Literature Searches with PubMed. Elke Rometsch
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1 Literature Searches with PubMed Elke Rometsch Taipei November 2015
2 Search the literature 2
3 What you will learn Literature Searches: What we need it for & how to ask the right questions Literature Databases: Overview Special focus: PubMed How to search effectively Useful features, e.g use of filters & MeSH terms Types of searches How to document 3
4 Literature Search: Why Answer clinical questions Find evidence (e.g. background information for manuscripts; systematic literature reviews) Form base for further developments of Devices Procedures Treatments paths Etc. 4
5 Literature Search: What Levels of evidence - pre-appraised sources 1a 1b 2a Systematic review (with homogeneity) of RCTs Individual RCT (with narrow confidence intervals) Systematic review (with homogeneity) of cohort studies 2b Individual cohort study (including low quality RCT; e.g., <80% follow-up) 3a 3b Systematic review (with homogeneity) of case-control studies Individual Case-Control Study 4 Case-series (and poor quality cohort and case-control-studies) 5 Expert opinion without explicit critical appraisal, or based on physiology, bench research or "first principles" Use pre-set filters!
6 Literature Search: How / what to ask PICO(T)!!! 6
7 Literature Search: How / what to ask Literature Search Planning Form Population Intervention Comparator (if applicable) Outcome Time - adults (1 8-65) - degenerative spondylolistesis fusion - physiotherapy - function: ODI min 1 2 months - SF fusion success Alternative wording (synonyms) - degenerative spondylistesis - circumferential fusion 7
8 Literature Search: Where to ask Databases Database Medline over PubMed / OvidSP EMBASE* Cochrane Library databases - Cochrane Central Register of Controlled Trials (CENTRAL) - Systematic Reviews - Database of Abstracts of Review of Effects (DARE) MEDPILOT Web of Science* Biosis* Google Scholar PLOS (Public Library of Science) Other specialized databases: URL b05ca?LANGUAGE=en science_products/a-z/biosis_previews/ Derwent Drug File, Psyndex, CCMed, Wiso 8 *institutional access
9 PubMed: The work horse 9
10 PubMed: The work horse Covers: Medicine Nursing Dentistry Veterinary medicine Healthcare systems Preclinical sciences >25 million citations/abstracts for biomedical literature > 4,500 journals From
11 PubMed: The work horse 11
12 PubMed: most important features 12
13 PubMed Exercise 1 I would like to get information about femoral head necrosis 13
14 PubMed Exercise 1 : Simple search Basic features 14
15 PubMed Search Basic Features Useful tools: 1. Boolean operators 15
16 Boolean Operators 16
17 PubMed Exercise 1 : Simple search Basic features 17
18 PubMed Feature: Link to publisher / full text
19 PubMed Feature: Indexed for MEDLINE
20 PubMed Feature: Indexed for MEDLINE
21 PubMed Feature: Indexed for MEDLINE
22 PubMed Feature: Query translation 23
23 PubMed Feature: Query translation 24
24 PubMed Search Basic Features Useful tools: 1. Boolean operators 2. Tags 25
25 PubMed Features: Tags Search field tags qualify terms, e.g.: Femur head necrosis [MeSH] Chan W [au] 2004 [dp] Injury [ta] English [la] Randomized controlled trial [pt] 26
26 PubMed Exercise 2 : Simple search Basic features 27
27 PubMed Features: Tags Most important tags: MeSH Terms [MH /MESH] MeSH Subheading [SH] All Fields [ALL] Author [AU] Language [LA] Affiliation [AD] Journal Title [TA] Issue [IP] Publication Type [PT] Publication Date [DP] 28
28 PubMed Exercise 3: Automatic filters I would like to know what works best in the treatment of radius fractures Useful tools: 1. Filters provided by PubMed 2. Clinical query function 29
29 PubMed: Automatic filters 30
30 PubMed special filter: Clinical Query 31
31 PubMed special filter: Clinical Query 32
32 PubMed special filter: Clinical Query Category therapy diagnosis etiology prognosis clinical prediction guides Optimized For Sensitive/ Specific sensitive/broad 99%/70% specific/narrow 93%/97% sensitive/broad 98%/74% PubMed Equivalent ((clinical[title/abstract] AND trial[title/abstract]) OR clinical trials as topic[mesh Terms] OR clinical trial[publication Type] OR random*[title/abstract] OR random allocation[mesh Terms] OR therapeutic use[mesh Subheading]) (randomized controlled trial[publication Type] OR (randomized[title/abstract] AND controlled[title/abstract] AND trial[title/abstract])) (sensitiv*[title/abstract] OR sensitivity and specificity[mesh Terms] OR diagnose[title/abstract] OR diagnosed[title/abstract] OR diagnoses[title/abstract] OR diagnosing[title/abstract] OR diagnosis[title/abstract] OR diagnostic[title/abstract] OR diagnosis[mesh:noexp] OR diagnostic * [MeSH:noexp] OR diagnosis,differential[mesh:noexp] OR diagnosis[subheading:noexp]) specific/narrow 64%/98% (specificity[title/abstract]) sensitive/broad 93%/63% specific/narrow 51%/95% sensitive/broad 90%/80% specific/narrow 52%/94% sensitive/broad 96%/79% (risk*[title/abstract] OR risk*[mesh:noexp] OR risk *[MeSH:noexp] OR cohort studies[mesh Terms] OR group[text Word] OR groups[text Word] OR grouped [Text Word]) ((relative[title/abstract] AND risk*[title/abstract]) OR (relative risk[text Word]) OR risks[text Word] OR cohort studies[mesh:noexp] OR (cohort[title/abstract] AND study[title/abstract]) OR (cohort[title/abstract] AND studies[title/abstract])) (incidence[mesh:noexp] OR mortality[mesh Terms] OR follow up studies[mesh:noexp] OR prognos*[text Word] OR predict*[text Word] OR course*[text Word]) (prognos*[title/abstract] OR (first[title/abstract] AND episode[title/abstract]) OR cohort[title/abstract]) (predict*[tiab] OR predictive value of tests[mh] OR score[tiab] OR scores[tiab] OR scoring system[tiab] OR scoring systems[tiab] OR observ*[tiab] OR observer variation[mh]) specific/narrow 54%/99% (validation[tiab] OR validate[tiab]) 33
