Toward Automated Data Extraction: A Pilot Survey of the Structure of Tabular Data in Clinical Comparative Literature (Preprint)

2021 ◽  
Author(s):  
Karl Holub ◽  
Nicole Hardy ◽  
Kevin M. Kallmes
Keyword(s):  
Data Extraction ◽  
Outcome Data ◽  
Free Text ◽  
Data Format ◽  
Quantitative Evidence ◽  
Reporting Practices ◽  
Pilot Survey ◽  
Report Data ◽  
Data Elements ◽  
Measurement Context

BACKGROUND Systematic reviews depend on time-consuming extraction of data from PDFs of underlying studies. To date, automation efforts have focused on extracting from the text, and no approach has yet succeeded in fully automating ingestion of quantitative evidence. However, the majority of relevant data is generally presented in tables, and tabular structure is more amenable to automated extraction than free-text. OBJECTIVE The purpose of this survey is to classify the structure and format of descriptive statistics reported in tables in the comparative medical literature. METHODS We sampled 100 published randomized controlled trials (RCTs) from the year 2019 from PubMed; these results were imported to the AutoLit platform. Studies were excluded if they were non-clinical, non-comparative, not in English, protocol-only, or not available in full text. In AutoLit, tables reporting baseline or outcome data in all studies were characterized based on reporting practices. Measurement context, meaning the structure in which the interventions of interest, patient arm breakdown, measurement timepoints, and data element descriptions were presented, was classified based on the number of contextual pieces and metadata reported. Then, the statistic formats for reported metrics (specific instances of reporting of data elements) were classified by location and broken down into reporting strategies for continuous, dichotomous, and categorical metrics. RESULTS We included 78 of 100 studies, one of which (1.3%) did not report data elements in tables. The remaining 77 studies reported baseline and outcome data in 174 tables, and 97% of these tables broke down reporting by patient arms. Fifteen structures were found for the reporting of measurement context, which were broadly grouped into: 1x1 Contexts, where two pieces of context are reported total (e.g. “arms in columns, data elements in rows); 2x1 Contexts, where two pieces of context are given on row headers (e.g. timepoints in columns, arms nested in data elements on rows); 1x2 Contexts, where two pieces of context are given on column headers. 1x1 contexts were present in 57% of tables, compared to 20% for 2x1 and 15% for 1x2 (8% used unique/other stratification). Statistic formats were reported in the headers or descriptions of 84% of studies. CONCLUSIONS In this pilot survey, we found a high density of information in tables, but with major heterogeneity in presentation of measurement context. The highest-density studies reported both baseline and outcome measures in tables, with arm-level breakout, intervention labels and arm sizes present, and reported both the statistic formats and units. The measurement context formats presented here, broadly classified into three classes that cover 92% of studies, form a basis for understanding the frequency of different reporting styles, supporting automated detection of data format for extraction of metrics.

scholarly journals What is the risk of prostate cancer mortality following negative systematic TRUS-guided biopsies? A systematic review

BMJ Open ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. e040965
Author(s):  
Sandra Miriam Kawa ◽  
Signe Benzon Larsen ◽  
John Thomas Helgstrand ◽  
Peter Iversen ◽  
Klaus Brasso ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Systematic Review ◽  
Data Extraction ◽  
Specific Antigen ◽  
Transrectal Ultrasound ◽  
Population Based ◽  
Free Text ◽  
Medical Subject Headings ◽  
Prognostic Information ◽  
Prostate Biopsies

ObjectiveTo investigate the risk of prostate cancer-specific mortality (PCSM) following initial negative systematic transrectal ultrasound-guided (TRUS) prostate biopsies.DesignSystematic review.Data sourcesPubMed and Embase were searched using a string combination with keywords/Medical Subject Headings terms and free text in the search builder. Date of search was 13 April 2020.Study selectionStudies addressing PCSM following initial negative TRUS biopsies. Randomised controlled trials and population-based studies including men with initial negative TRUS biopsies reported in English from 1990 until present were included.Data extractionData extraction was done using a predefined form by two authors independently and compared with confirm data; risk of bias was assessed using the Newcastle–Ottawa Scale for cohort studies when applicable.ResultsFour eligible studies were identified. Outcomes were reported differently in the studies as both cumulative incidence and Kaplan-Meier estimates have been used. Regardless of the study differences, all studies reported low estimated incidence of PCSM of 1.8%–5.2% in men with negative TRUS biopsies during the following 10–20 years. Main limitation in all studies was limited follow-up.ConclusionOnly a few studies have investigated the risk of PCSM following initial negative biopsies and all studies included patients before the era of MRI of the prostate. However, the studies point to the fact that the risk of PCSM is low following initial negative TRUS biopsies, and that the level of prostate-specific antigen before biopsies holds prognostic information. This may be considered when advising patients about the need for further diagnostic evaluation.PROSPERO registration numberCRD42019134548.

