The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.
Bio-ontologies: current trends and future directions
Open accessAbstract
In recent years, as a knowledge-based discipline, bioinformatics has been made more computationally amenable. After its beginnings as a technology advocated by computer scientists to overcome problems of heterogeneity, ontology has been taken up by biologists themselves as a means to consistently annotate features from genotype to phenotype. In medical informatics, artifacts called ontologies have been used for a longer period of time to produce controlled lexicons for coding schemes. In this article, we review the current position in ontologies and how they have become institutionalized within biomedicine. As the field has matured, the much older philosophical aspects of ontology have come into play. With this and the institutionalization of ontology has come greater formality. We review this trend and what benefits it might bring to ontologies and their use within biomedicine.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The unified medical language system (UMLS): integrating biomedical terminology
Bodenreider, O. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh061 · Cited by 4,356
Self-citation(2004) · Springer eBooks · doi:10.1007/978-3-540-24750-0 · Cited by 1,442
A reference ontology for biomedical informatics: the Foundational Model of Anatomy
Rosse, C., & Mejino, J. L. V. (2003) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2003.11.007 · Cited by 1,045
Relations in biomedical ontologies
Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A. L., & Rosse, C. (2005) · Genome Biology · doi:10.1186/gb-2005-6-5-r46 · Cited by 1,018
Antoniou, G., & van Harmelen, F. (2004) · Handbook on Ontologies · doi:10.1007/978-3-540-24750-0_4 · Cited by 1,017
The Gene Ontology (GO) project in 2006
Gene Ontology Consortium (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj021 · Cited by 1,016
The Sequence Ontology: a tool for the unification of genome annotations
Eilbeck, K., Lewis, S. E., Mungall, C. J., Yandell, M., Stein, L., Durbin, R., & Ashburner, M. (2005) · Genome Biology · doi:10.1186/gb-2005-6-5-r44 · Cited by 806
Völkel, M., Krötzsch, M., Vrandečić, D., Haller, H., & Rudi Studer, A. (2006) · International World Wide Web Conference (WWW) · doi:10.1145/1135777.1135863 · Cited by 476
Guarino, N., & Welty, C. A. (2009) · Springer eBooks · doi:10.1007/978-3-540-92673-3_9 · Cited by 464
Karp, P. D. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.56 · Cited by 449
Cited by
Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support
Bodenreider, O. (2008) · Yearbook of Medical Informatics · doi:10.1055/s-0038-1638585 · Cited by 368
Self-citationBiomedical ontologies: a functional perspective
Rubin, D. L., Shah, N. H., & Noy, N. F. (2007) · Briefings in Bioinformatics · doi:10.1093/bib/bbm059 · Cited by 287
Semantic Web meets Integrative Biology: a survey
Chen, H., Yu, T., & Chen, J. Y. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs014 · Cited by 65
Mortensen, J. M., Minty, E. P., Januszyk, M., Sweeney, T. E., Rector, A. L., Noy, N. F., & Musen, M. A. (2015) · Journal of the American Medical Informatics Association · doi:10.1136/amiajnl-2014-002901 · Cited by 63
Metadata
- Authors
- Bodenreider, O.
- Venue
- Briefings in Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-05-23
- Volume
- 7
- Issue
- 3
- Pages
- 256-274
- ISSN
- 1467-5463 (ISSN-L)
- 1477-4054
- OpenAlex
- W2127480960
- Cited by
- 377
- References
- 43
- FWCI
- 10.93
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Bio-ontologies: current trends and future directions. https://app.cochat.ai/papers/10.1093/bib/bbl027
- The paper
- Bodenreider, O. (2006). Bio-ontologies: current trends and future directions. Briefings in Bioinformatics. https://doi.org/10.1093/bib/bbl027
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
