Papers that cite the OBO Foundry

Antezana E, Tsiporkova E, Mironov V, et al. 2006 "A cell-cycle knowledge integration framework", Lecture Notes in Computer Science 4075: 19-34.

Aranguren ME, Bechoffer S, Lord P, Sattler U, Stevens R 2007 "Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL", BMC Bioinformatics, 8: 57.

Arnaiz O, Cain S, Cohen J, Sperling L 2006 "ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data", Nucleic Acids Res Dec 7.

Baker CJO, Shaban-Nejad A, Su X, Haarslev V, Butler G 2006 "Semantic Web infrastructure for fungal enzyme biotechnologists", J Web Semantics 4 (3).

Bard JBL 2005 "Anatomics: the intersection of anatomy and bioinformatics", Journal of Anatomy 206 (1): 1-16 Jan.

Bittner T, Goldberg LJ 2006 "The Qualitative and Time-Dependent Character of Spatial Relations in Biomedical Ontologies", O. Bodenreider, ed., Proceedings of KR-MED, 47-55.

Blake JA, Bult CJ 2006 "Beyond the data deluge: Data integration and bio-ontologies", Journal of Biomedical Informatics 39 (3): 314-320.

Bodenreider O. 2006 "Lexical, terminological and ontological resources for biological text mining", in Ananiadou S, McNaught J, (eds.) Text mining for biology and biomedicine, Artech House, 43-66.

Bontas EP, Schlangen D, Schrader T 2005 "Creating ontologies for content representation - The OntoSeed suite", Lecture Notes in Computer Science 3761: 1296-1313.

Burek P, Hoehndorf R, Loebe F, Visagie J, Herre H Kelso J. 2006 "A top-level ontology of functions and its application in the Open Biomedical Ontologies", Bioinformatics, Vol. 22 no. 14: e66-e73.

Castro AG, Rocca-Serra P, Stevens R, Taylor C, Nashar K, Ragan MA, Sansone SA 2006 "The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case", BMC Bioinformatics 25 (7): 267.

Ceusters W 2006 "Towards a Realism-Based Metric for Quality Assurance in Ontology Matching", Formal Ontology in Information Systems - Proceedings of the Fourth International Conference (FOIS 2006), Edited by Brandon Bennett, Christiane Fellbaum, New York: IOS Press, 321-332.

Ceusters W, Smith B 2006 "A Realism-Based Approach to the Evolution of Biomedical Ontologies", Proceedings of the Annual AMIA Symposium, Washington DC, 121-125.

Dameron O, Roques E, Rubin DL, Marquet G, and Burgun A 2006 "Grading lung tumors using OWL-DL based reasoning", In 9th International Protégé Conference.

Dolbey A, Ellsworth M, Scheffczyk J 2006 "BioFrameNet: A Domain-Specific FrameNet Extension with Links to Biomedical Ontologies", O. Bodenreider, ed., Proceedings of KR-MED, 87-94.

Donnelly M, Bittner T, Rosse C 2006 "A formal theory for spatial representation and reasoning in biomedical ontologies", Artificial Intelligence in Medicine 36 (1): 1-27.

Friedberg I 2006 "Automated protein function prediction - the genomic challenge", Briefings in Bioinformatics 7 (3): 225-242.

Friedman C, Borlawsky T, Shagina L, et al. 2006 "Bio-Ontology and text: bridging the modeling gap", Bioinformatics 22 (19): 2421-2429.

Fung KW, et al. 2005 "Integrating SNOMED CT into the UMLS: An Exploration of Different Views of Synonymy and Quality of Editing", Am Med Inform Assoc.

Gardner SP 2005 "Ontologies and semantic data integration", Drug Discovery Today, 10 (14): 1001-1007.\ ration.pdf+

Gkoutos, GV 2006 "Towards a phenotypic semantic web", Current Bioinformatics, 1 (2): 235-246.

Haendel, MA, Neuhaus, F, Osumi-Sutherland, DS, Mabee, PM, Mejino JLV, Mungall, CJ, and Smith, B 2007 "The Common Anatomy Reference Ontology", in: A Burger, et al. (eds.), Anatomy Ontologies for Bioinformatics: Principles and Practice, New York, Springer.

Hahn U, Schulz S, 2007 "Ontological Foundations for Biomedical Sciences", in Artificial Intelligence in Medicine, 39 (3): 179-82.