scholarly journals Gender disparity between authors in leading medical journals during the COVID-19 pandemic: a cross-sectional review

BMJ Open ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. e051224
Author(s):  
Vaidehi Misra ◽  
Frozan Safi ◽  
Kathryn A Brewerton ◽  
Wei Wu ◽  
Robin Mason ◽  
...  
Keyword(s):  
Data Extraction ◽  
Gender Disparity ◽  
High Impact ◽  
Original Research ◽  
Eligibility Criteria ◽  
Cross Sectional ◽  
Medical Journals ◽  
The Usa ◽  
Study Characteristics ◽  
Data Elements

ObjectivesEvaluate gender differences in authorship of COVID-19 articles in high-impact medical journals compared with other topics.DesignCross-sectional review.Data sourcesMedline database.Eligibility criteriaArticles published from 1 January to 31 December 2020 in the seven leading general medical journals by impact factor. Article types included primary research, reviews, editorials and commentaries.Data extractionKey data elements were whether the study topic was related to COVID-19 and names of the principal and the senior authors. A hierarchical approach was used to determine the likely gender of authors. Logistic regression assessed the association of study characteristics, including COVID-19 status, with authors’ likely gender; this was quantified using adjusted ORs (aORs).ResultsWe included 2252 articles, of which 748 (33.2%) were COVID-19-related and 1504 (66.8%) covered other topics. A likely gender was determined for 2138 (94.9%) principal authors and 1890 (83.9%) senior authors. Men were significantly more likely to be both principal (1364 men; 63.8%) and senior (1332 men; 70.5%) authors. COVID-19-related articles were not associated with the odds of men being principal (aOR 0.99; 95% CI 0.81 to 1.21; p=0.89) or senior authors (aOR 0.96; 95% CI 0.78 to 1.19; p=0.71) relative to other topics. Articles with men as senior authors were more likely to have men as principal authors (aOR 1.49; 95% CI 1.21 to 1.83; p<0.001). Men were more likely to author articles reporting original research and those with corresponding authors based outside the USA and Europe.ConclusionsWomen were substantially under-represented as authors among articles in leading medical journals; this was not significantly different for COVID-19-related articles. Study limitations include potential for misclassification bias due to the name-based analysis. Results suggest that barriers to women’s authorship in high-impact journals during COVID-19 are not significantly larger than barriers that preceded the pandemic and that are likely to continue beyond it.PROSPERO registration numberCRD42020186702.

scholarly journals Rapid Implementation of Inpatient Electronic Physician Documentation at an Academic Hospital

2012 ◽  
Vol 03 (02) ◽  
pp. 175-185 ◽  
Author(s):  
J.A. Bernstein ◽  
R.B. McKenzie ◽  
B.J. King ◽  
C.A. Longhurst ◽  
J.S. Hahn
Keyword(s):  
Essential Element ◽  
Cost Savings ◽  
Free Text ◽  
Academic Hospital ◽  
Electronic Documentation ◽  
Documentation System ◽  
Clinical Notes ◽  
System Data ◽  
Electronic Method ◽  
Data Elements

SummaryElectronic physician documentation is an essential element of a complete electronic medical record (EMR). At Lucile Packard Children’s Hospital, a teaching hospital affiliated with Stanford University, we implemented an inpatient electronic documentation system for physicians over a 12-month period. Using an EMR-based free-text editor coupled with automated import of system data elements, we were able to achieve voluntary, widespread adoption of the electronic documentation process. When given the choice between electronic versus dictated report creation, the vast majority of users preferred the electronic method. In addition to increasing the legibility and accessibility of clinical notes, we also decreased the volume of dictated notes and scanning of handwritten notes, which provides the opportunity for cost savings to the institution.

