Mark A Musen, Professor
Stanford University Stanford, Ca 94305
Grant 5U54HG004028-020001 from National Human Genome Research Institute IRG: ZRG1
Abstract: We propose to create the National Center for Biomedical Ontology (cBIO) that will develop tools and methods for assimilating, archiving, and accessing machine-processable representations of biomedical domain objects, processes, and relations to assist in the management, integration, visualization, analysis, and interpretation of the huge, distributed data sets that are now the hallmark of biomedical research. Our Center will be truly national in scope, with participation of leading scientific groups from Stanford, Lawrence Berkeley National Laboratory, the Mayo Clinic, SUNY Buffalo, and the University of Victoria. Our objectives are defined by the following seven cores (1) the development of computer science methods for ontology annotation, peer review, alignment, mapping, and management, leading to the creation of a virtual library of Open Biomedical Ontologies and a Web-based BioPortal to allow investigators and intelligent computer programs to access and use the ontology library; (2) the creation of tools to assist biomedical investigators in the use of ontologies accessible through BioPortal to annotate experimental data; to enable scientists to visualize, apply, and store their data and annotations in an online resource also accessible via BioPortal known as Open Biomedical Databases; to ensure that data annotations will change as the underlying ontologies evolve over time; and to facilitate cross-linking among ontologies and data accessed via BioPortal; (3) the promotion of driving biological projects - initially in the areas of (a) interpretation of genomic data in Drosophila (Cambridge, UK); (b) interpretation of genomic data in zebrafish (U. of Oregon); (c) analysis of clinical-trial data for therapy of HIV/AIDS (UCSF) - that can stimulate our research by highlighting the need to use ontologies for data analysis and data annotation; (4) the creation of a computational infrastructure to support our research, development, and dissemination activities; (5) the training of the next generation of biocomputational scientists in the area of biomedical ontology; (6) a set of comprehensive dissemination activities that include the creation of a novel program of workshops led by world-class faculty to assist the biomedical community to create and refine ontologies and to use the Center s technologies to enhance biomedical investigation; and (7) outstanding project administration conducted by a dedicated and talented management group. Our Center will accelerate the transition of biomedicine into the world of e-science, and will provide an essential complement to those National Centers for Biomedical Computation that focus on the development of algorithms.
Keywords: Internet, bioinformatics, computational biology, computer system design /evaluation, computer human interaction, cooperative study, human subject
Sponsored Links Excellgen http://Excellgen.com
NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY(RMI)
Mark A Musen, Professor
Stanford University, 340 Panama Street, Stanford, Ca 94305-6203
Grant 5U54HG004028-05 from Office Of The Director, National Institutes Of Health
Abstract: We propose to create the National Center for Biomedical Ontology (cBIO) that will develop tools and methods for assimilating, archiving, and accessing machine-processable representations of biomedical domain objects, processes, and relations to assist in the management, integration, visualization, analysis, and interpretation of the huge, distributed data sets that are now the hallmark of biomedical research. Our Center will be truly national in scope, with participation of leading scientific groups from Stanford, Lawrence Berkeley National Laboratory, the Mayo Clinic, SUNY Buffalo, and the University of Victoria. Our objectives are defined by the following seven cores (1) the development of computer science methods for ontology annotation, peer review, alignment, mapping, and management, leading to the creation of a virtual library of Open Biomedical Ontologies and a Web-based BioPortal to allow investigators and intelligent computer programs to access and use the ontology library; (2) the creation of tools to assist biomedical investigators in the use of ontologies accessible through BioPortal to annotate experimental data; to enable scientists to visualize, apply, and store their data and annotations in an online resource also accessible via BioPortal known as Open Biomedical Databases; to ensure that data annotations will change as the underlying ontologies evolve over time; and to facilitate cross-linking among ontologies and data accessed via BioPortal; (3) the promotion of driving biological projects - initially in the areas of (a) interpretation of genomic data in Drosophila (Cambridge, UK); (b) interpretation of