MEDLINE®/PubMed® PubMed for Trainers, revised Fall 2012 U.S. National Library of Medicine (NLM) and NLM Training Center An introduction

MEDLINE/PubMed PubMed for Trainers, revised Fall 2012 U.S. National Library of Medicine (NLM) and NLM Training Center An introduction

Objectives By the end of this presentation, you will be able to: Distinguish between a MEDLINE and non-MEDLINE record in PubMed. Define: MeSH headings MeSH Major Topics MeSH Subheadings Conduct a basic PubMed search Manipulate the results display Move from your PubMed results to other resources Identify where to customize your use of PubMed (My NCBI) Revised 2013/03 PubMed for Trainers 2

Overview We will answer the following questions: What is MEDLINE? What is the content of MEDLINE? Who selects MEDLINE journals? How has the scope of MEDLINE changed over time? What is included in each MEDLINE record? What are Medical Subject Headings? What is PubMed? How do you search PubMed? What are some of the features of the PubMed search? What other resources are linked from PubMed? How to customize PubMed using My NCBI Revised 2013/03 PubMed for Trainers 3

What is MEDLINE? Revised 2013/03 PubMed for Trainers 4

1964 MEDLINE - a database of citations to biomedical journal articles. 5 Revised 2013/03 PubMed for Trainers

Highlights of MEDLINE MEDLINE is a database of citations to published biomedical journal articles. Over 5,600 journals are currently indexed for MEDLINE. Journals must be approved by a review committee. NLM indexers use Medical Subject Headings (MeSH) to index over 50,000 articles each month. MEDLINE has over 20 million citations going back to the mid 1940s. Most of the citations are for English-language articles and include abstracts. Revised 2013/03 PubMed for Trainers 6

Who decides what journals are in MEDLINE? The Literature Selection Technical Review Committee Made up of medical experts and librarians. Meets 3 times per year. Considers approximately 180 titles each meeting. Selects roughly 20-25% of reviewed titles. Revised 2013/03 PubMed for Trainers 7

What criteria are used to select MEDLINE journals? Critical elements for inclusion: Scope and coverage Quality of content Quality of editorial work Production quality Audience Types of content See Fact Sheet for selection criteria. http://www.nlm.nih.gov/pubs/factsheets/jsel.html Revised 2013/03 PubMed for Trainers 8

How has the scope of MEDLINE changed over time? See Journals Recently Accepted for Inclusion in MEDLINE: http://www.nlm.nih.gov/bsd/lstrc/new_titles.html 9 Revised 2013/03 PubMed for Trainers

MEDLINE Basic Bibliographic Citation Journal Source Information Title of the journal article Names of the Authors First Author Affiliation Abstract published with the article Language in which the article was published Publication Type (description of the type of article, e.g., Review, Letter, etc.) Controlled Vocabulary search terms (Medical Subject Headings) 10 PubMed for Trainers

What are Medical Subject Headings? Revised 2013/03 PubMed for Trainers 11

MeSH (Medical Subject Headings) terms are added by NLM indexers to reflect the content of the article. Indexers assign the most specific term possible. 12

* = a major concept. Subheadings are used with MeSH headings to be more specific. 13 Mouth Mucosa/pathology Nail Diseases/immunology

What is PubMed? Revised 2013/03 PubMed for Trainers 14

PubMed http://www.pubmed.gov/ 15 Revised 2013/03 PubMed for Trainers

MEDLINE Licensees Revised 2013/03 PubMed for Trainers 16

Whats in PubMed? includes: records for online books & chapters out of scope articles Revised 2013/03 PubMed for Trainers 17

PubMed Record Status Tags Revised 2013/03 PubMed for Trainers 18

How to Search PubMed Revised 2013/03 PubMed for Trainers 19 aids drugs breast feeding

Search Results 20 Revised 2013/03 PubMed for Trainers

Automatic Term Mapping (ATM) ATM Checks these tables: Subjects (Medical Subject Headings) Journal Titles Authors PubMed uses Automatic Term Mapping which recognizes thousands of concepts and maps to an appropriate term. Revised 2013/03 21 PubMed for Trainers

Search details Revised 2013/03 PubMed for Trainers 22

The Search Details feature lets you see how your search was mapped. http://www.ncbi.nlm.nih.gov/mesh/82019380 23 Revised 2013/03PubMed for Trainers

See the Difference: aids drugs + breast feeding= 3 aids drugs breast feeding= 404 (processed using ATM) Revised 2013/03 PubMed for Trainers 24