Evaluating Intensive Family Preservation Programs: A Methodological Review

PEDIATRICS ◽  
1996 ◽  
Vol 97 (4) ◽  
pp. 535-542
Author(s):  
Amy M. Heneghan ◽  
Sarah M. Horwitz ◽  
John M. Leventhal
Keyword(s):  
At Risk ◽  
English Language ◽  
Data Extraction ◽  
Experimental Studies ◽  
Outcome Data ◽  
Family Preservation ◽  
Children At Risk ◽  
Quasi Experimental ◽  
Family Based ◽  
Family Preservation Program

Objectives. To determine the adequacy of evaluations of family preservation services (FPS), which are designed to support families and prevent out-of-home placements of children at risk of abuse or neglect, and to assess the effectiveness of FPS at reducing out-of-home placements of children. Data Sources. References published from 1977 to 1993 were identified from a computerized search of databases for English-language publications using the key phrases "family preservation," "child abuse," and "family-based services." Unpublished references were identified by mail or phone from a listing of more than 200 programs in a national directory. Selection of Studies. Of 802 references initially identified, 46 program evaluations were reviewed. Ten studies met the following inclusion criteria: (1) evaluated an intensive family preservation program, (2) included outcome data in the report, and (3) used a comparison group. Five were randomized trials, and 5 were quasi-experimental studies (nonrandomized). Data Extraction. Descriptive information about the programs and evaluations was collected. To determine methodological quality, two independent raters used a 15- item questionnaire to examine the assignment of families to treatment groups, the interventions provided, and the outcomes assessed. A composite score of 11 or greater represented an acceptable study, 6 to 10 represented an adequate study, and 5 or less represented an unacceptable study. Results. Only two studies were rated acceptable, four were adequate, and four were unacceptable. Methodological shortcomings included poorly defined assessment of risk, inadequate descriptions of the interventions provided, and nonblinded determination of the outcomes. Rates of out-of-home placements were 21% to 59% among families who received FPS and 20% to 59% among comparison families. The relative risk of placement was significantly reduced by FPS in only two studies (one randomized trial and one quasi-experimental study). Conclusions. Despite current widespread use of FPS to prevent out-of-home placements of children, evaluations of FPS are methodologically difficult and show no benefit in reducing rates of out-of-home placements of children at risk of abuse or neglect in 8 of 10 studies. Consistent, methodologically rigorous evaluations are needed to determine the effectiveness of FPS and to guide social policy for high-risk children and their families.

Abstract 198: Public Perceptions on Why Women Receive Less Bystander CPR Than Men in Out of Hospital Cardiac Arrest

Circulation ◽  
2018 ◽  
Vol 138 (Suppl_2) ◽  
Author(s):  
Sarah M Perman ◽  
Shelby K Shelton ◽  
Christopher Knoepke ◽  
Kathryn Rappaprt ◽  
Daniel D Matlock ◽  
...  
Keyword(s):  
Cardiac Arrest ◽  
National Sample ◽  
Public Perceptions ◽  
Free Text ◽  
Pilot Survey ◽  
Adequate Knowledge ◽  
Free Text Response ◽  
Bystander Cpr ◽  
To Receive ◽  
Hospital Cardiac Arrest

Introduction: Women who suffer an out of hospital cardiac arrest have been observed to receive less bystander cardiopulmonary resuscitation (CPR) than men. Potential reasons for why women receive less bystander CPR than men are largely unknown. Methods: Mechanical Turk (MTurk), Amazon’s crowdsourcing platform, was used to pilot a national survey asking participants why they believe women receive less bystander CPR than men. Eligible participants were adults (18 years or over) located in the US. Participants were reimbursed $1 for their participation. To ensure adequate knowledge on the subject, survey responses were excluded if they incorrectly defined CPR. Participant demographics as well as familiarity with CPR were queried. Participants were asked to answer the following free-text question “Do you have any ideas on why women may be less likely to receive CPR than men when they collapse in public?” Descriptive statistics were used to define the cohort. The free text response was coded using thematic analysis and major themes were identified via classical content analysis. Results: Within 55 minutes of deploying the pilot survey, 54 individuals responded. All respondents answered the knowledge question correctly, and none were excluded. Mean age was 36.9 ±9.6 years and 38.9% were female. Participants were geographically distributed as follows: 13% West, 13% Southwest, 16.7% Midwest, 27.8% Southeast, 29.6% Northeast. Predominant themes identified for why women might receive less bystander CPR than men are identified in Table 1. Within this cohort, 27.8% were trained in CPR, and only 5.6% of respondents had actually performed CPR on a person. Conclusions: In this pilot survey, public perceptions identified social norms regarding fear of inappropriate touching and hurting women as significant contributors to reasons for why women receive less bystander CPR than men. Additional work using a larger national sample to confirm and expand on these findings is ongoing.

scholarly journals P21 Feasibility of the Learning and Exercise to Avert Pain (LEAP) programme: an evaluation of a group therapy intervention for young people with chronic musculoskeletal pain

