| Literature DB >> 19767336 |
Amit X Garg1, Arthur V Iansavichus, Nancy L Wilczynski, Monika Kastner, Leslie A Baier, Salimah Z Shariff, Faisal Rehman, Matthew Weir, K Ann McKibbon, R Brian Haynes.
Abstract
OBJECTIVE: To develop and test a Medline filter that allows clinicians to search for articles within a clinical discipline, rather than searching the entire Medline database.Entities:
Mesh:
Year: 2009 PMID: 19767336 PMCID: PMC2746885 DOI: 10.1136/bmj.b3435
Source DB: PubMed Journal: BMJ ISSN: 0959-8138

Fig 1 Searching without using filter

Fig 2 Searching with use of filter

Fig 3 Data collection and filter development
Formulas for calculating sensitivity, specificity, precision, and accuracy of each filter to identify articles with renal information
| Filter (consisting of single or combined terms) | Manual review of each article | |
|---|---|---|
| Articles with renal information | Articles without renal information | |
| Article identified | a | b |
| Article not identified | c | d |
Sensitivity=a/(a+c): proportion of articles with renal information identified (also called recall in information retrieval studies).
Specificity=d/(b+d): proportion of articles without renal information not identified.
Precision=a/(a+b) (also referred to as positive predictive value in diagnostic test terminology): proportion of articles identified with renal information.
Accuracy=(a+d)/(a+b+c+d): proportion of all articles dealt with correctly by filter.
Division of 40 journals into development and validation sets
| Rank* | Journal | Total contributed articles (n=4657) | Articles with renal information (%) |
|---|---|---|---|
| 1 | Nephrology Dialysis Transplantation | 168 | 94.6 |
| 2 | Transplantation Proceedings | 171 | 59.7 |
| 3 | Journal of the American Society of Nephrology | 102 | 87.3 |
| 4 | American Journal of Kidney Diseases | 85 | 90.6 |
| 5 | Pediatric Nephrology | 83 | 67.5 |
| 6 | American Journal of Transplantation | 96 | 44.8 |
| 7 | New England Journal of Medicine | 376 | 3.7 |
| 8 | Diabetes Care | 184 | 5.4 |
| 9 | American Journal of Medicine | 107 | 7.5 |
| 10 | Journal of Hypertension | 89 | 9 |
| 11 | Radiology | 136 | 5.1 |
| 12 | Journal of Vascular Surgery | 73 | 6.8 |
| 13 | Lancet | 386 | 0.8 |
| 14 | Archives of Disease in Childhood | 87 | 3.4 |
| 15 | Journal of Trauma-Injury Infection & Critical Care | 120 | 1.7 |
| 16 | Diabetic Medicine | 60 | 1.7 |
| 17 | Surgical Endoscopy | 101 | 1 |
| 18 | Journal of the Association of Physicians of India | 50 | 2 |
| 19 | Calcified Tissue International | 22 | 4.5 |
| 20 | Journal of Human Genetics | 41 | 2.4 |
| 21 | Journal of Infection | 39 | 0 |
| 22 | Journal of Viral Hepatitis | 29 | 0 |
| 23 | American Journal of Clinical Oncology | 22 | 0 |
| 24 | Netherlands Journal of Medicine | 22 | 0 |
| Total | 2649 | 22.3 | |
| 1 | Kidney International | 187 | 79.7 |
| 2 | Transplantation | 168 | 37.5 |
| 3 | Peritoneal Dialysis International | 49 | 100 |
| 4 | Clinical Transplantation | 46 | 50 |
| 5 | Journal of Urology | 219 | 10.1 |
| 6 | Annals of Internal Medicine | 130 | 6.9 |
| 7 | BMJ | 477 | 1.3 |
| 8 | Annals of Thoracic Surgery | 289 | 1.7 |
| 9 | Investigative Radiology | 48 | 6.3 |
| 10 | Journal of Pediatrics | 96 | 2.1 |
| 11 | Clinical Pharmacology and Therapeutics | 30 | 3.3 |
| 12 | American Journal of Clinical Pathology | 58 | 1.7 |
| 13 | Bone Marrow Transplantation | 101 | 0 |
| 14 | Family Practice | 57 | 0 |
| 15 | East African Medical Journal | 31 | 0 |
| 16 | Diabetes/Metabolism Research Reviews | 22 | 0 |
| Total | 2008 | 16.6 | |
*Ranked by number of articles with renal information.