Pop Quiz! Revised 2013/03 PubMed for Trainers 25

Citation Sensor fauci cell 2007 Revised 2013/03 PubMed for Trainers 26

Citation Sensor 27 Revised 2013/03 PubMed for Trainers

Title Matcher Revised 2013/03 PubMed for Trainers 28

How to search Revised 2013/03 PubMed for Trainers 29

Abstract & Related Citations

Links Between Databases Revised 2013/03 32 PubMed for Trainers

Revised 2013/03 33 PubMed for Trainers

Customizing PubMed Using My NCBI My NCBI allows you to: Save records (Collections, My Bibliography) Save searches (Saved Searches) Customize your results (Filters, My NCBI Preferences) Revised 2013/03 PubMed for Trainers 34

My NCBI homepage Revised 2013/03 PubMed for Trainers 35

Register for an account Homework: Register for a My NCBI account if you dont already have one. Throughout the class, the instructors will point out useful features of My NCBI to use when searching PubMed Revised 2013/03 PubMed for Trainers 36

insert visual here PubMed Mobile Mobile-friendly version of PubMed Minimal feature set: Small HTML, CSS, JavaScript VIDEO: PubMed Mobile Demonstration

Online Help and Training

Summary The MEDLINE database of biomedical journal citations is the heart of PubMed. MEDLINE includes only good quality journals deemed important and relevant by a committee of experts. MEDLINE is available for free using PubMed, but it is also available from other database searching systems. MEDLINE is enhanced with Medical Subject Headings (MeSH), which improve access to the literature and can be used for searching. Revised 2013/03 PubMed for Trainers 39

Summary (continued) Search PubMed by entering the main concepts of your search without punctuation. Your terms will automatically map to MeSH. Enter components of references (author, title, journal) to find a known article or set of articles. The full text article may be linked from the PubMed record using an icon in the upper right of the abstract display. Explore related citations and related information from the right column of your search results and the abstract display. Customize your PubMed search experience using My NCBI Revised 2013/03 PubMed for Trainers 40

Conclusions You will now be able to: Distinguish between a MEDLINE and non- MEDLINE record in PubMed. Define: MeSH headings MeSH Major Topics MeSH Subheadings Conduct a basic PubMed search Manipulate the results display Move from your PubMed results to other resources Identify where to customize your use of PubMed (My NCBI) Revised 2013/03 PubMed for Trainers 41

Revised 2013/03 PubMed for Trainers 42

PubMed Searching: Automatic Term Mapping (ATM) PubMed for Trainers, Winter 2013 U.S. National Library of Medicine (NLM) and NLM Training Center

Objectives By the end of this session, you should be able to: Describe how PubMed processes a search using Automatic Term Mapping (ATM) Use Search Details to determine how PubMed processed your search Modify your PubMed search based on what you learn from Search details Revised 2012/09 44 PubMed for Trainers

Composing Your Search Be specific Use no punctuation (e.g., no quotation marks) Use no operators (e.g., AND) Use no tags Capitalization is unimportant Revised 2012/09 45 PubMed for Trainers

ATM in Action

ATM (contd) PubMed looks for: Subjects Journals Authors In that order. Revised 2012/09 48 PubMed for Trainers

MeSH (Subject) Translation Table Contains: MeSH Headings Subheadings Publication Types Entry Term mappings (also known as synonyms) for MeSH terms Supplementary Concepts and synonyms to the Supplementary Concepts Mappings derived from the Unified Medical Language System (UMLS) Revised 2012/09 49 PubMed for Trainers

When a Match is Found for your Subject Revised 2012/09 50 PubMed for Trainers Processing now stops!

Automatic Explosion: What you Dont See in Search Details Revised 2012/09 51 PubMed for Trainers

ATM (contd) If PubMed doesnt find a match in the MeSH subject table, it looks for: Subjects Journals Authors Revised 2012/09 54 PubMed for Trainers

Journals Translation Table Full journal title MEDLINE abbreviation International Standard Serial Number (ISSN) Revised 2012/09 55 PubMed for Trainers

When a Match is Found for your Journal Title 56 Revised 2012/09 PubMed for Trainers Processing now stops!

ATM (contd) If PubMed doesnt find a match in the journals table, it looks for: Subjects Journals Authors Revised 2012/09 58 PubMed for Trainers

Author Translation Tables Author Index In the format: Lastname Initials: Jennings BH Full Author Translation Table Author names in natural and inverted order: Barbara H Jennings Jennings, Barbara H Investigator Index Full Investigator Translation Table Revised 2012/09 59 PubMed for Trainers

When a Match is Found for an Author Name Revised 2012/09 60 PubMed for Trainers Processing now stops!