genomic data in zebrafish (U. of Oregon); (c) analysis of clinical-trial data for therapy of HIV/AIDS (UCSF) - that can stimulate our research by highlighting the need to use ontologies for data analysis and data annotation; (4) the creation of a computational infrastructure to support our research, development, and dissemination activities; (5) the training of the next generation of biocomputational scientists in the area of biomedical ontology; (6) a set of comprehensive dissemination activities that include the creation of a novel program of workshops led by world-class faculty to assist the biomedical community to create and refine ontologies and to use the Center´s technologies to enhance biomedical investigation; and (7) outstanding project administration conducted by a dedicated and talented management group. Our Center will accelerate the transition of biomedicine into the world of e-science, and will provide an essential complement to those National Centers for Biomedical Computation that focus on the development of algorithms
Keywords: No Project Terms available
Project start date: 2005-09-23
Project end date: 2010-07-31
Budget start date: 1-AUG-2009
Budget end date: 31-JUL-2010
PFA/PA: RFA-RM-04-022
5U54HG004028-05 (2009): $3474171
Mark A Musen, Professor
Stanford University, 340 Panama Street, Stanford, Ca 94305-6203
Grant 5U54HG004028-05_0001 from Roadmap Initiative, Office Of The Director
Abstract: We propose to create the National Center for Biomedical Ontology (cBIO) that will develop tools and methods for assimilating, archiving, and accessing machine-processable representations of biomedical domain objects, processes, and relations to assist in the management, integration, visualization, analysis, and interpretation of the huge, distributed data sets that are now the hallmark of biomedical research. Our Center will be truly national in scope, with participation of leading scientific groups from Stanford, Lawrence Berkeley National Laboratory, the Mayo Clinic, SUNY Buffalo, and the University of Victoria. Our objectives are defined by the following seven cores (1) the development of computer science methods for ontology annotation, peer review, alignment, mapping, and management, leading to the creation of a virtual library of Open Biomedical Ontologies and a Web-based BioPortal to allow investigators and intelligent computer programs to access and use the ontology library; (2) the creation of tools to assist biomedical investigators in the use of ontologies accessible through BioPortal to annotate experimental data; to enable scientists to visualize, apply, and store their data and annotations in an online resource also accessible via BioPortal known as Open Biomedical Databases; to ensure that data annotations will change as the underlying ontologies evolve over time; and to facilitate cross-linking among ontologies and data accessed via BioPortal; (3) the promotion of driving biological projects - initially in the areas of (a) interpretation of genomic data in Drosophila (Cambridge, UK); (b) interpretation of genomic data in zebrafish (U. of Oregon); (c) analysis of clinical-trial data for therapy of HIV/AIDS (UCSF) - that can stimulate our research by highlighting the need to use ontologies for data analysis and data annotation; (4) the creation of a computational infrastructure to support our research, development, and dissemination activities; (5) the training of the next generation of biocomputational scientists in the area of biomedical ontology; (6) a set of comprehensive dissemination activities that include the creation of a novel program of workshops led by world-class faculty to assist the biomedical community to create and refine ontologies and to use the Center´s technologies to enhance biomedical investigation; and (7) outstanding project administration conducted by a dedicated and talented management group. Our Center will accelerate the transition of biomedicine into the world of e-science, and will provide an essential complement to those National Centers for Biomedical Computation that focus on the development of algorithms
Keywords: AIDS/HIV; AIDS/HIV problem; Algorithms; Analysis, Data; Archives; Area; Automobile Driving; Biological; Biomedical Computing; Biomedical Research; Brachydanio rerio; Buffaloes; Clinic; Clinical Trials; Clinical Trials, Unspecified; Communities; Complement; Complement Proteins; Computer Programs and Programming; Danio rerio; Data; Data Analyses; Data Banks; Data Bases; Data Set; Databank, Electronic; Databanks; Database, Electronic; Databases; Dataset; Development; Development and Research; Drivings, Automobile; Drosophila; Drosophila genus; Educational workshop; Ensure; Evaluation; Evolution; Faculty; Fruit Fly, Drosophila; Genomics; Goals; Grant; HIV/AIDS; HIV/AIDS problem; Imagery; Internet; Investigation; Investigators; Knowledge; Laboratories; Libraries; Maps; Method LOINC Axis 