Best single term filters for high sensitivity (keeping specificity ≥50%), high specificity (keeping sensitivity ≥50%), and optimal balance of sensitivity and specificity, and performance of some other single term filters from 24 027 considered. Values are percentages (95% confidence intervals)
| Filters | Sensitivity | Specificity | Precision | Accuracy | ||
|---|---|---|---|---|---|---|
| Ovid† | PubMed translation‡ | Journal set | ||||
| kidney$.mp | kidney*[tw] | Development | 78.7 (75.4 to 82.0) | 97.2 (96.5 to 97.9) | 88.9 (86.2 to 91.6) | 93.0 (92.1 to 94.0) |
| Validation | 79.6 (75.25 to 83.9) | 95.6 (94.7 to 96.6) | 78.4 (74.0 to 82.8) | 93.0 (91.9 to 94.1) | ||
| exp *kidney diseases/ | “kidney diseases”[majr] | Development | 57.5 (53.5 to 61.5) | 98.6 (98.1 to 99.1) | 92.4 (89.7 to 95.1) | 89.5 (88.3 to 90.6) |
| Validation | 41.4 (36.1 to 46.7) | 97.6 (96.8 to 98.3) | 77.1 (70.9 to 83.3) | 88.2 (86.8 to 89.7) | ||
| kidney$.mp | kidney*[tw] | Development | 78.7 (75.4 to 82.0) | 97.2 (96.5 to 97.9) | 88.9 (86.2 to 91.6) | 93.0 (92.1 to 94.0) |
| Validation | 79.6 (75.25 to 83.9) | 95.6 (94.7 to 96.6) | 78.4 (74.0 to 82.8) | 93.0 (91.9 to 94.1) | ||
| *kidney transplantation/ | “kidney transplantation” [majr:noexp] | Development | 28.6 (24.9 to 32.2) | 99.7 (99.5 to 99.9) | 96.6 (93.9 to 99.3) | 83.8 (82.4 to 85.2) |
| Validation | 27.0 (22.3 to 31.8) | 99.9 (99.7 to 100) | 97.8 (94.8 to 100) | 87.8 (86.4 to 89.2) | ||
| glomerul$.mp | glomerul*[tw] | Development | 20.8 (17.5 to 24.1) | 99.3 (98.9 to 99.6) | 89.1 (83.9 to 94.3) | 81.8 (80.3 to 83.2) |
| Validation | 24.0 (19.4 to 28.6) | 99.5 (99.1 to 99.8) | 89.9 (83.6 to 96.2) | 86.9 (85.5 to 88.4) | ||
| glomerular filtration rate/ | “glomerular filtration rate”[mh:noexp] | Development | 6.3 (4.3 to 8.2) | 99.8 (99.7 to 100) | 92.5 (84.3 to 100) | 78.9 (77.4 to 80.5) |
| Validation | 7.2 (4.4 to 9.9) | 100 (100 to 100) | 100 (100 to 100) | 84.6 (83.0 to 86.2) | ||
| renal.ti. | renal[ti] | Development | 34.2 (30.4 to 38.0) | 99.5 (99.2 to 99.8) | 94.8 (91.9 to 97.8) | 84.9 (83.5 to 86.3) |
| Validation | 35.1 (30.0 to 40.3) | 98.7 (98.1 to 99.2) | 84.2 (78.1 to 90.2) | 88.1 (86.7 to 89.6) | ||
| *proteinuria/ | “proteinuria”[majr:noexp] | Development | 2.9 (1.5 to 4.2) | 99.9 (99.8 to 100) | 89.5 (75.7 to 100) | 78.3 (76.7 to 79.8) |
| Validation | 1.8 (0.4 to 3.2) | 100 (100 to 100) | 100 (100 to 100) | 83.7 (82.1 to 85.3) | ||
| exp renal replacement therapy/ | “renal replacement therapy”[mh] | Development | 48.1 (44.0 to 52.1) | 99.5 (99.2 to 99.8) | 96.6 (94.5 to 98.7) | 88.0 (86.8 to 89.3) |
| Validation | 50.5 (45.1 to 55.8) | 99.5 (99.1 to 99.8) | 94.9 (91.7 to 98.2) | 91.3 (90.1 to 92.6) | ||
| dialy$.mp. | dialy*[tw] | Development | 26.6 (23.0 to 30.1) | 99.9 (99.7 to 100) | 98.1 (96.0 to 100) | 83.5 (82.1 to 84.9) |
| Validation | 27.0 (22.3 to 31.8) | 99.9 (99.7 to 100) | 97.8 (94.8 to 100) | 87.8 (86.4 to 89.2) | ||
†Ovid fields: exp=exploded search term that automatically includes narrower indexing terms (for example, with exploded term kidney diseases, terms such as glomerulonephritis, renal insufficiency, uremia, and kidney failure are included in search); $=truncation character; mp=multiple posting (term appears in title, abstract, or MeSH); /=MeSH character; *=focused MeSH term; ti=term present in title.
‡PubMed fields: *=truncation character; [majr]=exploded and focused MeSH term; [majr:noexp]=not exploded and focused MeSH term; [tw]=text word present in title, abstract, or MeSH; [ti]=term present in title; [mh]=exploded MeSH term; [mh:noexp]=not exploded MeSH term.