ATM: Searching Multiple Concepts 62 Revised 2012/09 PubMed for Trainers

Combining Subjects, Journals & Authors: What does ATM Do? Revised 2012/09 63 PubMed for Trainers

No match in any of the translation tables? Revised 2012/09 64 PubMed for Trainers

Phrase Searching with Quotes Caution! Using quotes bypasses ATM & automatic explosion. Revised 2012/09 65 PubMed for Trainers

Revised 2012/09 PubMed for Trainers 66 Quoted Phrase Not Found

Exercise Search the following in PubMed: a. health planning b. health planning What is missed in the first search? Revised 2012/09 67 PubMed for Trainers

Searches that Bypass Automatic Term Mapping: 1. Using a search tag: Gene [author] Science [journal] 2. Forcing a phrase search with quotes: pressure point 3. Using the Single Citation Matcher 4. Using Advanced Search Revised 2012/09 68 PubMed for Trainers Use with caution!

Summary Revised 2012/09 PubMed for Trainers 69 For most PubMed searches just enter your terms and click Search. Always check Search details Automatic Term Mapping processes subjects, journals and authors, in that order.

Summary Revised 2012/09 PubMed for Trainers 70 With ATM, your MeSH terms will automatically explode to include narrower topics. The 3 ways to enter journal titles are: 1. Full journal title 2. MEDLINE journal title abbreviation 3. ISSN For the most comprehensive author search, use the format lastname initials (e.g., smith ja). If necessary, bypass ATM by using: Quotations or tags Single Citation Matcher Advanced Search (to be discussed later)

You should now be able to: Revised 2012/09 PubMed for Trainers 71 Describe how PubMed processes a search using Automatic Term Mapping Use Search Details to determine how PubMed processed your search Modify your PubMed Search depending on what you learn from Search Details

Evidence-Based Medicine in PubMed PubMed for Trainers, Winter 2013 U.S. National Library of Medicine (NLM) and NLM Training Center

Objectives To explore MeSH vocabulary and PubMed features that facilitate finding evidence-based research Define the term evidence based medicine Identify and discuss publication types and research design vocabulary available in MeSH Introduce and examine three PubMed topic-specific searches: clinical queries; systematic reviews; and comparative effectiveness research Introduce PubMed Health 74 Revised February 2013

What is Evidence-Based Medicine? 75 The use of the current best evidence in making clinical decisions See Sackett, D. Evidence-based Medicine - What it is and what it isn't. BMJ 1996; 312:71-72. http://www.bmj.com/cgi/content/full/312/7023/71 http://www.bmj.com/cgi/content/full/312/7023/71 Revised February 2013

76 The best evidence is usually found in clinically relevant research that has been conducted using sound methodology. (Sackett D, 2002) Revised February 2013

What do we mean by Evidence- Based Medicine in the context of PubMed? Identifying the best available evidence in the literature to inform clinical decision making using: Study characteristics (i.e., research design and methods) Reviews (including systematic reviews) of the literature 77 Revised February 2013

Useful Vocabulary to Describe Study Characteristics 78 Revised February 2013

Publication Types 79 Describe the item being indexed rather than its topic. There are 3 main categories: Publication Components, e.g., English Abstract Publication Formats, e.g., Lectures, Letter Study Characteristics, e.g., Clinical Trial, Twin Study Revised February 2013

Study Characteristics (PTs) 80 Case Reports Clinical Conference Clinical Trial + Comparative Study Consensus Development Conference + Evaluation Studies In Vitro Meta-Analysis Multicenter Study Scientific Integrity Review Twin Study Validation Studies Revised February 2013

81 Study Characteristics (PTs) Clinical Trial Clinical Trial, Phase I Clinical Trial, Phase II Clinical Trial, Phase III Clinical Trial, Phase IV Controlled Clinical Trial Multicenter Study Randomized Controlled Trial Revised February 2013

Clinical Trial Phases 82 Phase I Is it safe? Phase II Whats the right dose? Phase III How good is it compared to the standard treatment? Phase IV Does it have any rare or long term adverse effects? Revised February 2013

Publication Type vs. Method as Topic 83 Revised February 2013

Research Design MeSH Headings: Investigative Techniques (examples) Double-blind method (1990, Aug 1977) Matched-Pair Analysis (1992) Patient selection (1995) Random allocation (1991, 1978) 84 http://www.ncbi.nlm.nih.gov/mesh?term=Investigative%20Techniques Revised February 2013

MeSH Pop Quiz! 85 Revised February 2013

Exercise 86 Find studies comparing treatments for sleep apnea. Revised February 2013

Clinical Queries 87

Clinical Queries: Clinical Study Categories 88

Clinical Queries: Clinical Study Categories 89 Revised February 2013

Systematic Reviews Defined (by NLM) 1. One or more questions are posed. 2. Study results are collected. 3. Criteria are used to include or exclude studies. 4. Data extracted from the selected studies are combined and compared. 5. Conclusions are made. http://www.nlm.nih.gov/pubs/techbull/jf02/jf02_systematic_reviews.html 90 Revised February 2013

