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PubMed Nuts and Bolts

PubMed Nuts and Bolts. PubMed for Trainers, Spring 2014 U.S. National Library of Medicine (NLM) and NLM Training Center. Goals. Locate details and history about the information included in MEDLINE/PubMed records and S earch the fields of MEDLINE/PubMed records efficiently. Objectives.

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PubMed Nuts and Bolts

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  1. PubMed Nuts and Bolts PubMed for Trainers, Spring 2014 U.S. National Library of Medicine (NLM) and NLM Training Center

  2. Goals • Locate details and history about the information included in MEDLINE/PubMed records and • Search the fields of MEDLINE/PubMed records efficiently. PubMed for Trainers

  3. Objectives • After this session participants will be able to use: • the MEDLINE/PubMed Field Elements Descriptions documentation to find details about the MEDLINE data • the search tags table in PubMed Help to find searchable fields and learn how to search those fields • the Advanced Search page Search Builder to explore PubMed’s indexes • the NLM Catalog Journal search to find journals and build journal sets for searching in PubMed • History to combine searches PubMed for Trainers

  4. The point of the following slides: • MEDLINE/PubMed data structure can vary by field • MEDLINE/PubMed data inclusion has varied over time • PubMed indexing can vary by field • BUT you can search easily because there are tools at your disposal to: • Get details about MEDLINE/PubMed data • View PubMed indexing • Shortcut to the data you need PubMed for Trainers

  5. Part I: The Data PubMed for Trainers

  6. Fields Records PubMed for Trainers

  7. PMID- 22068643 OWN - NLM STAT- MEDLINE DA - 20111109 DCOM- 20120309 IS - 1438-8812 (Electronic) IS - 0013-726X (Linking) VI - 43 Suppl 2 UCTN DP - 2011 TI - Eosinophilic enteritis presenting as a perforated duodenal ulcer. PG - E358-9 AD - Department of Internal Medicine, King Fahad Specialist Hospital, Dammam, Saudi Arabia. ahsalsalem@hotmail.com FAU - Issa, H AU - Issa H FAU - Bseiso, B AU - Bseiso B FAU - Al-Salem, A H AU - Al-Salem AH LA - eng PT - Case Reports PT - Journal Article DEP - 20111108 PL - Germany TA - Endoscopy JT - Endoscopy JID - 0215166 RN - Eosinophilicenteropathy SB - IM MH - Adult MH - Duodenal Ulcer/complications/*etiology/surgery MH - Enteritis/*complications/*diagnosis/drug therapy MH - Eosinophilia/*complications/*diagnosis/drug therapy MH - Gastritis/*complications/*diagnosis/drug therapy MH - Humans MH - Intestinal Obstruction/*etiology/therapy MH - Male MH - Peptic Ulcer Perforation/*etiology/surgery EDAT- 2011/11/10 06:00 MHDA- 2012/03/10 06:00 CRDT- 2011/11/10 06:00 PHST- 2011/11/08 [epublish] AID - 10.1055/s-0030-1256526 [doi] PST - ppublish SO - Endoscopy. 2011;43 Suppl 2 UCTN:E358-9. Epub 2011 Nov 8. MEDLINE FORMAT WITH FIELD LABELS (Tags) PubMed for Trainers

  8. Data structure varies by field • Author [au] or Grant [gr] or Date fields • Highly structured vs. • Affiliation [ad] • NOT structured OR standardized vs. • Abstract [ab] • Sometimes partially structured PubMed for Trainers

  9. Highly Structured MEDLINE Field Examples: Author [au] Lastname initials suffix Examples: AU – Smith AB 3rd AU – McCrary SV Date fields [EDAT], [MHDA] etc. YYYY/MM/DD HH:MM Examples: EDAT – 2003/01/02 04:00 MHDA – 2005/08/03 09:00 Grant Number [gr] Number/code/agency/country Examples:GR - LM0577/LM/NLM NIH HHS/United StatesGR - 058423/Wellcome Trust/United Kingdom PubMed for Trainers

