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BioPortal: ontologies and integrated data resources at the click of a mouse
Open accessAbstract
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content by providing features to add notes to ontology terms, mappings between terms and ontology reviews based on criteria such as usability, domain coverage, quality of content, and documentation and support. BioPortal also enables integrated search of biomedical data resources such as the Gene Expression Omnibus (GEO), ClinicalTrials.gov, and ArrayExpress, through the annotation and indexing of these resources with ontologies in BioPortal. Thus, BioPortal not only provides investigators, clinicians, and developers 'one-stop shopping' to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources.
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Cited by
Controlled vocabularies and semantics in systems biology
Courtot, M., Juty, N., Knüpfer, C., Waltemath, D., Zhukova, A., Dräger, A., Dumontier, M., Finney, A., Golebiewski, M., Hastings, J., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.77 · Cited by 316
“KiSAO is an open ontology, accessible in OWL2 format via the project homepage (http://biomodels.net/kisao/) or through the NCBO BioPortal (ontology 1410, http://purl. bioontology.org/ontology/KiSAO).”
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Self-citationStojanov, R., Popovski, G., Cenikj, G., Koroušić Seljak, B., & Eftimov, T. (2021) · Journal of Medical Internet Research · doi:10.2196/28229 · Cited by 37
Automated clinical knowledge graph generation framework for evidence based medicine.
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Developing a knowledge base to support the annotation of ultrasound images of ectopic pregnancy
Dhombres, F., Maurice, P., Friszer, S., Guilbaud, L., Lelong, N., Khoshnood, B., Charlet, J., Perrot, N., Jauniaux, E., Jurkovic, D., et al. (2017) · Journal of Biomedical Semantics · doi:10.1186/s13326-017-0117-1 · Cited by 14
Metadata
- Authors
- Noy, N. F., Shah, N. H., Whetzel, P. L., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Rubin, D. L., Storey, M.-A., Chute, C. G., & Musen, M. A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-05-29
- Volume
- 37
- Issue
- Web Server
- Pages
- W170-W173
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2131660156
- Cited by
- 875
- References
- 0
- FWCI
- 23.28
- Type
- journal article
- Language
- en
- Open access
- gold
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- The paper
- Noy, N. F., Shah, N. H., Whetzel, P. L., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Rubin, D. L., Storey, M.-A., Chute, C. G., & Musen, M. A. (2009). BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research. https://doi.org/10.1093/nar/gkp440
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