Journal of Biomedical Semantics

Editors-in-Chief

Robert Hoehndorf, King Abdullah University of Science and Technology, Saudi Arabia

Founding Editor-in-Chief:
Dietrich Rebholz-Schuhmann, ZB Med, Germany

Aims and scope

Journal of Biomedical Semantics addresses issues of semantic enrichment and semantic processing in the biomedical and clinical domain. The scope of the journal covers two main areas:

Infrastructure for biomedical semantics: focusing on semantic resources and repositories, ontology design, meta-data standards and management, resource description, knowledge representation and semantic frameworks, the Biomedical Semantic Web, and semantic interoperability.

Semantic mining, annotation, and analysis: focusing on approaches and applications of semantic resources; and tools for investigation, reasoning, prediction, artificial intelligence modelling, and discoveries in biomedicine.

Open Collections

2023
Ontologies for Infectious and Immune-Mediated Disease Data Science
Journal of Biomedical Semantics
Edited by: Asiyah Yu Lin, Alexander Diehl, John Beverley & Lindsay G. Cowell

Vaccine and Drug Ontologies (Call for papers)
Journal of Biomedical Semantics
Edited by: Yongqun Oliver He, Cui Tao & Junguk Hur

International Conference on Biomedical Ontologies (ICBO)
Journal of Biomedical Semantics
Edited by: Karin Slater & Robert Hoehndorf

2022
International Society of Molecular Biology (ISMB) Bio-Ontologies Community of Special Interest
Journal of Biomedical Semantics
Edited by: Tiffany Callahan & Maxat Kulmanov

Data and Research Objects Planning and Management for Linked Open Science (DaMaLOS)
Journal of Biomedical Semantics
Edited by: Leyla Jael Garcia-Castro & Nuria Queralt-Rosinach

The SPHN Schema Forge – transform healthcare semantics from human-readable to machine-readable by leveraging semantic web technologies

Authors: Vasundra Touré, Deepak Unni, Philip Krauss, Abdelhamid Abdelwahed, Jascha Buchhorn, Leon Hinderling, Thomas R. Geiger and Sabine Österle

Content type: Software 8 May 2025
Sentences, entities, and keyphrases extraction from consumer health forums using multi-task learning

Authors: Tsaqif Naufal, Rahmad Mahendra and Alfan Farizki Wicaksono

Content type: Research 6 May 2025
Semantics in action: a guide for representing clinical data elements with SNOMED CT

Authors: Julien Ehrsam, Christophe Gaudet-Blavignac, Mirjam Mattei, Monika Baumann and Christian Lovis

Content type: Research 27 March 2025
Digital evolution: Novo Nordisk’s shift to ontology-based data management

Authors: Shawn Zheng Kai Tan, Shounak Baksi, Thomas Gade Bjerregaard, Preethi Elangovan, Thrishna Kuttikattu Gopalakrishnan, Darko Hric, Joffrey Joumaa, Beidi Li, Kashif Rabbani, Santhosh Kannan Venkatesan, Joshua Daniel Valdez and Saritha Vettikunnel Kuriakose

Content type: Research 22 March 2025
Standardizing free-text data exemplified by two fields from the Immune Epitope Database

Authors: Sebastian Duesing, Jason Bennett, James A. Overton, Randi Vita and Bjoern Peters

Content type: Research 22 March 2025

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The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside

Authors: Joanne S Luciano, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Tim Clark, Christine K Denney, Christopher Domarew, Thomas Gambet, Lee Harland, Anja Jentzsch, Vipul Kashyap, Peter Kos, Julia Kozlovsky, Timothy Lebo, Scott M Marshall, Jamie P McCusker…

Content type: Proceedings 17 May 2011
Semantic querying of relational data for clinical intelligence: a semantic web services-based approach

Authors: Alexandre Riazanov, Artjom Klein, Arash Shaban-Nejad, Gregory W Rose, Alan J Forster, David L Buckeridge and Christopher JO Baker

Content type: Research 13 March 2013
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Authors: Melissa A Haendel, James P Balhoff, Frederic B Bastian, David C Blackburn, Judith A Blake, Yvonne Bradford, Aurelie Comte, Wasila M Dahdul, Thomas A Dececchi, Robert E Druzinsky, Terry F Hayamizu, Nizar Ibrahim, Suzanna E Lewis, Paula M Mabee, Anne Niknejad, Marc Robinson-Rechavi…

Content type: Research 19 May 2014
The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

Authors: Mark D Wilkinson, Benjamin Vandervalk and Luke McCarthy

Content type: Database 24 October 2011
MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank

Authors: Yuqing Mao and Zhiyong Lu

Content type: Research 17 April 2017

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Current Open Calls-for-Papers

Journal of Biomedical Semantics welcomes Collections/Thematic Series in emerging and hot topics, relevant to the aims and scope of the journal. Collections can also originate from well-established and upcoming conferences or focus on the research legacy of a pioneer in the field as well.

You can view all present and past collections by following the "Collections" link in the header at the top of the page. The journal's currently open Calls-for-Papers can be seen here or by following the link in the right-hand sidebar toward the top of this page.

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Journal of Biomedical Semantics

Editors-in-Chief

Aims and scope

Open Collections

Articles

The SPHN Schema Forge – transform healthcare semantics from human-readable to machine-readable by leveraging semantic web technologies

Sentences, entities, and keyphrases extraction from consumer health forums using multi-task learning

Semantics in action: a guide for representing clinical data elements with SNOMED CT

Digital evolution: Novo Nordisk’s shift to ontology-based data management

Standardizing free-text data exemplified by two fields from the Immune Epitope Database

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside

Semantic querying of relational data for clinical intelligence: a semantic web services-based approach

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank

Current Open Calls-for-Papers

Annual Journal Metrics

Journal of Biomedical Semantics

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