don’t!), they would order the results differently Ganesha Associates

15. How do humans find things ? • They don’t look beyond the first page • They select articles by title or (less often) author, rarely by journal • They often make little attempt to modify their search terms if they cannot find what they want Ganesha Associates

16. So, use keywords carefully Question 1: What is the optimal management strategy for radial head fractures based on randomized controlled trials? Keywords: radial head fractures randomized Result: 9 records found, one judged highly relevant Question 2: Paper by Glasziou on radial fractures in the BMJ in 2007? Keywords: glasziou fractures bmj 2007 Result: 1 record (the target) found. Question 3: Review article on the state of vitreous body (of the eye) and time of death? Keywords: vitreous body time death Result: 7 records found, several relevant. Note: These examples are from PubMed Ganesha Associates

17. Improving recall precision Keywords. Trained indexers supply a list of words and their synonyms that describe the subject of the text, e.g. MeSH Field-restricted search. Some search engines enable users to limit free text searches to a particular field within a stored data record, such as "Title" or "Author.“ Boolean queries. Searches that use Boolean operators (for example, “drug" AND “side effect" NOT “headache") can dramatically increase the precision of a free text search. Ganesha Associates

18. Improving recall precision Phrase search. A phrase search matches only those documents that contain a specified phrase, such as “cancerous growth" Proximity search. A phrase search matches only those documents that contain two or more words that are separated by a specified number of words Wildcard search. A search that substitutes one or more characters in a search query for a wildcard character such as an asterisk. For example, "s*n" will find "sin", "son", "sun", etc. in a text. Ganesha Associates

19. Real queries - Google • pharmacogenomics and disorders • bacteria growth casein media effect • waal pseudomonas • TRPM2 PCR mouse • Chitinases in carnivorous plants • glycerophosphoinositol 4-phosphate • Dai N, Gubler C, Hengstler P, Meyenberger C, Bauerfeind P. Improved capsule endoscopy after bowel preparation. GastrointestEndosc 2005;61(1) 28-31. Ganesha Associates

20. Real queries - PubMed • ATR1 HAL2 • Fuzzy[ALL] AND Hanage[AU] AND 2005[DP] • arndt and rhabdomyosarcoma • "Vorster HH"[Author] • (rotavirus infections[majr] OR rotavirus[majr]) AND english[la] AND humans[mh] NOT (editorial[pt] OR letter[pt]) Ganesha Associates

21. More examples of search terms - PubMed hurley M J [auth] AK230159 cytokinin signalling in arabidopsis A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors cytochrome P450cam gene sequence target of wingless in drosophila Ganesha Associates

22. Search terms – PubMed via Google Diabetes high blood pressure losartan potassium ET-1 AND sepsis AND heart 17[volume] AND 17[page] AND 2004[pdat] beta-galactosidase + plant + flower "transient K+ current" motoneuron determining time of death by body temperature Ganesha Associates

23. Query changes people actually make • Query 1 • latrunculin • latrunculin fm3a cell arrest • latrunculin fm3a arrest • latrunculin fm3a • latrunculin FM3A • Query 2 • cytokininsignalling in arabidopsis • "cytokininsignalling in arabidopsis" • cytokinin delta • spindly arabidopsis • Results • Remember to look beyond the first page. Compare the reults of Query 1 in PubMed and Google (add the term PubMed) Ganesha Associates

24. Search terms - summary • Make sure you understand the search term syntax used by your preferred site, i.e. AND, +, “ ”, etc • Search engines ‘see’ only certain words, not sentences • Do not use ‘stop’ words, i.e. a, the, of, before unless they are part of “a text string search” • Google can be an effective tool for searching Entrez(PubMed) databases Ganesha Associates

25. Special features: Google • Unlike PubMed, Google searches web pages. • Google supports OR and NOT Boolean operators. • Submitting a query to Google in the form [propanolol hypertension] will return all the web pages that match both "propanolol" and "hypertension" exactly • However, some of the terms may reside not on the retrieved page itself, but on pages that link to the retrieved page • Instead of returning web pages chronologically, Google employs a unique method called PageRank and sophisticated text-matching techniques to find pages that are both important and relevant to a query. Ganesha Associates

26. Special features : PubMed • PubMed is a service of the National Library of Medicine that includes over 15 million bibliographic citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. • The full text of articles is not stored by the system – only “header” information (title, authors names, abstract, etc) • Each article is indexed according to multiple fields, including title, abstract, author names, journal name, language of publication, year of publication, etc. Ganesha Associates

27. Special features : PubMed • Each article in MEDLINE is also indexed using a controlled vocabulary, called Medical Subject Headings (MeSH), which is used to describe the main topics discussed. • The set of MeSH terms is manually assigned by biomedical experts who scan each article. • Results are ranked in reverse chronological order (default setting) Ganesha Associates

