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The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
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Taylor, C. F., Field, D., Sansone, S.-A., Aerts, J., Apweiler, R., Ashburner, M., Ball, C. A., Binz, P.-A., Bogue, M., Booth, T., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt.1411 · Cited by 558
Self-citationBard, J., Rhee, S. Y., & Ashburner, M. (2005) · Genome biology · doi:10.1186/gb-2005-6-2-r21 · Cited by 416
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Research works printed but not linked: 45
- Yue, L. & Reisdorf, W.C. Pathway and ontology analysis: emerging approaches connecting transcriptome data and clinical endpoints. Curr. Mol. Med. 5, 11–21 (2005). · DOI
- Gene Ontology Consortium. The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 34 (database issue), D322–D326 (2006). · DOI · Paper page
- Camon, E. et al. The Gene Ontology Annotation (GOA) Project. Genome Res. 13, 662–672 (2003). · DOI · Paper page
- Kohane, I.S. et al. Building national electronic medical record systems via the World Wide Web. J. Am. Med. Inform. Assoc. 3, 191–207 (1996). · DOI
- Bodenreider, O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 32 (database issue), D267–D270 (2004). · DOI · Paper page
- Ceusters, W., Smith, B., Kumar, A. & Dhaen, C. Mistakes in medical ontologies: where do they come from and how can they be detected? Stud. Health Technol. Inform. 102, 145–164 (2004).
- Ceusters, W., Smith, B. & Goldberg, L. A terminological and ontological analysis of the NCI Thesaurus. Methods Inf. Med. 44, 498–507 (2005). · DOI
- Campbell, K.E., Oliver, D.E. & Shortliffe, E.H. The Unified Medical Language System. Toward a collaborative approach for solving terminologic problems. J. Am. Med. Inform. Assoc. 5, 12–16 (1998). · DOI
- Buetow, K.H. Cyberinfrastructure: empowering a 'third way' in biomedical research. Science 308, 821–824 (2005). · DOI
- Smith, B. & Ceusters, W. HL7 RIM: an incoherent standard. Stud. Health Technol. Inform. 124, 133–138 (2006).
- Ashburner, M., Mungall, C.J. & Lewis, S.E. Ontologies for biologists: a community model for the annotation of genomic data. Cold Spring Harb. Symp. Quant. Biol. 68, 227–236 (2003). · DOI
- Rubin, D.L. et al. National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. OMICS 10, 185–198 (2006). · DOI
- Rosse, C. & Mejino, J.L.F. The Foundational Model of Anatomy ontology. In Anatomy Ontologies for Bioinformatics (eds. Burger, A. et al.) (Springer, New York, in the press).
- Haendel, M. et al. CARO: the Common Anatomy Reference Ontology. In Anatomy Ontologies for Bioinformatics (eds. Burger, A. et al.) (Springer, New York, in the press).
- Leontis, N.B. et al. The RNA Ontology Consortium: an open invitation to the RNA community. RNA 12, 533–541 (2006). · DOI
- Natale, D.A. et al. Framework for a protein ontology. BMC Bioinformatics [online] (in the press).
- Kelso, J. et al. eVOC: a controlled vocabulary for unifying gene expression data. Genome Res. 13, 1222–1230 (2003). · DOI
- Mabee, P.M. et al. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol. Evol. 22, 345–350 (2007). · DOI
- Whetzel, P.L. et al. The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 22, 866–873 (2006). · DOI
- Whetzel, P.L. et al. Development of FuGO: an ontology for functional genomics investigations. OMICS 10, 199–204 (2006). · DOI
- Golbreic, C. et al. OBO and OWL: leveraging semantic web technologies for the life sciences. In Proceedings 6th International Semantic Web Conference (ISWC 2007), (Springer, in the press).
- Brinkley, J.F., Detwiler, L.T., Gennari, J.H., Rosse, C. & Suciu, D. A framework for using reference ontologies as a foundation for the semantic web. Proc. AMIA Fall Symposium, 2006, 95–100.
- Lacy, L.W. Owl: Representing Information Using the Web Ontology Language (Trafford Publishing, Victoria, BC, Canada, 2005).
- Smith, B., Köhler, J. & Kumar, A. On the application of formal principles to life science data: a case study in the Gene Ontology. Data Integration in the Life Sciences (DILS) Workshop 2004, 79–94. · DOI
- Smith, B. et al. Relations in biomedical ontologies. Genome Biol. [online] 6, R46 (2005). · DOI · Paper page
- Bittner, T. & Goldberg, L.J. Spatial location and its relevance for terminological inferences in bio-ontologies. BMC Bioinformatics 23, 1674–1682 (2007). · DOI
- Ramírez, M.J. et al. Linking of digital images to phylogenetic data matrices using a morphological ontology. Syst. Biol. 56, 283–294 (2007). · DOI
- Schober, D., et al. Towards naming conventions for use in controlled vocabulary and ontology engineering. Bio-Ontologies Workshop, ISMB/ECCB, Vienna, 20 July 2007, 87–90.