  10. An Unstructured MEDLINE Field Example: Affiliation [ad] PubMed for Trainers

  11. Over time, MEDLINE data inclusion has varied Examples: • Author policy • “New” fields: • Full author name (2002-) • Grant number (1981-) • Location Identifier (2008-) • “Old” fields (no new data): • Gene Symbol (1991-1995) • Number of References (-2010) PubMed for Trainers

  12. Exercise: MEDLINE/PubMed Elements (the data) • Explore the MEDLINE/PubMed Elements documentation • Google MEDLINE, • Go to MEDLINE/PubMed Resources Guide • Under Data Structure, choose Detailed Field/Data Element Descriptions • Look at the author policy • Compare these two records: • PMID 10595696 and • PMID 22922874 PubMed for Trainers

  13. Part II: Indexing PubMed for Trainers

  14. Indexes Records PubMed for Trainers

  15. Search Tags antimicrobial [ti] PubMed for Trainers

  16. Search Tags • Search specific PubMed fields using tags. • Syntax is term [tag], e.g.: Warning! Using search tags turns off Automatic Term Mapping (ATM) PubMed for Trainers

  17. Search Tags (Look in PubMed Help) All PubMed Search indexes are not created equal PubMed for Trainers

  18. Article Title [ti] • [ti] can be used to search for words and phrases in the title field • NOT for the entire title PubMed for Trainers

  19. Journal Title [ta] • [ta] can be used to search for the exact title or MEDLINE title abbreviation • NOT for extracted words or phrases PubMed for Trainers

  20. Combined Index PubMed for Trainers

  21. Title/Abstract [tiab] • [tiab] finds words and numbers included in the title, abstract, and other abstract of a citation. • [tiab] is often used by searchers to find topic-related keywords, BUT: • [tiab] does NOT find terms from the subject fields of PubMed records. PubMed for Trainers

  22. Text word • [tw] includes: • Title • Abstract • MeSH headings & subheadings • Publication Types • Other Terms field • Chemical Names of Substances • Secondary Source Identifier • Personal Name as Subject PubMed for Trainers

  23. Building Phrase Indexes in PubMed • A speech analyzer identifies new noun phrases from the title and abstract fields of PubMed • The phrase is added if it: • occurs at least 3 times in the database • contains at least 1 alphabetic character • has at most 6 words • Phrases are added to the PubMed indexes twice per month PubMed for Trainers

  24. Explore the Indexes • Searchable indexes are accessible from the Search Builder on the PubMed Advanced Search page. PubMed for Trainers

  25. Explore the Indexes (continued) PubMed for Trainers

  26. Exercise: PubMed Indexes Using only the Show Index feature of the PubMed Advanced Search Builder, answer the following questions: • How many PubMed records are for articles in Esperanto? • Is the phrase “finger to nose” indexed in PubMed? PubMed for Trainers

  27. Part III: The Tools PubMed for Trainers

  28. Part III: The Tools • Previously covered: • MEDLINE/PubMed Elements Page • Table of Search Tags in Help • Index on Advanced Search Builder • Next up: • NLM Catalog Journal Search • Search History features PubMed for Trainers

  29. NLM Catalog Journal Search PubMed for Trainers

  30. PubMed for Trainers

  31. PubMed for Trainers

  32. PubMed Search Results: All citations from the International Journal of Oncology PubMed for Trainers

  33. PubMed for Trainers

  34. Broad Subject Terms PubMed for Trainers

  35. Find Related Data PubMed for Trainers

  36. Combining Searches in History PubMed for Trainers

  37. Combining searches in History (cont.) PubMed for Trainers

  38. PubMed for Trainers

  39. Exercise • Use the NLM Catalog Journal Broad Subject Terms to find MEDLINE journals about audiology.  • Search for all citations in PubMed from these audiology journals. • Using History, combine the audiology journal search with a search for cochlear implants. • Limit your search to those that are included in the Systematic Reviews subset. PubMed for Trainers

  40. Summary After this session participants will be able to use: • the MEDLINE/PubMed Field Elements Descriptions documentation to find details about the MEDLINE data • the search tags table in PubMed Help to find searchable fields and learn how to search those fields • the Advanced Search page Search Builder to explore PubMed’s indexes • the NLM Catalog Journal search to find journals and build journal sets for searching in PubMed • History to combine searches PubMed for Trainers

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