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Publications
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Publications by Project
There are 52 publications for the project "NCBO".
- BMIR-2011-1482
- Proposed SKOS Extensions for BioPortal Terminology Services
- C. Tao, N. F. Noy, H. Solbrig, N. H. Shah, M. A. Musen, C. G. Chute
- Joint International Semantic Technology Conference (JIST 2011), Hangzhou, China. Published in 2011
- BMIR-2011-1481
- How orthogonal are the OBO Foundry ontologies?
- A. Ghazvinian, N. F. Noy, M. A. Musen
- Journal of Biomedical Semantics, 2(Suppl 2), S2. Published in 2011
- BMIR-2011-1480
- NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources,information retrieval, biomedical data and ontologies
- C. Jonquet, P. LePendu, S. M. Falconer, A. Coulet, N. F. Noy, M. A. Musen, N. H. Shah
- Journal of Web Semantics: Science, Services and Agents on the World Wide Web, 9, 3. Published in 2011
- BMIR-2011-1478
- Document Annotation Support Using Biomedical Ontologies
- T. Thanh, Y. Ma, N. F. Noy
- Workshop on Web Scale Knowledge Extraction at ISWC 2011, Bonn, Germany. Published in 2011
- BMIR-2011-1477
- The Quad Economy of a Semantic Web Ontology Repository
- M. Salvadores, P. R. Alexander, M. A. Musen, N. F. Noy
- Workshop on Scalable Semantic Web Knowledge Base Systems at ISWC 2011, Bonn, Germany. Published in 2011
- BMIR-2011-1476
- BioPortal: Enhanced Functionality via New Web services from the National Center for Biomedical Ontology to Access and Use Ontologies in Software Applications
- T. Whetzel, N. F. Noy, N. H. Shah, P. R. Alexander, C. I. Nyulas, T. Tudorache, M. A. Musen
- Nucleic Acid Research, 39(Web Server issue), W541-5. Published in 2011
- BMIR-2011-1468
- The National Center for Biomedical Ontology
- M. A. Musen, N. F. Noy, C. G. Chute, M. A. Storey, B. Smith, N. H. Shah
- . Published in 2011
- BMIR-2011-1443
- BioDBCore working group. Towards BioDBcore: a community-defined information specification for biological databases.
- P. Gaudet, A. Bairoch, D. Field, S. A. Sansone, C. Taylor, C. Yamasaki
- Nucleic Acids Research, Nucleic Acids Res., 39, Database Issue, D7-10. Published in 2011
- BMIR-2011-1442
- Semantic Infrastructure to Enable Collaboration in Ontology Development
- P. R. Alexander, C. I. Nyulas, T. Tudorache, T. Whetzel, N. F. Noy, M. A. Musen
- International Workshop on Semantic Technologies for Information-Integrated Collaboration (STIIC 2011), Philadelphia, PA. Published in 2011
 - BMIR-2011-1441
- The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research.
- J. Tenenbaum, T. Whetzel, K. Anderson, C. D. Borromeo, I. D. Dinov, D. Gabriel, B. Kirschner, B. Mirel, T. Morris, N. F. Noy, C. I. Nyulas, D. Rubenson, P. R. Saxman, H. Singh, N. Whelan, Z. Wright, B. D. Athey, M. J. Becich, G. S. Ginsburg, M. A. Musen, K. A. Smith, A. F. Tarantal, D. L. Rubin, P. Lyster
- Journal of Biomedical Informatics, J Biomed Inform., 44, 1, 137-145. Published in 2011
- BMIR-2011-1413
- Where to Publish and Find Ontologies? A Survey of Ontology Libraries.
- M. d’Aquin, N. F. Noy
- Journal of Web Semantics. In Press in 2011
- BMIR-2010-1433
- Using text to build semantic networks for pharmacogenomics
- A. Coulet, Y. Garten, M. A. Musen, N. H. Shah, R. B. Altman
- Journal of Biomedical Informatics, JBI. Published in 2010
- BMIR-2010-1432
- Building a Biomedical Ontology Recommender Web Service
- C. Jonquet, M. A. Musen, N. H. Shah
- Journal of Biomedical Semantics, 22, 1, Suppl 1:S1. Published in 2010
 - BMIR-2010-1431
- The ontology life cycle: Integrated tools for editing, publishing, peer review, and evolution of ontologies
- N. F. Noy, T. Tudorache, C. I. Nyulas, M. A. Musen
- AMIA Annual Symposium, Washington, DC. Published in 2010
- BMIR-2010-1430
- Optimize First, Buy Later: Analyzing Metrics to Ramp-up Very Large Knowledge Bases
- P. LePendu, N. F. Noy, C. Jonquet, P. R. Alexander, N. H. Shah, M. A. Musen
- 9th International Conference on Semantic Web (ISWC 2010), Shanghai, China, Springer. Published in 2010
- BMIR-2010-1429
- Lost in Translation? Empirical Analysis of Mapping Compositions for Large Ontologies
- A. Tordai, A. Ghazvinian, J. van Ossenbruggen, M. A. Musen, N. F. Noy
- The fifth International Workshop on Ontology Matching (OM 2010), at ISWC 2010, Shanghai, China. Published in 2010
- BMIR-2010-1415
- How Orthogonal are the OBO Foundry Ontologies?
