Core 2: Driving Biological Projects Our Center currently supports three Driving Biological Projects (DBPs) that represent a broad range of biomedical research endeavors. The DBPs provide """"""""application pull"""""""" and serve as early adopters and evaluators of our technology's utility in enhancing their research. Their feedback is critical in defining the requirements of our technology-development activities as well as in shaping the overall thrust of our engineering efforts. The work conducted by the DBPs is coordinated with the Center's aims by Dr. Whetzel. Dr. Whetzel is in constant contact with DBP groups to learn about their requirements, to suggest how they might take better advantage of NCBO offerings, and to elicit feedback that she can bring back to our development team. The current ongoing DBPs were chosen via a widely advertised open call in the spring of 2008, and will remain as key drivers through August 2011. When the current DBPs terminate in 2011, we will initiate three new DBPs. We have already selected two of these new projects for their strategic importance to our Center, and we will use an open call to select the third new DBP that will start that year. We also propose to add a fourth DBP?the i2b2 National Center for Biomedical Computing?starting with our first year of renewed funding in 2010. Both the current DBPs and those due to start in July 2011 cover a broad spectrum of activities spanning ontology development, management, and evaluation, as well as creation of ontology-based annotations of biomedical data sources and annotation analysis for translational research.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Specialized Center--Cooperative Agreements (U54)
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Special Emphasis Panel (ZRG1-BST-K)
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Stanford University
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Kamdar, Maulik R; Walk, Simon; Tudorache, Tania et al. (2018) Analyzing user interactions with biomedical ontologies: A visual perspective. Web Semant 49:16-30
Ochs, Christopher; Perl, Yehoshua; Geller, James et al. (2017) An empirical analysis of ontology reuse in BioPortal. J Biomed Inform 71:165-177
van der Weyden, Louise; Arends, Mark J; Campbell, Andrew D et al. (2017) Genome-wide in vivo screen identifies novel host regulators of metastatic colonization. Nature 541:233-236
Kamdar, Maulik R; Musen, Mark A (2017) Mechanism-based Pharmacovigilance over the Life Sciences Linked Open Data Cloud. AMIA Annu Symp Proc 2017:1014-1023
Kamdar, Maulik R; Walk, Simon; Tudorache, Tania et al. (2017) BiOnIC: A Catalog of User Interactions with Biomedical Ontologies. Semant Web ISWC 10588:130-138
Martínez-Romero, Marcos; O'Connor, Martin J; Shankar, Ravi D et al. (2017) Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. AMIA Annu Symp Proc 2017:1272-1281
Martínez-Romero, Marcos; Jonquet, Clement; O'Connor, Martin J et al. (2017) NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. J Biomed Semantics 8:21
Kamdar, Maulik R; Musen, Mark A (2017) PhLeGrA: Graph Analytics in Pharmacology over the Web of Life Sciences Linked Open Data. Proc Int World Wide Web Conf 2017:321-329
van der Weyden, Louise; Karp, Natasha A; Swiatkowska, Agnieszka et al. (2017) Genome wide in vivo mouse screen data from studies to assess host regulation of metastatic colonisation. Sci Data 4:170129
Mortensen, Jonathan M; Telis, Natalie; Hughey, Jacob J et al. (2016) Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology. J Biomed Inform 60:199-209

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