PubMed Systematic Review query also includes: meta-analyses reviews of clinical trials evidence-based medicine consensus development conferences guidelines, and citations to articles from journals specializing in clinical review studies. 92 Filter strategy: http://www.nlm.nih.gov/bsd/pubmed_subsets/sysreviews_strategy.html http://www.nlm.nih.gov/bsd/pubmed_subsets/sysreviews_strategy.html Revised February 2013

Exercise: Clinical Queries 93 Using the Clinical Queries page, find studies exploring the effect of weight loss on obstructive sleep apneaClinical Queries Look at the Systematic Reviews and click See all to view them in PubMed Revised February 2013

Comparative Effectiveness 94 effectiveness [sb] http://www.nlm.nih.gov/nichsr/cer/cerqueries.html Revised February 2013

RCTs PubMed CER Searches Conceptual Structure Outcomes ALL of the Above Systematic Reviews Cohort Administrative Data/Registries/ EHRs Health Disparities Simulations Modeling Comparative OR Effective Costs & Cost Analysis Outcomes About CER AND OR Clinical Studies Observational Studies Systematic Reviews Comparative OR Effective 95 http://www.nlm.nih.gov/nichsr/cer/CER_search_strategies.html Revised February 2013

Exercise: Comparative Effectiveness Research 96 Use the comparative effectiveness search page to search for weight loss on obstructive sleep apneacomparative effectiveness search page Look at results for Observational Studies Look at results for Systematic Reviews, Simulations, Models Compare your results for CER search on Systematic Reviews with the Clinical Queries Systematic Reviews search results http://www.nlm.nih.gov/nichsr/cer/cerqueries.html Revised February 2013

Full-text online collection of systematic reviews (or summaries) Curated Some not in PubMed http://www.ncbi.nlm.nih.gov/pubmedheal th/ Revised February 2013 97 Another EBM Resource:

More about Comparative Effectiveness Research 98 Webinar: Comparative Effectiveness Research (from the Pacific Northwest RML): https://webmeeting.nih.gov/p77505591/ https://webmeeting.nih.gov/p77505591/ Finding Evidence for Comparing Medical Interventions (AHRQ Guide on comparative effectiveness reviews) http://www.ncbi.nlm.nih.gov/pubmed/21433408 http://www.ncbi.nlm.nih.gov/pubmed/21433408 Systematic Review Workshop: The Nuts and Bolts for Librarians (3-day workshop) http://www.hsls.pitt.edu/systematicreview/ http://www.hsls.pitt.edu/systematicreview/ Revised February 2013

More about Evidence-Based Medicine 99 Online tutorial: http://www.hsl.unc.edu/services/Tutorials/EBM/we lcome.htm http://www.hsl.unc.edu/services/Tutorials/EBM/we lcome.htm Work by Dr. John Ioannidis (see profile in the Atlantic http://www.theatlantic.com/magazine/archive/201 0/11/lies-damned-lies-and-medical-science/8269/ and/or search PubMed for ioannidis jp) http://www.theatlantic.com/magazine/archive/201 0/11/lies-damned-lies-and-medical-science/8269/ Revised February 2013

Summary 100 Vocabulary Study Characteristics (PTs) Investigative Techniques headings PubMed Clinical and Special Queries Clinical Study Categories (Clinical Queries page) Systematic Reviews (Clinical Queries page) Comparative Effectiveness (NICHSR Web site) PubMed Health for full-text systematic reviews Revised February 2013

Searching for Drug Information In PubMed PubMed for Trainers Winter 2013 U.S. National Library of Medicine (NLM) and NLM Training Center

Revised 2013/01 103 PubMed for Trainers Goal: To gain familiarity with the NLM MeSH vocabulary related to chemicals and drugs and to get comfortable with searching for drug information in PubMed.

Objectives: Revised 2013/01 104 PubMed for Trainers By the end of this session you will be able to: Explain how chemicals, drugs and other substances are described in MeSH. Search for drugs or chemicals in PubMed. Search using pharmacological action terms.

Help, Im not a Chemist! Revised 2013/01 105 PubMed for Trainers

Drugs and Chemicals in MeSH Revised 2013/01 106 PubMed for Trainers

Many Synonyms, One Preferred Name, Same Concept 107 Revised 2013/01 PubMed for Trainers

Common v. Chemical Names Revised 2013/01 108 PubMed for Trainers Mimosine 3-Hydroxy-4-oxo-1(4H) pyridinealanine C 8 H 10 N 2 O 4 Aspirin Acetylsalicylic Acid Always exceptions 1,2-dinitrobenzene Look at the Drug Handout

Exercise: Preferred Term Revised 2013/01 PubMed for Trainers 109 Develop a good PubMed search for information on Zantac.

