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PubMed for Trainers Winter 2015 U.S. National Library of Medicine (NLM) and NLM Training Center PubMed Nuts and Bolts.

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Presentation on theme: "PubMed for Trainers Winter 2015 U.S. National Library of Medicine (NLM) and NLM Training Center PubMed Nuts and Bolts."— Presentation transcript:

1 PubMed for Trainers Winter 2015 U.S. National Library of Medicine (NLM) and NLM Training Center PubMed Nuts and Bolts

2 Goals Revised January 2015 Locate details and history about the information included in MEDLINE/PubMed records and Search the fields of MEDLINE/PubMed records efficiently.

3 Objectives Revised January 2015 After this session participants will be able to use: the MEDLINE/PubMed Data Element (Field) Descriptions 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

4 The point of the following slides: Revised January 2015 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

5 Part I: The Data Revised January 2015

6 PMID TITLEEosinophils in the gastrointestinal tract AUTHORStraumann A LANGUAGEEnglish SOURCEActa Gastroenterol Belg Sep;75(3):310-5 PMID TITLEChanging antimicrobial resistance pattern AUTHORJain S LANGUAGEEnglish SOURCEJ Assoc Physicians India May;60:27-8, 33 PMID TITLEGut bacteria and antimicrobial resistance AUTHORKanerva M LANGUAGEFinnish SOURCEDuodecim. 2012;128(17): Records Fields Revised January 2015

7 PMID OWN - NLM STAT- MEDLINE DA DCOM IS (Electronic) IS X (Linking) VI - 43 Suppl 2 UCTN DP TI - Eosinophilic enteritis presenting as a perforated duodenal ulcer. PG - E358-9 LID /s [doi] AD - Department of Internal Medicine, King Fahad Specialist Hospital, Dammam, Saudi Arabia. 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 PL - Germany TA - Endoscopy JT - Endoscopy JID RN - Eosinophilic enteropathy 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 /s [doi] PST - ppublish SO - Endoscopy. 2011;43 Suppl 2 UCTN:E Epub 2011 Nov 8. Revised January 2015 MEDLINE format with field labels (Tags)

8 Data structure varies by field Revised January 2015 Highly Structured: Author [au] or Grant [gr] or Date fields vs. NOT structured OR standardized Affiliation [ad] vs. Sometimes partially structured Abstract [ab]

9 Highly-structured MEDLINE field examples Revised January 2015 Author [au]Format:Lastname initials suffix Examples:AU – Smith AB 3 rd AU – McCrary SV Date fields [edat], [mhda], etc. Format:YYYY/MM/DD HH:MM Examples:EDAT – 2003/01/02 04:00 MHDA – 2005/08/03 09:00 Grant Number [gr] Format:Number/code/agency/country Examples: GR – LM0577/LM/NLM NIH HHS/United States GR – /Wellcome Trust/United Kingdom

10 An unstructured MEDLINE field example: Affiliation [ad] Revised January 2015

11 Over time, MEDLINE data inclusion has varied Revised January 2015 Author policy “New” fields: Full author name (2002-) Grant number (1981-) Location Identifier (2008-) “Old” fields (no new data): Gene Symbol ( ) Number of References (-2010)

12 Exercise: MEDLINE/PubMed Elements (the data) Revised January 2015 Explore the MEDLINE/PubMed Data Element (Field) DescriptionsMEDLINE/PubMed Data Element (Field) Descriptions 1. Google MEDLINE 2. Go to MEDLINE/PubMed Resources Guide 3. Under Data Structure, choose Detailed Field/Data Element Descriptions 4. Look at the author policy 5. Compare these two records: PMID and PMID PMID

13 Part II: Indexing Revised January 2015

14 PMID TITLEChanging antimicrobial resistance pattern AUTHORJain S LANGUAGEEnglish SOURCEJ Assoc Physicians India May;60:27-8, 33 PMID TITLEGut bacteria and antimicrobial resistance AUTHORKanerva M LANGUAGEFinnish SOURCEDuodecim. 2012;128(17): AUTHOR INDEX Jain Jain S Kanerva Kanerva M TITLE INDEX antimicrobial antimicrobial resistance bacteria changing gut gut bacteria pattern resistance Indexes Records Revised January 2015

15 TITLE INDEX antimicrobial antimicrobial resistance changing eosinophils gastrointestinal gastrointestinal tract pattern resistance Search Tags antimicrobial [ti] PMID TITLEChanging antimicrobial resistance pattern AUTHORJain S LANGUAGEEnglish SOURCEJ Assoc Physicians India May;60:27-8, 33 PMID TITLEAntimicrobial resistance in the ICU AUTHORSoman R LANGUAGEEnglish SOURCEJ Assoc Physicians India May;60:9. Revised January 2015

16 Search Tags Revised January 2015 Search specific PubMed fields using tags Syntax is term [tag] Warning! Using search tags turns off Automatic Term Mapping (ATM)

17 Search Tags (Look in PubMed Help) Revised January 2015

18 Article Title [ti] Revised January 2015 [ti] can be used to search for words and phrases in the title field NOT for the entire title

19 Journal Title [ta] Revised January 2015 [ta] can be used to search for the exact title or MEDLINE title abbreviation NOT for extracted words or phrases

20 TITLE INDEX antimicrobial antimicrobial resistance changing eosinophils ABSTRACT INDEX achievement acinetobacter aeruginosa amikacin changing eosinophils TITLE/ABSTRACT INDEX achievement acinetobacter aeruginosa amikacin antimicrobial antimicrobial resistance changing eosinophils Combined Index Revised January 2015

21 Title/Abstract [tiab] Revised January 2015 [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.

22 Text word Revised January 2015 [tw] includes: Title Abstract MeSH headings & subheadings Publication Types Other Terms field Corporate Author Comment/Correction Notes Chemical Names of Substances Secondary Source Identifier Personal Name as Subject

23 Building Phrase Indexes in PubMed Revised January 2015 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

24 Explore the Indexes  Searchable indexes are accessible from the Search Builder on the PubMed Advanced Search page. Revised January 2015

25 Explore the Indexes (continued) Revised January 2015

26 Exercise: PubMed Indexes Revised January 2015 Using only the Show Index feature of the PubMed Advanced Search Builder, answer the following questions: 1. How many PubMed records are for articles in the Esperanto language? 2. Is the phrase “finger to nose” indexed in PubMed?

27 Part III: The Tools Revised January 2015

28 Part III: The Tools Revised January 2015 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

29 NLM Catalog Journal Search Revised January 2015

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32 PubMed Search Results: All citations from the International Journal of Oncology Revised January 2015

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34 Broad Subject Terms Revised January 2015

35 Find related data Revised January 2015

36 Combining searches in History Revised January 2015

37 Combining searches in History (cont.) Revised January 2015

38 Combining searches in History (cont.)

39 Exercise Revised January Use the NLM Catalog Journal Broad Subject Terms to find MEDLINE journals about audiology. 2. Search for all citations in PubMed from these audiology journals. 3. Using History, combine the audiology journal search with a search for cochlear implants. 4. Limit your search to those that are included in the Systematic Reviews subset.

40 Summary Revised January 2015 After this session participants will be able to use: the MEDLINE/PubMed Data Element (Field) Descriptions 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


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