- A. Ghazvinian, N. F. Noy, N. F. Noy
- Bio-Ontologies SIG at ISMB, Boston, MA, USA. Published in 2010
 - BMIR-2009-1444
- Building Web Applications with Protégé
- C. I. Nyulas, T. Tudorache
- . Published in 2009
 - BMIR-2009-1404
- Harnessing the Power of the Community in a Library of Biomedical Ontologies
- N. F. Noy, M. V. Dorf, N. Griffith, C. I. Nyulas, M. A. Musen
- Workshop on Semantic Web Applications in Scientific Discourse at ISWC 2009, Chantilly, VA, http://CEUR-WS.org/Vol-523. Published in 2009
- BMIR-2009-1398
- Comparison of Concept Recognizers for building the Open Biomedical Annotator
- N. H. Shah, B. Nipun, C. Jonquet, A. P. Chiang, D. L. Rubin, M. A. Musen
- BMC Bioinformatics, 10, (Suppl 9):S14. Published in 2009
- BMIR-2009-1387
- BioPortal: ontologies and integrated data resources at the click of a mouse
- N. F. Noy, N. H. Shah, T. Whetzel, B. Dai, M. V. Dorf, N. B. Griffith, C. Jonquet, M. A. Storey, C. G. Chute, D. L. Rubin, M. A. Musen
- Nucleic Acids Research, 37, Web Server Issue. Published in 2009
- BMIR-2009-1386
- What Four Million Mappings Can Tell You About Two Hundred Ontologies
- A. Ghazvinian, N. F. Noy, C. Jonquet, N. H. Shah, M. A. Musen
- 8th International Semantic Web Conference (ISWC 2009), Washington, DC, Springer, Volume 5823/2009, 229-242. Published in 2009
 - BMIR-2009-1382
- Ontology-Driven Software: What We Learned From Using Ontologies As Infrastructure For Software
- C. I. Nyulas, N. F. Noy, M. V. Dorf, N. Griffith, M. A. Musen
- 5th International Workshop on Semantic Web Enabled Software Engineering (SWESE) at ISWC 2009, Chantilly, VA. Published in 2009
- BMIR-2009-1378
- Prototyping a Biomedical Ontology Recommender Service
- C. Jonquet, N. H. Shah, M. A. Musen
- Bio-Ontologies: Knowledge in Biology, SIG, ISMB ECCB 2009, Stockholm, Sweden. Published in 2009
- BMIR-2009-1364
- Creating Mappings For Ontologies in Biomedicine: Simple Methods Work
- A. Ghazvinian, N. F. Noy, M. A. Musen
- 2009 AMIA Annual Symposium, San Francisco, CA. Published in 2009
- BMIR-2009-1357
- The Open Biomedical Annotator
- C. Jonquet, N. H. Shah, M. A. Musen
- AMIA Summit on Translational Bioinformatics, San Francisco, CA, USA, 56-60. Published in 2009
- BMIR-2009-1356
- Ontology-driven Indexing of Public Datasets for Translational Bioinformatics
- N. H. Shah, C. Jonquet, A. P. Chiang, A. J. Butte, R. Chen, M. A. Musen
- BMC Bioinformatics, Volume 10. Published in 2009
 - BMIR-2009-1325
- Ontologies for formal representation of biological systems
- N. H. Shah, M. A. Musen
- Handbook on Ontologies, Rudi Studer and Steffen Staab, Springer, New York, second, 445-462. Published in 2009
- BMIR-2008-1343
- Collecting Community-Based Mappings in an Ontology
- N. F. Noy, N. B. Griffith, M. A. Musen
- 7th International Semantic Web Conference (ISWC 2008), Karlsruhe, Germany, Springer. Published in 2008
- BMIR-2008-1332
- Comparing Concept Recognizers for Ontology-Based Indexing: MGREP vs. MetaMap
- N. Bathia, N. H. Shah, A. P. Chiang, D. L. Rubin, M. A. Musen
- . Published in 2008
- BMIR-2008-1324
- Biomedical Data/Content Acquisition, Curation
- N. H. Shah
- Encyclopedia of Database Systems, Ling Liu and M. Tamer Ozsu, Springer, New York. Published in 2008
 - BMIR-2008-1323
- UMLS-Query: A Perl Module for Querying the UMLS
- N. H. Shah, M. A. Musen
- AMIA Annual Symposium, Washington DC, American Medical Informatics Association, AMIA Annu Symp Proc, 2008, 652–656. Published in 2008
- BMIR-2008-1317
- Help will be provided for this task: Ontology-Based Annotator Web Service
- C. Jonquet, M. A. Musen, N. H. Shah
- . Published in 2008
- BMIR-2008-1307
- A System for Ontology-Based Annotation of Biomedical Data
- C. Jonquet, M. A. Musen, N. H. Shah
- International Workshop on Data Integration in The Life Sciences 2008, DILS'08, Evry, France, Springer-Verlag, 5109, Lecture Notes in BioInformatics, 144-152. Published in 2008
- BMIR-2008-1306
- Ontology-driven Indexing of Public Datasets for Translational Bioinformatics
- N. H. Shah, A. P. Chiang, A. J. Butte, R. Chen, M. A. Musen
- American Medical Informatics Association Symposium on Translational Bioinformatics, San Francisco, CA, March 10-12, 2008. Published in 2008
- BMIR-2008-1298
- BioPortal: A Web Portal to Biomedical Ontologies
- D. L. Rubin, D. de Abreu Moreira, P. P. Kanjamala, M. A. Musen
- AAAI Spring Symposium Series, Symbiotic Relationships between Semantic Web and Knowledge Engineering, Stanford University, (in press). Published in 2008
 - BMIR-2008-1288
- Biomedical ontologies: a functional perspective
- D. L. Rubin, N. H. Shah, N. F. Noy
- Briefings in Bioinformatics, 9, 1, 75-90. Published in 2008
- BMIR-2007-1314
- Knowledge Zone: a public repository of peer-reviewed biomedical ontologies.