Rheumatology ◽  
2019 ◽  
Vol 58 (Supplement_4) ◽  
Author(s):  
Hannah Wong ◽  
Margaret Wheeler ◽  
Jennifer Nisbet ◽  
Janet McDonagh ◽  
Verna Cuthbert
Keyword(s):  
Young People ◽  
Musculoskeletal Pain ◽  
Conflicts Of Interest ◽  
Outcome Data ◽  
Free Text ◽  
Electronic Patient Records ◽  
Structured Interviews ◽  
Group Setting ◽  
Adolescent Anxiety

Abstract Background Chronic idiopathic musculoskeletal pain (CIMSKP) has become increasingly recognised as a major cause of morbidity in adolescents. In view of increasing referrals to a paediatric rheumatology centre, the Learning and Exercise to Avert Pain (LEAP) intervention was designed as an approach to pain management within a group setting, led by an occupational therapist and a physiotherapist. It involves 2 hour weekly sessions for 6 weeks and includes education, gym activities and relaxation sessions with routine collection of Pain VAS, CHAQ, Bath Pain questionnaires (adolescent BAPQ and parent BAPQ-p forms) at baseline, end of LEAP and 3 months follow-up. We aim to assess the feasibility and impact of LEAP for adolescents with CIMSKP. Methods Young people who had been referred for the LEAP programme were identified (n = 46). Basic demographics and questionnaire scores were collected from electronic patient records and therapy notes. Feasibility was assessed by delivery of programme and percentage completion of questionnaires at three time-points. Semi-structured interviews were conducted with healthcare professionals involved in the programme and analysed using thematic analyses as were any free text comments on the BAPQ from adolescents and parents. Statistical analysis of the outcome data was performed using paired t-tests and SPSS software (v22). Results 46 adolescents were identified: 85% female, median age 16 years (range 10 to 19). 34 participated in LEAP, 12 received 1:1 therapy. Feasibility of programme delivery was achieved with completion of all six sessions. Completion rates for all 3 measures for adolescents/parents at baseline, end of programme review and follow up were 78.6/71.4%, 64.3/71.4%, and 45.5/36.4% respectively. Adolescent scores indicated a significant increase in impairment in the development subscale scores on BAPQ from baseline to programme end (p = 0.021) although not at follow up. Parent scores for adolescent anxiety and pain-specific anxiety on BAPQ-p increased significantly from end of programme to follow-up (p = 0.017, p = 0.034 respectively). Parents scored higher than adolescents for most outcomes. The qualitative data (available for 11 adolescents, 12 parents) revealed that parents and adolescents appreciated learning coping techniques and gaining a greater understanding of chronic pain. The intervention was perceived to be socially beneficial in particular but imperfect in terms of data collection by the professionals interviewed (n = 2). Conclusion Baseline demographics of the LEAP participants echoed current literature. Delivery of the programme was feasible and the programme was positively received by young people, their parents and professionals alike. The increase in adolescent development subscale scores following the programme could represent increased self-reflection and/or peer to peer observations as a result of the group setting but needs longer term follow-up data to clarify further. The increase in parental anxiety highlights the need for a concurrent session for parents. Routine collection of objective measures remains challenging in non-research setting. Conflicts of Interest The authors declare no conflicts of interest.

scholarly journals Code Orange: A Systematic Review of Psychosocial Disaster Response

2019 ◽  
Vol 34 (s1) ◽  
pp. s69-s70 ◽  
Author(s):  
Melissa B. Korman ◽  
Lauren Goldberg ◽  
Cailtin Klein ◽  
Marjan Khanjani ◽  
Gemma Cox ◽  
...  
Keyword(s):  
Disaster Response ◽  
Psychological Treatment ◽  
Data Extraction ◽  
Mass Casualty ◽  
Lessons Learned ◽  
Free Text ◽  
Evidence Based ◽  
Inclusion Criteria ◽  
Mass Trauma ◽  
Disaster Situation

Introduction:Survivors of mass casualty incidents are vulnerable to both physical and psychological injuries. Hospitals need to triage the walking wounded victims, their loved ones, and witnesses for symptoms of emotional distress to ensure that those who are traumatized benefit from proactive psychological treatment. Hospitals must also manage the influx of searching family and friends, and be able to reunite them with their loved ones, to reduce chaos and prevent hospital skipping.Aim:To analyze previous research on institutional psychosocial disaster response, what has or has not worked, and lessons learned in order to develop evidence-based future planning suggestions.Methods:A literature search was conducted on the following electronic databases: (Medline 2007 to July 2018), (Embase 2007 to July 2018), (PsycInfo 2007 to July 2018). A combination of subject headings and free text keywords were used to perform the searches. After removing duplicates, abstracts were screened independently by two reviewers for the following inclusion criteria: 1) crisis intervention (in a disaster situation), 2) mention of psychosocial response or lack thereof and lessons learned, 3)relevant outcomes, 4) OECD countries, and 5) journal articles published 2007–Present. Review articles were excluded. Primary and secondary reviewers are in the process of discussing discrepancies. Data extraction will be conducted from all articles that meet the inclusion criteria. Key themes to be analyzed include psychological casualties, searching family and friends, and family reunification plans.Results:The initial search yielded 6,267 results. 5,294 articles remained after duplicates were removed. Of the 4,890 reviewed thus far, 269 articles met inclusion criteria.Discussion:Although a wealth of existing literature notes the need for an effective psychosocial response in mass trauma and disaster situations, no prior study has analyzed the efficacy of such interventions or laid out an evidence-based plan. This study will fill this much-needed gap in the literature.