The Chemicals and Drugs Category in MeSH Inorganic Chemicals Organic Chemicals Heterocyclic Compounds Polycyclic Compounds Macromolecular Substances Hormones, Hormone Substitutes, and Hormone Antagonists Enzymes and Coenzymes Carbohydrates Lipids Amino Acids, Peptides, and Proteins Nucleic Acids, Nucleotides, and Nucleosides Complex Mixtures Biological Factors Biomedical and Dental Materials Pharmaceutical Preparations Chemical Actions and Uses 110 Revised 2013/01

Medical Subject Headings (MeSH Vocabulary) MeSH Vocabulary TypeExamples HeadingsBody Weight, Kidney, Dental Cavity Preparation, Self Medication, Brain Edema, Oseltamivir Subheadingsadverse effects, genetics, contraindications, ultrastructure Publication TypesLetter, Review, Practice Guideline, Twin Study Supplementary Concept Recordscordycepin, albuterol-ipratopium, carbon monoxyde dehydrogenase, nocturnin Revised 2013/01 111 PubMed for Trainers

Supplementary Concepts Revised 2013/01 112 PubMed for Trainers

Supplementary Concepts (cont.) Revised 2013/01 113 PubMed for Trainers

Supplementary Concepts (cont.) 114 Revised 2013/01 PubMed for Trainers

Mapped to MeSH 115 Revised 2013/01 PubMed for Trainers

MeSH Heading v. SCRs: Why Both? Revised 2013/01 116 PubMed for Trainers MeSH Headings Supplementary Concepts Located in hierarchy Subheadings Updated annually Pharmacologic Actions Entry Terms Not located in hierarchy no explosion No subheadings Updated weekly Pharmacologic Actions Entry Terms Heading Mapped To Can become MeSH Heading

SCRs Are Revised 2012/10 PubMed for Trainers 117 Updated Weekly Update SCRs

SCRs Do Not Revised 2012/10 PubMed for Trainers 118 Take Subheadings

SCRs Are Not Revised 2012/10 PubMed for Trainers 119 In the MeSH Hierarchy. No explosion!

Exercise: Headings, Subheadings and Supplementary Concepts Revised 2013/01 PubMed for Trainers 120 What MeSH Heading/Subheading combination would be applied to a citation for an article about the synthesis of sordarin? What search would retrieve only highly relevant citations on this topic?

Searching Tip: Use Tags Sparingly Revised 2013/01 121 PubMed for Trainers Use [mh] for drugs that you know are MeSH Headings: oseltamivir [mh] dibenzazepines [mh] You can use [nm] for drugs that are Supplementary Concepts OR MeSH Headings: metapramine [nm] dibenzazepines [nm] water [nm] BUT headings will not explode if searched with [nm].

Best way to search for a drug: No tags Revised 2013/01 122 PubMed for Trainers SearchResults (# records) Xanthophylls [nm]2000 Xanthophylls [mh]2923 Xanthophylls3166

Pharmacological Action Terms Revised 2013/01 123 PubMed for Trainers The way a chemical or drug behaves in the body http://www.sciencephoto.com/media/282094/enlarge

Pharmacological action terms Revised 2013/01 124 PubMed for Trainers

Pharmacological Action Terms Revised 2013/01 PubMed for Trainers 126

The MeSH Heading Record Revised 2013/01 PubMed for Trainers 127

Drug AND MeSH Heading 128 Revised 2013/01 PubMed for Trainers

Pharmacological Action Record 129 Revised 2013/01 PubMed for Trainers

MeSH Record vs. PA Record Revised 2013/01 PubMed for Trainers 130 MeSH Record: A concept / topic PA record: A tool (list of drugs with that PA)

Disease AND Pharmacological Action [pa] 131 Revised 2013/01 PubMed for Trainers

Review 2 Ways to Use PAs Revised 2013/01 PubMed for Trainers 133 1. Drug AND Pharmacological Action tagged [mh] Example: lithium carbonate AND antidepressive agents [mh] retrieves articles about lithium carbonate as an antidepressive agent. 2. Disease AND Pharmacological Action tagged [pa] Example: panic disorder AND antidepressive agents [pa] retrieves articles about any antidepressive chemical or drug and panic disorder.

Teachback Revised 2012/02 PubMed for Trainers 134 In groups of 2 or 3, explain to each other when and why you would use the [mh] or [pa] tags to search for pharmacologic actions with a drug or disease. Use these examples: Find articles about Bismuth or Magnesium Hydroxide used as antacids. Find articles about treating GERD or Heartburn with antacids.

Exercise: Pharmacological Actions Revised 2013/01 PubMed for Trainers 135 Recently there has been some interest in thalidomide as an angiogenesis inhibitor. How might you search to find relevant records?