- K. S. Supekar, D. L. Rubin, N. F. Noy, M. A. Musen
- MEDINFO, Brisbane, Australia, 812-6. Published in 2007
- BMIR-2007-1294
- Interpretation Errors Related to the GO Annotation File Format
- D. de Abreu Moreira, N. H. Shah, M. A. Musen
- AMIA Annual Symposium Proceedings, Chicago, IL, 759-764. Published in 2007
- BMIR-2007-1289
- Ontrez Project Report
- N. H. Shah, C. Jonquet
- . Published in 2007
- BMIR-2007-1284
- Searching Ontologies Based on Content: Experiments in the Biomedical Domain
- H. Alani, N. F. Noy, N. H. Shah, M. A. Musen
- The Fourth International Conference on Knowledge Capture (K-CAP 2007), Whistler, BC, Canada, ACM, 55-62. Published in 2007
- BMIR-2007-1283
- Ontology Mapping - A User Survey
- , N. F. Noy, M. A. Storey
- The Second International Workshop on Ontology Matching at ISWC 07 + ASWC 07, Busan, Korea. Published in 2007
- BMIR-2007-1262
- Using annotations from controlled vocabularies to find meaningful associations
- W. Lee, L. Raschid, P. Srinivasan, N. H. Shah, D. L. Rubin, N. F. Noy
- Lecture Notes in Bioinformatics, LNBI, 4544, 247-263. Published in 2007
- BMIR-2007-1252
- Current progress in network research: toward reference networks for key model organisms
- B. Srinivasan, N. H. Shah, J. A. Flannick, E. Abeliuk, A. F. Novak, S. Batzoglou
- Briefings in Bioinformatics, 10.1093/bib/bbm038. Published in 2007
 - BMIR-2007-1249
- Annotation and query of tissue microarray data using the NCI Thesaurus
- N. H. Shah, D. L. Rubin, I. Espinosa, K. Montgomery, M. A. Musen
- BMC Bioinformatics, 8, 296. Published in 2007
- BMIR-2007-1247
- Which Annotation did you mean?
- N. H. Shah, M. A. Musen
- . Published in 2007
- BMIR-2007-1242
- UMLS-Query: A Perl Module for Querying the UMLS
- N. H. Shah, M. A. Musen
- . Published in 2007
- BMIR-2007-1234
- Translating the Foundational Model of Anatomy into OWL
- N. F. Noy, D. L. Rubin
- Journal of Web Semantics, 6, 2. Published in 2007
- BMIR-2006-1248
- Clench2.0: Cluster enrichment analysis and visualization of expression, annotation and transcription factor binding site data
- N. H. Shah, N. V. Fedoroff, M. A. Musen
- . Published in 2006
- BMIR-2006-1233
- Ontology-based Annotation and Query of Tissue Microarray Data
- N. H. Shah, K. S. Supekar, D. L. Rubin, M. A. Musen
- AMIA Annual Symposium, Washington DC, AMIA, 709-713. Published in 2006
- BMIR-2006-1118
- The National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge.
- D. L. Rubin, N. F. Noy, J. D. Richter, B. Smith, M. A. Storey, H. Solbrig, C. G. Chute, I. Sim, M. Ashburner, M. Westerfield, S. Misra, C. J. Mungall, S. E. Lewis, M. A. Musen
- OMICS: A Journal of Integrative Biology, 10, 2, 185-198. Published in 2006
 - BMIR-2000-1290
- Computers in Radiology: Interactive Software for Generation and Vizualization of Structured Findings in Radiology Reports
- U. Sinha, B. Dai, D. B. Johnson, R. Taira, M. Golamco, H. Kangarloo
- American Journal of Roentgenology, AJR, 175, 3, 609-612. Published in 2000
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