- Ruttenberg, A., Rees, J., & Zucker, J. What BioPAX communicates and how to extend OWL to help it. OWL: Experiences and Directions Workshop Series < http://owl-workshop.man.ac.uk/acceptedLong/submission_26.pdf > (2006).
- Hunter, L. & Bada. M. Enrichment of OBO ontologies. J. Biomed. Inform. 40, 300–315 (2007). · DOI
- Hill, D.P., Blake, J.A., Richardson, J.E. & Ringwald, M. Extension and integration of the Gene Ontology (GO): combining GO vocabularies with external vocabularies. Genome Res. 12, 1982–1991 (2002). · DOI
- Mungall, C.J. Obol: integrating language and meaning in bio-ontologies. Comp. Funct. Genomics 5, 509–520 (2004). · DOI
- Camon, E. et al. The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res. 32 (database issue), D262–D266 (2004). · DOI · Paper page
- Blake, J., Hill, D.P. & Smith, B. Gene Ontology annotations: what they mean and where they come from. Bio-Ontologies Workshop, ISMB/ECCB, Vienna, 20 July 2007, 79–82.
- Sjoblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268–274 (2006). · DOI · Paper page
- Lee, J.A. et al. Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinformatics [online] 7, 237 (2006). · DOI
- Rebholz-Schuhmann, D., Kirsch, H. & Couto, F. Facts from text—is text mining ready to deliver? PLoS Biol. [online] 3, e65 (2005). · DOI
- Witte, R., Kappler, T. & Baker, C.J.O. Ontology design for biomedical text mining. In Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. Baker C.J.O. & Cheung, K.-H.) 281–313 (Springer, New York, 2007). · DOI
- Zhang, S. & Bodenreider, O. Aligning multiple anatomical ontologies through a reference. International Workshop on Ontology Matching (OM 2006) 193–197 (2006).
- Luo, F. et al. Modular organization of protein interaction networks. Bioinformatics 23, 207–214 (2007). · DOI
- Martone, M.E., Gupta, A. & Ellisman, M.H. E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nat. Neurosci. 7, 467–472 (2004). · DOI
- Fong, L. et al. An ontology-driven knowledge environment for subcellular neuroanatomy. OWL Experiences and Directions, 3rd International Workshop, Innsbruck, Austria, June 6–7, 2007 (in the press).
- Brazma, A. et al. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nat. Genet. 29, 365–371 (2001). · DOI · Paper page
- Sansone, S.A. et al. A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group. OMICS 10, 164–171 (2006). · DOI
- Grenon, P., Smith, B. & Goldberg, L. Biodynamic ontology: applying BFO in the biomedical domain. In Ontologies in Medicine (ed. Pisanelli, D.M.) 20–38 (IOS, Amsterdam, 2004).
Cited by
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
Welter, D., MacArthur, J., Morales, J., Burdett, T., Hall, P., Junkins, H., Klemm, A., Flicek, P., Manolio, T., Hindorff, L., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1229 · Cited by 2,707
The human phenotype ontology: a tool for annotating and analyzing human hereditary disease
Robinson, P. N., Köhler, S., Bauer, S., Seelow, D., Horn, D., & Mundlos, S. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.09.017 · Cited by 1,034
Gateways to the FANTOM5 promoter level mammalian expression atlas
Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S., Abugessaisa, I., Fukuda, S., Hori, F., Ishikawa-Kato, S., et al. (2015) · Genome Biology · doi:10.1186/s13059-014-0560-6 · Cited by 871
Self-citationUberon, an integrative multi-species anatomy ontology
Mungall, C. J., Torniai, C., Gkoutos, G. V., Lewis, S. E., & Haendel, M. A. (2012) · Genome biology · doi:10.1186/gb-2012-13-1-r5 · Cited by 732
“We believe that Uberon meets the current need for an integrative cross-species anatomy ontology amongst the OBO Foundry suite [66].”
BackgroundOMERO: flexible, model-driven data management for experimental biology
Allan, C., Burel, J.-M., Moore, J., Blackburn, C., Linkert, M., Loynton, S., MacDonald, D., Moore, W. J., Neves, C., Patterson, A., et al. (2012) · Nature Methods · doi:10.1038/nmeth.1896 · Cited by 653
Metadata
- Authors
- The OBI Consortium, Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L. J., Eilbeck, K., Ireland, A., Mungall, C. J., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S.-A., Scheuermann, R. H., Shah, N., Whetzel, P. L., & Lewis, S.
- Venue
- Nature Biotechnology
- Published
- 2007-11
- Volume
- 25
- Issue
- 11
- Pages
- 1251-1255
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2113142309
- Cited by
- 2,560
- References
- 2
- FWCI
- 53.28
- Type
- journal article
- Language
- en
- Open access
- green
- Licence
- www.springer.com/tdm (tdm)
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- The paper
- The OBI Consortium, Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L. J., Eilbeck, K., Ireland, A., Mungall, C. J., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S.-A., Scheuermann, R. H., Shah, N., Whetzel, P. L., & Lewis, S. (2007). The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology. https://doi.org/10.1038/nbt1346
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Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.