Top filters yielding highest sensitivity (keeping specificity >90%) and highest specificity (keeping sensitivity >90%) based on combination of up to 14 terms. Values are percentages (95% confidence intervals)
| Filter | Sensitivity | Specificity | Precision | Accuracy | ||
|---|---|---|---|---|---|---|
| Ovid† | PubMed translation‡ | Journal set | ||||
| exp kidney diseases/OR exp renal replacement therapy/OR renal.mp OR kidney$.mp OR nephr$.mp. OR proteinuria.mp | “kidney diseases”[mh] OR “renal replacement therapy”[mh] OR renal[tw] OR kidney*[tw] OR (nephre*[tw] OR nephri*[tw] OR nephroc*[tw] OR nephrog*[tw] OR nephrol*[tw] OR nephron*[tw] OR nephrop*[tw] OR nephros*[tw] OR nephrot*[tw]) OR proteinuria[tw] | Development | 97.8 (96.6 to 99.0) | 95.0 (94.1 to 95.9) | 84.9 (82.2 to 87.6) | 95.6 (94.8 to 96.4) |
| Validation | 96.7 (94.8 to 98.6) | 93.9 (92.8 to 95.1) | 75.9 (71.9 to 80.0) | 94.4 (93.4 to 95.4) | ||
| (exp *renal replacement therapy/OR exp *kidney diseases/OR kidney$.ti. OR nephr$.ti. OR renal.ti. OR *kidney/OR exp renal dialysis/OR exp *kidney function tests/OR *proteinuria/OR glomerul$.ti.) NOT (exp *kidney neoplasms/OR *pyelonephritis/OR exp *urinary tract infections/OR exp *nephrolithiasis/) | (“renal replacement therapy”[majr] OR “kidney diseases”[majr] OR kidney*[ti] OR nephr*[ti] OR renal[ti] OR “kidney”[majr:noexp] OR “renal dialysis”[mh] OR “kidney function tests”[majr] OR “proteinuria”[majr:noexp] OR glomerul*[ti]) NOT (“kidney neoplasms”[majr] OR pyelonephritis[majr:noexp] OR “urinary tract infections”[majr] OR “nephrolithiasis”[majr]) | Development | 93.4 (91.4 to 95.4) | 98.5 (98.0 to 99.0) | 94.7 (92.9 to 96.5) | 97.4 (96.7 to 98.0) |
| Validation | 91.3 (88.3 to 94.3) | 98.9 (98.4 to 99.4) | 94.4 (91.9 to 96.9) | 97.7 (97.0 to 98.3) | ||
†Ovid fields: exp=exploded MeSH term; $=truncation character; mp=multiple posting (term appears in title, abstract, or MeSH); /=MeSH character; *=focused MeSH; ti=term present in title.
‡PubMed fields: *=truncation character; [majr]=exploded and focused MeSH term; [majr:noexp]=not exploded and focused MeSH term; [tw]=text word present in title, abstract, or MeSH; [ti]=term present in title; [mh]=exploded MeSH term.
Number of relevant articles retrieved with and without search filters
| Clinical question* | No of relevant articles retrieved | No of non-relevant articles retrieved† | |||||
|---|---|---|---|---|---|---|---|
| Clinician’s search alone | Clinician’s search with most sensitive renal content filter | Clinician’s search with most specific renal content filter | Clinician’s search alone | Clinician’s search with most sensitive renal content filter | Clinician’s search with most specific renal content filter | ||
| What are the effects of statins on change in kidney function and urinary protein excretion? (24 relevant articles) | 6 | 20 | 16 | 86 | 48 | 39 | |
| What is the impact of fenoldopam on acute kidney injury, patients’ mortality, and length of hospital stay in critically ill patients? (12 relevant articles) | 1 | 11 | 11 | 7 | 32 | 21 | |
| When tacrolimus is compared directly with ciclosporin in the treatment of kidney transplant recipients, what is the evidence on transplant outcomes, toxicity, and adverse effects? (63 relevant articles) | 10 | 60 | 60 | 18 | 20 | 15 | |
| What is the efficacy of low dose dopamine (<5 μg/kg of body weight per minute) compared with no therapy in patients with or at risk for acute renal failure? (52 relevant articles) | 6 | 15 | 12 | 13 | 16 | 15 | |
| How does intradermal | 6 | 10 | 10 | 22 | 34 | 31 | |
*Five clinicians were asked to type in a PubMed search to answer a focused clinical question for which relevant articles were summarised in a recent systematic review.33-37 Each search was restricted to search dates provided in methods of each review. Search phrases as determined and typed in by clinicians were: “statins and kidney function”, “fenoldopam and acute kidney injury”, “‘kidney transplant outcome tacrolimus cyclosporin”, “low-dose dopamine and acute renal failure”, and “hepatitis b vaccination in chronic kidney disease”. Renal terms were removed when the clinician’s search was performed with renal content filters.
†Number of non-relevant articles retrieved is expressed per relevant article, rounded up to nearest whole number.