Email updates

Keep up to date with the latest news and content from BMC Research Notes and BioMed Central.

Open Access Technical Note

Jointly creating digital abstracts: dealing with synonymy and polysemy

Steven Vercruysse* and Martin Kuiper

Author Affiliations

Systems Biology group, Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway

For all author emails, please log on.

BMC Research Notes 2012, 5:601  doi:10.1186/1756-0500-5-601

Published: 30 October 2012

Abstract

Background

Ideally each Life Science article should get a ‘structured digital abstract’. This is a structured summary of the paper’s findings that is both human-verified and machine-readable. But articles can contain a large variety of information types and contextual details that all need to be reconciled with appropriate names, terms and identifiers, which poses a challenge to any curator. Current approaches mostly use tagging or limited entry-forms for semantic encoding.

Findings

We implemented a ‘controlled language’ as a more expressive representation method. We studied how usable this format was for wet-lab-biologists that volunteered as curators. We assessed some issues that arise with the usability of ontologies and other controlled vocabularies, for the encoding of structured information by ‘untrained’ curators. We take a user-oriented viewpoint, and make recommendations that may prove useful for creating a better curation environment: one that can engage a large community of volunteer curators.

Conclusions

Entering information in a biocuration environment could improve in expressiveness and user-friendliness, if curators would be enabled to use synonymous and polysemous terms literally, whereby each term stays linked to an identifier.

Keywords:
Structured digital abstract; Biocuration; Community curation; Ontology; Controlled vocabulary