Summary Revised 2013/01 136 PubMed for Trainers You should now be able to: Explain how chemicals, drugs and other substances are described in MeSH. Search for drugs or chemicals in PubMed. Search using pharmacological action terms.

PubMed for Trainers, Winter 2013 U.S. National Library of Medicine (NLM) and NLM Training Center PubMed Nuts and Bolts

Goals Revised 2012/12 PubMed for Trainers 139 Locate details and history about the information included in MEDLINE/PubMed records and Search the fields of MEDLINE/PubMed records efficiently.

Objectives Revised 2012/12 PubMed for Trainers 140 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 PubMeds 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 2012/12 PubMed for Trainers 141 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

Part I: The Data Revised 2012/12 PubMed for Trainers 142

PMID 23082700 TITLEEosinophils in the gastrointestinal tract AUTHORStraumann A LANGUAG E English SOURCEActa Gastroenterol Belg. 2012 Sep;75(3):310-5 PMID 23029718 TITLEChanging antimicrobial resistance pattern AUTHORJain S LANGUAG E English SOURCEJ Assoc Physicians India. 2012 May;60:27-8, 33 PMID 23033785 TITLEGut bacteria and antimicrobial resistance AUTHORKanerva M LANGUAG E Finnish SOURCEDuodecim. 2012;128(17):1755-61. Record s Field s Revised 2012/12 PubMed for Trainers 143

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. [email protected] 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 2012/12 PubMed for Trainers 144 MEDLINE FORMAT WITH FIELD LABELS (Tags)

Data structure varies by field Revised 2012/12 PubMed for Trainers 145 Author [au] or Grant [gr] or Date fields Highly structured vs. Affiliation [ad] NOT structured OR standardized vs. Abstract [ab] Sometimes partially structured

Highly Structured MEDLINE Field Examples: Revised 2012/12 PubMed for Trainers 146 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 States GR - 058423/Wellcome Trust/United Kingdom

An Unstructured MEDLINE Field Example: Affiliation [ad] Revised 2012/12 PubMed for Trainers 147

Over time, MEDLINE data inclusion has varied Revised 2012/12 PubMed for Trainers 148 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)

Exercise: MEDLINE/PubMed Elements (the data) Revised 2012/12 PubMed for Trainers 149 Explore the MEDLINE/PubMed Elements documentationMEDLINE/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 10595696 PMID 22922874

Part II: Indexing Revised 2012/12 PubMed for Trainers 150

PMID 23029718 TITLEChanging antimicrobial resistance pattern AUTHORJain S LANGUAG E English SOURCEJ Assoc Physicians India. 2012 May;60:27-8, 33 PMID 23033785 TITLEGut bacteria and antimicrobial resistance AUTHORKanerva M LANGUAG E Finnish 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 PubMed for Trainers 151 Records

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 LANGUAG E English SOURCEJ Assoc Physicians India. 2012 May;60:27-8, 33 PMID 23029713 TITLEAntimicrobial resistance in the ICU AUTHORSoman R LANGUAG E English SOURCEJ Assoc Physicians India. 2012 May;60:9. Revised 2012/12 PubMed for Trainers 152

Search Tags Revised 2012/12 PubMed for Trainers 153 Search specific PubMed fields using tags. Syntax is term [tag], e.g.: Warning! Using search tags turns off Automatic Term Mapping (ATM)

Search Tags (Look in PubMed Help) Revised 2012/12 PubMed for Trainers 154

Article Title [ti] Revised 2012/12 PubMed for Trainers 155 [ti] can be used to search for words and phrases in the title field NOT for the entire title

Journal Title [ta] Revised 2012/12 PubMed for Trainers 156 [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 Combine d Index Revised 2012/12 PubMed for Trainers 157

Title/Abstract [tiab] Revised 2012/12 PubMed for Trainers 158 [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 2012/12 PubMed for Trainers 159 [tw] includes: Title Abstract MeSH headings & subheadings Publication Types Other Terms field Chemical Names of Substances Secondary Source Identifier Personal Name as Subject

Building Phrase Indexes in PubMed Revised 2012/12 PubMed for Trainers 160 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 2012/12 PubMed for Trainers 161

Explore the Indexes (continued) Revised 2012/12 PubMed for Trainers 162

Exercise: PubMed Indexes Revised 2012/12 PubMed for Trainers 163 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 Esperanto? 2. Is the phrase finger to nose indexed in PubMed?

