Toward Automated Data Extraction According to Tabular Data Structure: Cross-sectional Pilot Survey of the Comparative Clinical Literature (Preprint)
Authors: Holub Karl , Hardy Nicole , Kallmes Kevin 
Published: September 2021

BACKGROUND

Systematic reviews depend on time-consuming extraction of data from the PDFs of underlying studies. To date, automation efforts have focused on extracting data 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 the tabular structure is more amenable to automated extraction than free text.

OBJECTIVE

The purpose of this study was 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 from 2019 based on a search in PubMed; these results were imported to the AutoLit platform. Studies were excluded if they were nonclinical, noncomparative, not in English, protocols, 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 time points, and data element descriptions were presented, was classified based on the number of contextual pieces and metadata reported. The statistic formats for reported metrics (specific instances of reporting of data elements) were then classified by location and broken down into reporting strategies for continuous, dichotomous, and categorical metrics.

RESULTS

We included 78 of 100 sampled 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 96% (69/72) of these tables broke down reporting by patient arms. Fifteen structures were found for the reporting of measurement context, which were broadly grouped into: 1×1 contexts, where two pieces of context are reported in total (eg, arms in columns, data elements in rows); 2×1 contexts, where two pieces of context are given on row headers (eg, time points in columns, arms nested in data elements on rows); and 1×2 contexts, where two pieces of context are given on column headers. The 1×1 contexts were present in 57% of tables (99/174), compared to 20% (34/174) for 2×1 contexts and 15% (26/174) for 1×2 contexts; the remaining 8% (15/174) used unique/other stratification methods. Statistic formats were reported in the headers or descriptions of 84% (65/74) of studies.

CONCLUSIONS

In this cross-sectional pilot review, 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% (71/78) of studies, form a basis for understanding the frequency of different reporting styles, supporting automated detection of the data format for extraction of metrics.