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[bioontology-support] NCBO Ontology Recommender 2.0 paper

Marcos Martinez Romero marcosmr at
Tue Jun 13 17:02:29 PDT 2017

Dear BioPortal community,

We are pleased to announce the recent publication of a paper describing the NCBO Ontology Recommender 2.0 in the Journal of Biomedical Semantics (

As you may already know, the Ontology Recommender is a system that suggests appropriate ontologies to annotate biomedical textual data. It is openly available both via the BioPortal Web-based UI ( and via a Web service API (

The Ontology Recommender 2.0 has been available at BioPortal since August 2015, and it has been widely used by many of you since then. This paper describes in detail the algorithm used to generate the recommendations and compares it to the old system.

We hope you enjoy it!

Best regards,


Marcos Martínez-Romero, PhD
Research Software Developer
Center for Expanded Data Annotation and Retrieval (CEDAR)
Stanford Center for Biomedical Informatics Research (BMIR)
Stanford University

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