Part III: The Tools Revised 2012/12 PubMed for Trainers 164

Part III: The Tools Revised 2012/12 PubMed for Trainers 165 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 2012/12 PubMed for Trainers 166

PubMed Search Results: All citations from the International Journal of Oncology Revised 2012/12 PubMed for Trainers 169

Broad Subject Terms Revised 2012/12 PubMed for Trainers 171

Find Related Data Revised 2012/12 PubMed for Trainers 172

Combining Searches in History Revised 2012/12 PubMed for Trainers 173

Combining searches in History (cont.) Revised 2012/12 PubMed for Trainers 174

Exercise Revised 2012/12 PubMed for Trainers 176 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 2012/12 PubMed for Trainers 177 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 PubMeds indexes the NLM Catalog Journal search to find journals and build journal sets for searching in PubMed History to combine searches

Searching for Disease Information in PubMed: Building Searches with MeSH PubMed for Trainers, Winter 2013 U.S. National Library of Medicine (NLM) and NLM Training Center

Objectives: Revised 2012/12 PubMed for Trainers 180 1. Build a PubMed search using the MeSH Database. 2. Recognize and identify how NLM indexers assign terms to MEDLINE records, with a focus on disease and treatment terms. 3. Apply indexing rules to improve your search technique. 4. Create searches by free-floating subheadings. 5. Enhance your search by using subject populations terms. 6. Locate, and when appropriate, search using the AIDS and Cancer subject subsets.

Building a Search in the MeSH Database PubMed for Trainers 181 Revised 2012/12

PubMed for Trainers 182 Building a Search in the MeSH Database (cont.)

Revised 2012/12 PubMed for Trainers 183 Building a Search in the MeSH Database (cont.)

Revised 2012/12 PubMed for Trainers 184 Building a Search in the MeSH Database (cont.)

Exercise Revised 2012/12 PubMed for Trainers 185 Use the MeSH Database and the PubMed search builder to find articles discussing multiple sclerosis as the main focus of the article. Narrow your results to those citations also discussing sarcoidosis.

MEDLINE Indexing: From the Indexers point-of- view Revised 2012/12 PubMed for Trainers 186

Indexing: Specificity Revised 2012/12 PubMed for Trainers 187 Indexers use the hierarchy to find the most specific MeSH heading. Example: Chronic hepatitis B Hepatitis B, Chronic (not Liver diseases or Hepatitis or Hepatitis B) Search tip: Use the most specific term appropriate for searching.

Indexing: Depth of Indexing Revised 2012/12 PubMed for Trainers 188 For most research articles, every concept substantively discussed should be covered by at least one MeSH heading Negative results (i.e. supporting the null hypothesis) are indexed if discussed For articles discussing many subjects, general headings (but as specific as possible) may be used to group related concepts rather than indexing them individually

Indexing: Rule of Three Revised 2012/12 PubMed for Trainers 189 If more than 3 related concepts are discussed in an article, the more general MeSH heading under which they are all treed is usually indexed. The specific headings may be indexed, but not as major topics. Example: Article discusses infections by Helicobacter pylori, Clostridium difficile, peptostreptococci, and vancomycin-resistant enterococci indexed with BACTERIAL INFECTIONS

Required (if applicable) Headings Revised 2012/12 PubMed for Trainers 190 Some headings are considered for every article (check tags) Include: Species (including Humans) Sex Age groups (for humans) Also historical time periods and pregnancy Usually are indexed even if merely mentioned, unlike other MeSH headings

Required (if applicable) Headings Revised 2012/12 PubMed for Trainers 191 Search tip: Use terms for species, sex and age in your search if appropriate.

Indexing: When a Concept isnt Found Revised 2012/12 PubMed for Trainers 192 If an exact heading does not exist, indexers use the most specific heading available. Example: Ashi points in acupuncture Acupuncture points

Exercise Revised 2012/12 PubMed for Trainers 193 How would an article about preventing heart diseases in women be indexed for MEDLINE?

Indexing: Coordination Revised 2012/12 PubMed for Trainers 194 Because most concepts cannot be adequately described with a single MeSH term: indexers use a combination of the appropriate: MeSH headings, subheadings, and other terms to index a concept as specifically as possible. This is called coordination.

Indexing: Coordination Revised 2012/12 PubMed for Trainers 195 We will discuss four types of coordination: 1. Subheading 2. Multiple headings 3. Multiple subheadings 4. Pre-coordinated headings

Indexing: Coordination (Using Subheadings) Revised 2012/12 PubMed for Trainers 196 Coordination can be done using a subheading to describe a specific aspect of a topic. Example: Radiographic imaging of a lung tumor. Lung Neoplasms/radiography

Indexing: Coordination (Using Multiple Headings) Revised 2012/12 PubMed for Trainers 197 Coordination can be done using two or more headings. Mucinous adenocarcinoma of the ovary Adenocarcinoma, Mucinous Ovarian Neoplasms

Indexing: Coordination (Using Two or More Subheadings) Revised 2012/12 PubMed for Trainers 198 Coordination can be done using two or more subheadings. /drug therapy on a disease term /therapeutic use on a drug term Example: Treatment of HIV infections with HIV protease inhibitors. HIV Infections/drug therapy HIV Protease Inhibitors/therapeutic use

Exercise: Coordinated Indexing Revised 2012/12 PubMed for Trainers 199 Use the MeSH Database and the PubMed search builder to find article discussing prostate cancer as the main focus of the article. Narrow your results to those involving treatment by leuprolide.