33 PubMed Exercise 4: Combined topics/ filters I want to find papers where operative treatment of radius fractures is compared with conservative treatment Useful tools: automatic mapping filters 34
34 PubMed Exercise 4: Combined topics/ filters 35
35 PubMed Filters: Pitfalls and solutions Limitations when using filters: Some filters (e.g. ptyp, MeSH) only work after the article has been indexed ( lag-phase) Some filters do not work well for whatever reason (e.g. humans ) How to get around these problems: Hand- enter the filter, e.g. Rather than checking the randomized controlled trial / review field in the filters add AND random* / review to the query instead of using the filter humans add NOT (sheep OR dog OR animal..) to your query 36
36 PubMed Exercise 5: Entering filters by hand I have identified papers where operative treatment of radius fractures is compared with conservative treatment by using the filter function for RCTs and comparative trials. What can I do to make sure the latest publications are included? Useful tool: hand-search of indexed filter information 37
37 PubMed Exercise 5: Entering filters by hand 38
38 PubMed Feature: Advanced search builder 39
39 PubMed: Further Modalities: MeSH search Truncation Limitations of Automatic Mapping MeSH indexing - how to circumvent its drawbacks Related Data Clipboard Documentation 40
40 PubMed features: MeSH search MeSH (Medical Subject Headings) is the NLM controlled vocabulary thesaurus used for indexing articles for PubMed uses synonyms and a hierarchy with major headings and subheadings only linked to an article after it has been indexed indexing sometimes inconsistent no MeSH yet exists for the latest substances & terms lag-phase of up to a year applicable articles are not always identified for most recent articles: use hand-search, but get inspired by MeSH 41
41 PubMed MeSH search 42
42 PubMed types of searches: Hand search Truncation: e.g. infect* rather than infection 45
43 PubMed types of searches: Hand search Truncation: e.g. infect* rather than infection OR infectopyrones[all Fields] OR infector[all Fields] OR infectoria[all Fields] OR infectoriae[all Fields] OR infectors[all Fields] OR infectoscab[all Fields] OR infectosi[all Fields] OR infectosia[all Fields] OR infectosome[all Fields] OR infectosomes[all Fields] OR infectosomes'[all Fields] OR infectous[all Fields] OR infectouse[all Fields] OR infectovac[all Fields] OR infectra[all Fields] OR infectro[all Fields] OR infectrons[all Fields] OR infects[all Fields] OR infects'[all Fields] OR infectsiei[all Fields] OR infectsii[all Fields] OR infectsiia[all Fields] OR infectsiiakh[all Fields] OR infectsionnogo[all Fields] OR infectsionnom[all Fields] OR infectsionnykh[all Fields] OR infectsionnym[all Fields] OR infectspodoptera[all Fields] OR infectti[all Fields] OR infecttion[all Fields] OR infecttive[all Fields] OR infecttivity[all Fields] OR infectueuse[all Fields] OR infectueuses[all Fields] OR infectueux[all Fields] OR infectuosa[all Fields] OR infectuosas[all Fields] OR infectuous[all Fields] OR infectus[all Fields] OR infectvac[all Fields] OR infectve[all Fields] OR infectyions[all Fields])
44 PubMed hand search: Automatic mapping when does it not work? Truncation (instrument*) Search field tags ([au]) Quotation marks ( spinal fusion ) 47
45 Exercise 6: MeSH - how to circumvent the indexing lag-phase I want to find as many papers as possible on patellar dislocation. It is very important that the latest papers are also identified Useful tool: MeSH Hand Search Advanced Search Builder Also see exercise 5 48
46 Exercise 6: MeSH & alternatives
47 Exercise 6: MeSH & alternatives
48 PubMed Features: Related Data 51
49 PubMed Features (advanced): Clipboard 52
50 Documentation of your search Reproducibility is essential! Think of how you document the surgeries you do Same applies to literature searches (not forget to document the search date!) What always works: copy-paste your search strings & limits (may use search details field) take notes on the individual steps not forget to document how related searches got implemented 55
51 Documentation of your search PubMed s little helper 1 : Save Search 56
52 Documentation of your search PubMed s little helper 2: copy paste (display settings!) 57
53 Documentation of your search PubMed s little helper 2: copy paste (display settings) 58
54 Documentation of your search PubMed s little helper 3: Send to file 59
55 Documentation of your search advanced PubMed s little helper : copy paste or send to file incl. indexing 60
56 Documentation of your search advanced PubMed s little helper : copy paste or send to file incl. indexing 61
57 Literature Search with PubMed: Summary We now know why, what, how and where to search We ve practiced using PubMed tools like filters to focus our search on what we really need and are also aware of their pitfalls and know what to do to work around them We also know how important and easy it is to properly document the search 62
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