scholarly journals Issues in reporting of systematic review methods in health app-focused reviews: A scoping review

2020 ◽  
Vol 26 (4) ◽  
pp. 2930-2945
Author(s):  
Rebecca Grainger ◽  
Hemakumar Devan ◽  
Bahram Sangelaji ◽  
Jean Hay-Smith
Keyword(s):  
Systematic Review ◽  
Clinical Efficacy ◽  
Scoping Review ◽  
Data Extraction ◽  
Reporting Standard ◽  
Systematic Review Methods ◽  
Protocol Registration ◽  
Mobile Health Apps ◽  
Review Protocol ◽  
Data Elements

No guidelines exist for the conduct and reporting of manuscripts with systematic searches of app stores for, and then appraisal of, mobile health apps (‘health app-focused reviews’). We undertook a scoping review including a systematic literature search for health app-focused reviews describing systematic app store searches and app appraisal, for apps designed for patients or clinicians. We created a data extraction template which adapted data elements from the PRISMA guidelines for systematic literature reviews to data elements operationalised for health app-focused reviews. We extracted the data from included health app-focused reviews to describe: (1) which elements of the adapted ‘usual’ methods of systematic review are used; (2) methods of app appraisal; and (3) reporting of clinical efficacy and recommendations for app use. From 2798 records, the 26 included health app-focused reviews showed incomplete or unclear reporting of review protocol registration; use of reporting guidelines; processes of screening apps; data extraction; and appraisal tools. Reporting of clinical efficacy of apps or recommendations for app use were infrequent. The reporting of methods in health app-focused reviews is variable and could be improved by developing a consensus reporting standard for health app-focused reviews.

scholarly journals Documentation of social determinants in electronic health records with and without standardized terminologies: A comparative study

2018 ◽  
Vol 28 (1) ◽  
pp. 39-47 ◽  
Author(s):  
Karen A Monsen ◽  
Joyce M Rudenick ◽  
Nicole Kapinos ◽  
Kathryn Warmbold ◽  
Siobhan K McMahon ◽  
...  
Keyword(s):  
Electronic Health Records ◽  
Free Text ◽  
Snomed Ct ◽  
Health Records ◽  
Behavioral Determinants ◽  
Omaha System ◽  
Standardized Terminology ◽  
Electronic Health ◽  
Data Elements ◽  
Improve Health

Background: Electronic health records (EHRs) are a promising new source of population health data that may improve health outcomes. However, little is known about the extent to which social and behavioral determinants of health (SBDH) are currently documented in EHRs, including how SBDH are documented, and by whom. Standardized nursing terminologies have been developed to assess and document SBDH. Objective: We examined the documentation of SBDH in EHRs with and without standardized nursing terminologies. Methods: We carried out a review of the literature for SBDH phrases organized by topic, which were used for analyses. Key informant interviews were conducted regarding SBDH phrases. Results: In nine EHRs (six acute care, three community care) 107 SBDH phrases were documented using free text, structured text, and standardized terminologies in diverse screens and by multiple clinicians, admitting personnel, and other staff. SBDH phrases were documented using one of three standardized terminologies ( N = average number of phrases per terminology per EHR): ICD-9/10 ( N = 1); SNOMED CT ( N = 1); Omaha System ( N = 79). Most often, standardized terminology data were documented by nurses or other clinical staff versus receptionists or other non-clinical personnel. Documentation ‘unknown’ differed significantly between EHRs with and without the Omaha System (mean = 26.0 (standard deviation (SD) = 8.7) versus mean = 74.5 (SD = 16.5)) ( p = .005). SBDH documentation in EHRs differed based on the presence of a nursing terminology. Conclusions: The Omaha System enabled a more comprehensive, holistic assessment and documentation of interoperable SBDH data. Further research is needed to determine SBDH data elements that are needed across settings, the uses of SBDH data in practice, and to examine patient perspectives related to SBDH assessments.

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