Indexing: Coordination (Using Two or More Subheadings) Revised 2012/12 PubMed for Trainers 200 /secondary on the site to which a cancer has metastasized /secondary on the histologic/tissue type term /pathology on the primary/original organ neoplasm term Example: Liver Neoplasms/secondary metastasized site Adenocarcinoma/secondary tissue type Colonic Neoplasms/pathology primary/original site

Indexing: Coordination (Using a Pre-coordinated Heading) Revised 2012/12 PubMed for Trainers 201 Coordination can be done using a "pre-coordinated" MeSH heading which combines two concepts into one. Example: Staphylococcal pneumonia Pneumonia, Staphylococcal Rather than: Pneumonia (or Pneumonia, Bacterial) Staphylococcal Infections

Exercise: Coordinated Indexing Revised 2012/12 PubMed for Trainers 202 What MeSH term(s) would indexers use to describe osteoarthritis of the knee?

Free-Floating Subheadings Revised 2012/12 PubMed for Trainers 203 It may be useful to search a subheading unattached to a Heading. Examples from homework: breast neoplasms[mh] AND trends[sh] hypertension [majr] AND toxicity [sh] [sh] allows you to search the subheading attached to any MeSH heading

Useful Vocabulary to Describe Study Populations Revised 2012/12 PubMed for Trainers 204

Persons Category Revised 2012/12 PubMed for Trainers 205 Abortion Applicants Adult Children Age Groups + Alcoholics Athletes Caregivers Child, Abandoned Child, Exceptional + Child of Impaired Parents Child, Orphaned Child, Unwanted Consultants Crime Victims + Criminals Disabled Persons + Drug Users Emigrants and Immigrants Famous Persons Friends Homebound Persons Homeless Persons + Jehovah's Witnesses Legal Guardians + Medically Uninsured Men + Mentors Minors Multiple Birth Offspring + Occupational Groups + Parents + Patients + Population Groups + Prisoners Refugees Research Personnel + Research Subjects Sexual Partners Siblings Single Person Spouses Students + Survivors + Terminally Ill Tissue Donors + Transients and Migrants Veterans Visitors to Patients Voluntary Workers + Vulnerable Populations Women +

Age Groups Revised 2012/12 PubMed for Trainers 206 Adolescent Adult Aged Aged, 80 and over Frail Elderly Middle Aged Young Adult Child Child, Preschool Infant Infant, Newborn +

Population Groups Revised 2012/12 PubMed for Trainers 207 Continental Population Groups African Continental Ancestry Group + American Native Continental Ancestry Group + Asian Continental Ancestry Group + European Continental Ancestry Group Oceanic Ancestry Group Ethnic Groups African Americans Arabs Asian Americans Gypsies Hispanic Americans + Inuits Jews

Exercise: Study Populations Revised 2012/12 PubMed for Trainers 208 Use the MeSH Database and PubMed to find ways to encourage elderly black Americans to follow treatment programs for type 2 diabetes.

AIDS and Cancer Subsets Revised 2012/12 PubMed for Trainers 209 Subsets are on Filters sidebar but also searchable with tags Strategies can be found at http://www.nlm.nih.gov/bsd/pubmed_subsets.html (use PubMed Help) http://www.nlm.nih.gov/bsd/pubmed_subsets.html aids [sb] developed from AIDSLINE work cancer [sb] developed with the National Cancer Institute All strategies reviewed at least annually

Summary Revised 2012/12 PubMed for Trainers 210 Find and combine terms for your PubMed search using the MeSH Database. Identify subheadings to describe specific aspects of the topic of interest for better results. Restrict your search to MeSH major topic for higher relevancy. Find the most specific term available to describe topics of an article. Indexers use the most specific term, you should too. Search terms for species, sex, age, historical time period and pregnancy when applicable. These terms are added by indexers. Consider using these for searching.

Summary Revised 2012/12 PubMed for Trainers 211 Coordinate multiple headings to describe complex topics. For example: disease/drug therapy and drug/therapeutic use Try free-floating a subheading to search for the subheading applied to any heading. Enhance your search by using subject populations terms. Locate, and when appropriate, search using the AIDS and Cancer subject subsets.

Questions? Revised 2012/12 PubMed for Trainers 212

Documents

MEDLINE®/PubMed® PubMed for Trainers, revised Fall 2012 U.S. National Library of Medicine (NLM) and NLM Training Center An introduction