Harris MA, Clark JI, Ireland A, et al./Gene Ontology Consortium. 2006 "The Gene Ontology (GO) project in 2006", Nucleic Acids Research 34: D322-D326 Sp. Iss. SI Jan1.

Henrich T, Ramialison M, Wittbrodt B, Assouline B, Bourrat F, Berger A, Himmelbauer H, Sasaki T, Shimizu N, Westerfield M, Kondoh H, and Wittbrodt J 2005 "MEPD: a resource for medaka gene expression patterns", Bioinformatics 2005 21(14):3195-3197; doi:10.1093/bioinformatics/bti478 .

Hsing, M., Cherkasov, A. 2006 "Integration of Biological Data with Semantic Networks", Current Bioinformatics, 1 (3): 273-290.

Ingenerf J., Linder R. 2006 "Ontological Principles Applied to Biomedical Vocabularies".

Johansson I. 2006 "Bioinformatics and biological reality", Journal of Biomedical Informatics 39 (3): 274-287.

Kosseim L, Reda Siblini, Christopher J.O. Baker and Sabine Bergler 2006 "Using Selectional Restrictions to Query an OWL Ontology", Formal Ontology in Information Systems - Proceedings of the Fourth International Conference (FOIS 2006), Edited by Brandon Bennett, Christiane Fellbaum, New York: IOS Press, 360-371.

Louie B, Mork P, Martin-Sanchez F, et al. 2007 "Data integration and genomic medicine", Journal of Biomedical Informatics, 40 (1): 5-16.

Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M 2007 "Connecting evolutionary morphology to genomics using ontologies: A case study from Cypriniformes including zebrafish", J Exp Zoolog B Mol Dev Evol. 2007 Sep 15;308(5):655-6.

Maglia AM, et al. 2007 "An anatomical ontology for amphibians", Pacific Symposium on Biocomputing, 12: 367-378.

Malmstrom L, Marko-Varga G, Westergren-Thorsson G, et al. 2006 "2DDB - a bioinformatics solution for analysis of quantitative proteomics data", BMC Bioinformatics 7.

Masseroli M, Pinciroli F 2006 "Using Gene Ontology and genomic controlled vocabularies to analyze high-throughput gene lists: Three tool comparison", Computers in Biology and Medicine, 36 (7-8): 731-747.

Morrison N, Cochrane G, Faruque N, et al. 2006 "Concept of sample in OMICS technology", Omics - A Journal of Integrative Biology 10 (2): 127-137.

Myhre S, Tveit H, Mollestad T, et al. 2006 "Additional Gene Ontology structure for improved biological reasoning", Bioinformatics 22 (16): 2020-2027.

DA Natale, CN Arighi, W Barker, J Blake, TC Chang, Z Hu, H Liu, B Smith, and CH Wu 2006 "Framework for a Protein Ontology", Proceedings of the 1st international workshop on Text mining in bioinformatics, Arlington, Virginia, 29-36.

Neuhaus F, et al. "Modelling Principles and Methodologies: Relations in Anatomical Ontologies", in: A Burger et al. (eds.), Anatomy Ontologies for Bioinformatics: Principles and Practice, New York: Springer, in press.

Okada M, Sugimoto Y, Yoshikawa S, et al. 2006 "Drug Interaction Ontology (DIO) and the resource-sensitive logical inferences", Lecture Notes in Computer Science; 4060: 616-642.

Paul S, et al. 2006 "A semantically enabled formalism for the knowledge management of Parkinson's disease". Medical Informatics and the Internet in Medicine.

Philippi S, Kohler J 2006 "Addressing the problems with life-science databases for traditional uses and systems biology", Nature Reviews Genetics 7 (6): 482-488.

Rogers JE 2006 "Quality assurance of medical ontologies", Methods of Information in Medicine 45 (3): 267-274.

Rosenbloom ST, Miller RA, Johnson KB, et al. 2006 "Interface terminologies: Facilitating direct entry of clinical data into electronic health record systems", Journal of the American Medical Informatics Association 13 (3): 277-288.

Ruttenberg A, Clark T, et al. 2007 "Advancing translational research with the Semantic Web", BMC Bioinformatics, 8(Suppl 3):S2.

Ruttenberg A, Rees JA, Luciano JS 2005 "Experience using OWL DL for the exchange of biological pathway information", in OWL Experiences and Directions.

