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:
PubMed for Trainers Winter 2015 U.S. National Library of Medicine (NLM) and NLM Training Center PubMed Nuts and Bolts
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.
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
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
PMID 23082700 TITLEEosinophils in the gastrointestinal tract AUTHORStraumann A LANGUAGEEnglish SOURCEActa Gastroenterol Belg. 2012 Sep;75(3):310-5 PMID 23029718 TITLEChanging antimicrobial resistance pattern AUTHORJain S LANGUAGEEnglish SOURCEJ Assoc Physicians India. 2012 May;60:27-8, 33 PMID 23033785 TITLEGut bacteria and antimicrobial resistance AUTHORKanerva M LANGUAGEFinnish SOURCEDuodecim. 2012;128(17):1755-61. Records Fields Revised January 2015
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 LID - 10.1055/s-0030-1256526 [doi] AD - Department of Internal Medicine, King Fahad Specialist Hospital, Dammam, Saudi Arabia. email@example.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 - 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 - 10.1055/s-0030-1256526 [doi] PST - ppublish SO - Endoscopy. 2011;43 Suppl 2 UCTN:E358-9. Epub 2011 Nov 8. Revised January 2015 MEDLINE format with field labels (Tags)
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]
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 – 058423/Wellcome Trust/United Kingdom
An unstructured MEDLINE field example: Affiliation [ad] Revised January 2015
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 (1991-1995) Number of References (-2010)
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 10595696 and PMID 10595696 PMID 22922874
PMID 23029718 TITLEChanging antimicrobial resistance pattern AUTHORJain S LANGUAGEEnglish SOURCEJ Assoc Physicians India. 2012 May;60:27-8, 33 PMID 23033785 TITLEGut bacteria and antimicrobial resistance AUTHORKanerva M LANGUAGEFinnish SOURCEDuodecim. 2012;128(17):1755-61. AUTHOR INDEX Jain23029718 Jain S23029718 Kanerva23033785 Kanerva M23033785 TITLE INDEX antimicrobial23029718 23033785 antimicrobial resistance23029718 23033785 bacteria23033785 changing23029718 gut23033785 gut bacteria23033785 pattern23029718 resistance23029718 23033785 Indexes Records Revised January 2015
TITLE INDEX antimicrobial23029718 23029713 antimicrobial resistance23029718 changing23029718 eosinophils23082700 gastrointestinal23082700 gastrointestinal tract23082700 pattern23029718 resistance23029718 Search Tags antimicrobial [ti] PMID 23029718 TITLEChanging antimicrobial resistance pattern AUTHORJain S LANGUAGEEnglish SOURCEJ Assoc Physicians India. 2012 May;60:27-8, 33 PMID 23029713 TITLEAntimicrobial resistance in the ICU AUTHORSoman R LANGUAGEEnglish SOURCEJ Assoc Physicians India. 2012 May;60:9. Revised January 2015
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)
Search Tags (Look in PubMed Help) Revised January 2015
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
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
TITLE INDEX antimicrobial23029718 23082700 antimicrobial resistance23029718 changing23029718 eosinophils23082700 ABSTRACT INDEX achievement23029718 acinetobacter 23029718 aeruginosa23029718 amikacin23029718 changing23029718 eosinophils23082700 TITLE/ABSTRACT INDEX achievement23029718 23082700 acinetobacter 23029718 aeruginosa23029718 amikacin23029718 antimicrobial23029718 23082700 antimicrobial resistance23029718 changing23029718 eosinophils23082700 Combined Index Revised January 2015
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.
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
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
Explore the Indexes Searchable indexes are accessible from the Search Builder on the PubMed Advanced Search page. Revised January 2015
Explore the Indexes (continued) Revised January 2015
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?
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
NLM Catalog Journal Search Revised January 2015
Exercise Revised January 2015 1. 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.
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