Goals and Strategies for the Indexing of Publication Types and Study Designs

TL;DR

This paper discusses the unique goals and challenges of indexing publication types and study designs in biomedical literature, emphasizing the need for comprehensive, probabilistic, and automated approaches to improve retrieval and evidence synthesis.

Contribution

It introduces a unified hierarchy for publication types and study designs and highlights the importance of probabilistic scoring for automated indexing systems.

Findings

Created a unified hierarchy for publication types and study designs.

Emphasized the need for probabilistic goodness-of-fit prediction scores.

Proposed automated systems for real-time, comprehensive PT indexing.

Abstract

Objectives. Major research and implementation efforts have been devoted to indexing articles according to the major topics discussed, but much less effort to indexing their publication types and study designs (collectively, PTs). In this Perspective, we discuss how indexing PTs differs from topical MeSH indexing and requires a different approach. Materials and Methods. Rather than focus on the technical aspects of machine learning-based indexing models, we emphasize the goals and purposes for which biomedical articles are indexed, and the surprisingly thorny question of how indexing systems should be evaluated. Results. Topical Medical Subject Heading (MeSH) terms are assigned to articles that cover the major topics discussed; when more than one term is applicable, only the most specific term is assigned. In contrast, PTs are assigned to articles that have a given structure or use a particular design. To meet the needs of end-users, particularly groups involved in evidence syntheses, PT indexing needs to be comprehensive and employ probabilistic goodness-of-fit prediction scores. Whereas existing NLM hierarchies place publication types and study design-related terms on separate trees from each other, we have created a unified hierarchy that permits more appropriate retrieval via automatic expansion. Discussion. Automated PT indexing systems should allow users to input article records or full-text PDFs and receive scores in real time. This will offer consistent indexing across bibliographic databases, as well as preprints and unpublished manuscripts. Conclusions. Automated PT indexing systems, properly designed and implemented, hold the promise of greatly improving the retrieval of biomedical articles, saving substantial effort when writing evidence syntheses and benefiting other users as well.