Ruttenberg A, Rees J, Zucker J. 2007 "What BioPAX communicates and how to extend OWL to help it", OWLED.

Schulz S, Elena Beisswanger, Udo Hahn, Joachim Wermter, Anand Kumar and Holger Stenzhorn 2006 "From GENIA to BIOTOP: Towards a Top-Level Ontology for Biology", Formal Ontology in Information Systems - Proceedings of the Fourth International Conference (FOIS 2006), Ed. by B. Bennett, C. Fellbaum, New York: IOS Press, 103-114.

Schulz S, Hanser S, Hahn U, et al. 2006 "The semantics of procedures and diseases in SNOMED CT", Methods of Information in Medicine 45 (4): 354-358.

Schulz S, Jansen L 2006 "Lmo-2 interacts with elf-2" On the Meaning of Common Statements in Biomedical Literature, O. Bodenreider, ed., Proceedings of KR-MED, 37-45.

Schulz S, Kumar A, Bittner T 2006 "Biomedical ontologies: What part-of is and isn't", Journal of Biomedical Informatics 39 (3): 350-361.

Schulz S., S. Hanser, U. Hahn, J. Rogers 2006 "The Semantics of Procedures and Diseases in SNOMED CT", Methods of Information in Medicine, 45/4.

Skusa A, Ruegg A, Kohler J 2005 "Extraction of biological interaction networks from scientific literature", Briefings in Bioinformatics 6 (3): 263-276.

Slaughter LA, et al. 2005 "Semantic representation of consumer questions and physician answers". Int J Med Inform.

Smith B, Ashburner M, Rosse C, Bard C, Bug W, Ceusters W, Goldberg L J, Eilbeck K, Ireland A, Mungall C J, The OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone S-A, Scheuermann R H, Shah N, Whetzel P L and Lewis S (2007). "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration", Nature Biotechnology 25, 1251 - 1255.

Soldatova LN, Clare A, Sparkes A, King RD 2006 "An ontology for a robot scientist", Bioinformatics 22 (14): e464–e471.

Sprague J, et al. 2006 "The Zebrafish Information Network: the zebrafish model organism database", Nucleic Acids Res. 34, D581-D585.

Strizh IG 2006 "Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study", Bioessays 28 (2): 199-210.

Thomas CJ, Sheth AP, and York WS 2006 "Modular Ontology Design Using Canonical Building Blocks in the Biochemistry Domain", Formal Ontology in Information Systems - Proceedings of the Fourth International Conference (FOIS 2006), Ed. by B. Bennett, C. Fellbaum, NY: IOS Press, 115-127.

van Gurp M, Decoene M, Holvoet M, Casella dos Santos M 2006 "LinKBase, a Philosophically-Inspired Ontology for NLP/NLU Applications", O. Bodenreider, ed., Proceedings of KR-MED, 67-75.

Vizenor L, Bodenreider O 2006 "Using dependence relations in MeSH as a framework for the analysis of disease information in Medline", Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM-2006): 76-83.

Vizenor L, Bodenreider O, Peters L, McCray AT 2006 "Enhancing biomedical ontologies through alignment of semantic relationships: Exploratory approaches", Proc AMIA Annual Symp: 804-808.

Whetzel PL, et al. 2006 "The development of FuGO--An ontology for functional genomics experiments", Omics: A Journal of Integrative Biology, 10 (2), 199-204.

Zhang S, Bodenreider O. 2006 "NLM anatomical ontology alignment system. Results of the 2006 ontology alignment contest", Proceedings of the Ontology Alignment Evaluation Initiative 2006 Campaign (OAEI):145-156.

Zhang S, Bodenreider O 2006 "Law and order: Assessing and enforcing compliance with ontological modeling principles in the Foundational Model of Anatomy", Computers in Biology and Medicine 36 (7-8): 674-693.

Zhang W, Zhang Y, Zheng H, Zhang C, Xiong W, Olyarchuk JG, Walker M, Xu W, Zhao M, Zhao S, Zhou Z, Wei L 2006 "SynDB: a Synapse protein DataBase based on synapse ontology", Nucleic Acids Res, Nov 10.

Zhou L, Tao Y, Cimino JJ, et al. 2006 "Terminology model discovery using natural language processing and visualization techniques", Journal of Biomedical Informatics 39 (6): 626-636.