Molecular Connections: Enrich your database with an intelligent ontology framework.

Nature Publishing Group (NGP) is a leading publisher of academic journals, magazines, and online databases that serves the research community by publishing the most significant discoveries.



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With an increase in the volume of scholarly literature, Nature Publishing sought to create an ontology that reflected its content to ensure accurate search and retrieval. The company approached Molecular Connections’ to deliver ontology enhancements for its key subject terms and semantic tagging for its back files (archives) and enable more intuitive searches across their literature databases.

The existing ontology lacked granularity, structure, definitions, synonyms, and was a mere list of keywords stored in an excel spreadsheet. The challenge was to decide between developing an existing ontology or creating an ontology from scratch. The team had to arrive at a logical decision of merging the ontologies and decide on the size of the ontology based on its number of levels and comprehensibility. The framework had to incorporate storing of custom metadata retrieved from the data source associated with the candidate terms to provide granularity.


As a leader in delivering world-class ontology solutions, the team decided on creating a system for user-controlled accounting of versioning and re-engineering of the ontology for effective collaboration. Engineering an ontology and data structure facilitated interoperability and integration into other platforms.

The existing ontology was extended by extracting terms from public repositories and also by article indexing. For better navigation, definitions and synonyms of the candidate terms were added, and a structural hierarchy was also built with new parent-child relationships.

The ontology was built on a flexible platform that supported new terms and improved the specificity of the ontological terms through the interlinking of different concept terms within the framework. Further, the workflow management system within the platform was phase-centric (build phases, quality control, and release) and the changes within the ontology could be traced with ease.


Molecular Connections helped the client achieve its business objective by enriching its ontology from 700 terms to a set of 2,000 basic terms. The ontology was standardised extensively with reference to public ontologies for better integration and covered major concepts such as biological entities, chemistry, physical science, techniques, and models. The areas covered by the ontology include basic sciences such as biology, chemistry, physics, environmental sciences, social sciences, and health sciences. Further, the ontology was hosted on the publisher’s article hosting platform for indexing and improved search navigation.

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