28. The Medical Subject Headings classification • Controlled vocabulary, thesaurus. • MeSH terms are arranged in a hierarchy of "MeSH Tree Structures". • When PubMed searches a MeSH term, it will automatically include narrower terms in the search, if applicable. This is also called "automatic explosion." • When you click Go, PubMed will look for a match in up to four lists. It looks first for a match in the MeSH Translation Table. If it doesn't find a match, it looks in the Journals Translation Table, then in the Phrase List, and finally in the Author Index. Ganesha Associates

29. Special features : Scopus • Scopus is the largest abstract and citation database. It covers: • 15,000 peer-reviewed journals from more than 4,000 international publishers, including coverage of: • Over 1200 Open Access journals • 500 Conference Proceedings • Over 600 Trade Publications • 200 book series • 33 million records, of which: • 16 million records include references going back to 1996 (75% include references) • 17 million pre-1996 records go back as far as 1841 • Scopus also covers 386 million quality web sources, including 22 million patents. Ganesha Associates

30. Special features : ScienceDirect • ScienceDirect (Elsevier) contains over 25% of the world's science, technology and medicine full text and bibliographic information. • Apart from online eBooks, Reference Works, Handbooks and Book Series ScienceDirect offers a rich journal collection of over 2,500 titles. • In addition, the Backfiles program offers the ability to search a historical archive of over 6.75 million articles directly from your desktop, back to Volume 1, Issue 1. The collections contain four million articles prior to 1995, and 2.75 million articles from after 1994. Ganesha Associates

31. Special features : Web of Science • The Web of Science provides seamless access to current and retrospective multidisciplinary information from approximately 8,700 of the most prestigious, high impact research journals in the world. • Web of Science also provides a unique search method, cited reference searching. • With it, users can navigate forward, backward, and through the literature, searching all disciplines and time spans to uncover all the information relevant to their research. • Users can also navigate to electronic full-text journal articles. Ganesha Associates

32. Search engine ‘arms race’ • Scopus and Web of Science will continue to compete to provide user friendly tools for document retrieval • Their coverage will gradually expand to include all jouenals (including national ones) • PubMed (and NCBI) will focus on making it easier to search across different types of biomedical data • Journal coverage will remain limited compared to Scopus and Web of Science Ganesha Associates

33. Additional features • Related articles • PubMed • Cited by • Scopus, WoS • Curated links to other forms of related material • PubMed • Personalisation features e.g. MyNCBI • PubMed, Scopus, WoS Ganesha Associates

34. Set up alerts • Search alerts send new results from a previous search directly to your mailbox. • Document citation alerts notify you when an article you specify is cited by another article. • Author citation alerts to notify you when any of an author's publications get cited. • The alerts can run daily, weekly or monthly and deliver new results to you by e-mail. Ganesha Associates

35. About RSS • RSS (Really Simple Syndication) is an XML-based syndication format for distributing content on the Web. Many kinds of content can be distributed using the RSS format including Scopus® search and citation results. • Scopus offers XML-based feeds so you can receive updates on your desktop of all newly loaded content matching your search criteria. Each feed contains a list of the most recent titles which link back to the appropriate article in Scopus. Scopus content is refreshed every day. • Scopus feeds are in RSS 2.0 format. To use a Scopus RSS feed, you must have an RSS reader. Ganesha Associates

36. Cited by… Ganesha Associates

37. Why things sometimes don’t work Ganesha Associates

38. Managing your literature research on your computer • Download PDF/HTML versions of important documents • Give the files concise explanatory titles so you will remember what they are about • Ditto folder names • Download Google Desktop Search, a utility that indexes all the files on your PC and displays results in a Google search page Ganesha Associates

39. Citation management software • Zoteroand Mendeley are freeapplications that help you collect, manage, and cite your research sources • Use EndNote to search online bibliographic databases, organize references, images and PDFs in any language, and create bibliographies and figure lists • Reference Manager is the industry standard software tools for publishing and managing bibliographies on the Windows and Macintosh desktop • Confused ? Go to Wikipedia for a comparison of the features of these and other software packages Ganesha Associates

40. Starting to search Ganesha Associates

41. ? Scielo CAPES Portal Web of Science Scopus PubMed Google National Literature OA: BMC Or PLoS Science Direct Springer Link HighWire Other Databases, e.g. NCBI Initial choices Ganesha Associates

42. BLAST results AbstractPlus AbstractPlus AbstractPlus Full Text Full Text Full Text NCBI full_report Search results Search results GOOGLE search GOOGLE search Anatomy of a session Ganesha Associates

43. Google search Ganesha Associates

44. PubMed search Ganesha Associates

45. Scopus search Ganesha Associates

46. Access to full-text depends on whether… The journal is on CAPES list CAPES has a current subscription with the publisher The publisher has provided linking information to PubMed/Scopus, etc The link points to a source which recognises your institution as a CAPES subscriber The journal has an open access policy after 0, 6, 12, 24 months Many journals are available from more than one site, but not all may recognise you as a subscriber Remember: Subscribed-to content is only available on campus Ganesha Associates

47. PubMed search Ganesha Associates

48. PubMed Search Ganesha Associates

49. PubMed Search Ganesha Associates

50. Scopus search Ganesha Associates