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About Journal of Biomedical Semantics

This page includes information about the aims and scope of Journal of Biomedical Semantics, editorial policies, open access and article-processing charges, the peer review process and other information. For details of how to prepare and submit a manuscript through the online submission system, please see the instructions for authors.

Aims & scope

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

Infrastructure for biomedical semantics: focusing on semantic resources and repositories, meta-data management and 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, and discoveries in biomedicine.

Research in biology and biomedicine relies on various types of biomedical data, information, and knowledge, represented in databases with experimental and/or curated data, ontologies, literature, taxonomies, and so on. Semantics is essential for accessing, integrating, and analyzing such data. The ability to explicitly extract, assign, and manage semantic representations is crucial for making computational approaches in the biomedical domain productive for a large user community.

Journal of Biomedical Semantics addresses issues of semantic enrichment and semantic processing in the biomedical domain, and comprises practical and theoretical advances in biomedical semantics research with implications for data analysis.

In recent years, the availability and use of electronic resources representing biomedical knowledge has greatly increased, covering ontologies, taxonomies, literature, databases, and bioinformatics services. These electronic resources contribute to advances in the biomedical domain and require interoperability between them through various semantic descriptors. In addition, the availability and integration of semantic resources is a key part in facilitating semantic web approaches for life sciences leading into reasoning and other advanced ways to analyse biomedical data.

Open access

All articles published by Journal of Biomedical Semantics are made freely and permanently accessible online immediately upon publication, without subscription charges or registration barriers. Further information about open access can be found here.

Authors of articles published in Journal of Biomedical Semantics are the copyright holders of their articles and have granted to any third party, in advance and in perpetuity, the right to use, reproduce or disseminate the article, according to the BioMed Central copyright and license agreement.

For authors who are US government employees or are prevented from being copyright holders for similar reasons, BioMed Central can accommodate non-standard copyright lines. Please contact us if further information is needed.

Article-processing charges

Open access publishing is not without costs. Journal of Biomedical Semantics therefore levies an article-processing charge of £1370/$2145/€1745 for each article accepted for publication. If the corresponding author's institution is a Member, the cost of the article-processing charge is covered by the membership, and no further charge is payable. In the case of authors whose institutions are Supporter Members, however, a discounted article-processing charge is payable by the author. We routinely waive charges for authors from low-income countries. For other countries, article-processing charge waivers or discounts are granted on a case-by-case basis to authors with insufficient funds. Authors can request a waiver or discount during the submission process. For further details, see our article-processing charge page.

Indexing services

All articles published in Journal of Biomedical Semantics are included in PubMed, the most widely used biomedical bibliographic database service, which is run by the US National Library of Medicine. Other bibliographic databases that index articles published in Journal of Biomedical Semantics include:

  • Citebase
  • DBLP
  • DOAJ
  • Google Scholar
  • OAIster
  • PubMed
  • PubMed Central
  • Scopus
  • Zetoc

The full text of all research articles is deposited in PubMed Central, the US National Library of Medicine's full-text repository of life science literature, and other digital archives including e-Depot (The Netherlands).

The full text of all research articles published by BioMed Central is also available on SpringerLink.

Journal of Biomedical Semantics is tracked by Thomson Reuters (ISI) and has an Impact Factor of 2.26.

Publication and peer review process

Criteria for publication

Journal of Biomedical Semantics considers the following types of articles:

  • Research: original and novel research on practical and theoretical advances in biomedical semantics research with implications for data analysis.
  • Short reports: brief reports on case studies, experiments, tests, evaluations and procedures that use semantic resources for biomedical research, including tools and services that have been developed to support knowledge-based and semantics-driven approaches to biomedical research.
  • Database articles: descriptions of a new or a substantially improved database or other resource (including ontologies, taxonomies, terminologies, corpora and repositories), that have been developed to support knowledge-based and semantics-driven biomedical research.
  • Reviews: comprehensive, authoritative, descriptions of any subject within the scope of the journal. These articles are usually written by experts in the field, who have been invited by the Editorial Board.

Peer-review policies

Journal of Biomedical Semantics operates a closed peer review system. Manuscripts submitted to the journal are reviewed by at least two experts selected by the Editors, with the aim of reaching a decision as soon as possible. Reviewers are required to declare any competing interests.

Authors will be able to check the progress of their manuscript through the submission system at any time by logging into My Journal of Biomedical Semantics, a personalized section of the site.


High-quality, bound reprints can be purchased for all articles published. Please see our reprints website for further information about ordering reprints.


Journal of Biomedical Semantics will consider supplements based on proceedings (full articles or meeting abstracts), reviews or research. All articles submitted for publication in supplements are subject to peer review. Published supplements are fully searchable and freely accessible online and can also be produced in print. All full length articles (proceedings, reviews or research articles) are indexed by PubMed. PubMed displays the title of the supplement only in the case of meeting abstract collections. For further information, please contact us.

Editorial policies

All manuscripts submitted to Journal of Biomedical Semantics should adhere to BioMed Central's editorial policies.

Citing articles in Journal of Biomedical Semantics

Articles in Journal of Biomedical Semantics should be cited in the same way as articles in a traditional journal. Because articles are not printed, they do not have page numbers; instead, they are given a unique article number.

Article citations follow this format:

Authors: Title. J Biomed Sem [year], [volume number]:[article number].

e.g. Roberts LD, Hassall DG, Winegar DA, Haselden JN, Nicholls AW, Griffin JL: Increased hepatic oxidative metabolism distinguishes the action of Peroxisome Proliferator-Activated Receptor delta from Peroxisome Proliferator-Activated Receptor gamma in the Ob/Ob mouse. J Biomed Sem 2009, 1:115.

refers to article 115 from Volume 1 of the journal.

Why publish your article in Journal of Biomedical Semantics?

High visibility

Journal of Biomedical Semantics's open access policy allows maximum visibility of articles published in the journal as they are available to a wide, global audience. Articles that have been especially highly accessed are highlighted with a 'Highly accessed' graphic, which appears on the journal's contents pages and search results.

Speed of publication

Journal of Biomedical Semantics offers a fast publication schedule whilst maintaining rigorous peer review; all articles must be submitted online, and peer review is managed fully electronically (articles are distributed in PDF form, which is automatically generated from the submitted files). Articles will be published with their final citation after acceptance, in both fully browsable web form, and as a formatted PDF; the article will then be available through Journal of Biomedical Semantics, BioMed Central and PubMed Central and will also be included in PubMed.


Online publication in Journal of Biomedical Semantics gives authors the opportunity to publish large datasets, large numbers of color illustrations and moving pictures, to display data in a form that can be read directly by other software packages so as to allow readers to manipulate the data for themselves, and to create all relevant links (for example, to PubMed, to sequence and other databases, and to other articles).

Promotion and press coverage

Articles published in Journal of Biomedical Semantics are included in article alerts and regular email updates. Some may be included in abstract books mailed to academics and are highlighted on Journal of Biomedical Semantics's pages and on the BioMed Central homepage.

In addition, articles published in Journal of Biomedical Semantics may be promoted by press releases to the general or scientific press. These activities increase the exposure and number of accesses for articles published in Journal of Biomedical Semantics. A list of articles recently press-released by journals published by BioMed Central is available here.

Authors of articles published in Journal of Biomedical Semantics retain the copyright of their articles and are free to reproduce and disseminate their work (for further details, see the BioMed Central copyright policy and license agreement).

For further information about the advantages of publishing in a journal from BioMed Central, please click here.