6; Methodology; Methods; NIH; National Institutes of Health; National Institutes of Health (U.S.); On-Line Systems; Online Systems; Ontology; Oregon; Peer Review; Process; Programs (PT); Programs [Publication Type]; R & D; R&D; Research; Research Personnel; Research Resources; Researchers; Resources; Scientist; Stimulus; Technology; Time; Training; United States National Institutes of Health; Universities; Update; Virtual Library; Visualization; WWW; Workshop; Zebra Danio; Zebra Fish; Zebrafish; analytical method; base; biomedical computation; biomedical ontology; clinical data repository; clinical data warehouse; clinical investigation; cluster computing; computational grid; computer infrastructure; computer program; computer programming; computer science; cross-link; crosslink; data grid; data repository; datagrid; distributed computing; distributed data; driving; e-science; escience; federated computing; federated data; federated database; fruit fly; grid computing; improved; next generation; novel; online computer; open source; programs; relational database; research and development; tool; web; web based; world wide web
Budget start date: 1-AUG-2009
Budget end date: 31-JUL-2010
PFA/PA: RFA-RM-04-022
5U54HG004028-05_0001 (2009): $3749171
National Center For Biomedical Ontology
Mark A Musen, Professor
Stanford University Stanford, Ca 94305
Grant 5U54HG004028-03 from National Human Genome Research Institute IRG: ZRG1
Abstract: We propose to create the National Center for Biomedical Ontology (cBIO) that will develop tools and methods for assimilating, archiving, and accessing machine-processable representations of biomedical domain objects, processes, and relations to assist in the management, integration, visualization, analysis, and interpretation of the huge, distributed data sets that are now the hallmark of biomedical research. Our Center will be truly national in scope, with participation of leading scientific groups from Stanford, Lawrence Berkeley National Laboratory, the Mayo Clinic, SUNY Buffalo, and the University of Victoria. Our objectives are defined by the following seven cores (1) the development of computer science methods for ontology annotation, peer review, alignment, mapping, and management, leading to the creation of a virtual library of Open Biomedical Ontologies and a Web-based BioPortal to allow investigators and intelligent computer programs to access and use the ontology library; (2) the creation of tools to assist biomedical investigators in the use of ontologies accessible through BioPortal to annotate experimental data; to enable scientists to visualize, apply, and store their data and annotations in an online resource also accessible via BioPortal known as Open Biomedical Databases; to ensure that data annotations will change as the underlying ontologies evolve over time; and to facilitate cross-linking among ontologies and data accessed via BioPortal; (3) the promotion of driving biological projects - initially in the areas of (a) interpretation of genomic data in Drosophila (Cambridge, UK); (b) interpretation of genomic data in zebrafish (U. of Oregon); (c) analysis of clinical-trial data for therapy of HIV/AIDS (UCSF) - that can stimulate our research by highlighting the need to use ontologies for data analysis and data annotation; (4) the creation of a computational infrastructure to support our research, development, and dissemination activities; (5) the training of the next generation of biocomputational scientists in the area of biomedical ontology; (6) a set of comprehensive dissemination activities that include the creation of a novel program of workshops led by world-class faculty to assist the biomedical community to create and refine ontologies and to use the Center s technologies to enhance biomedical investigation; and (7) outstanding project administration conducted by a dedicated and talented management group. Our Center will accelerate the transition of biomedicine into the world of e-science, and will provide an essential complement to those National Centers for Biomedical Computation that focus on the development of algorithms.
Keywords: Internet, bioinformatics, computational biology, computer system design /evaluation, cooperative study, NIH Roadmap Initiative tag, clinical research, human subject
Project start date: 2005-09-23
Project end date: 2010-07-31
5U54HG004028-03 (2007): $3638519
Mark A Musen, Professor
Stanford University Stanford, Ca 94305
Grant 5U54HG004028-030001 from National Human Genome Research Institute IRG: ZRG1
Abstract: We propose to create the National Center for Biomedical Ontology (cBIO) that will develop tools and methods for assimilating, archiving, and accessing machine-processable representations of biomedical domain objects, processes, and relations to assist in the management, integration, visualization, analysis, and interpretation of the huge, distributed data sets that are now the hallmark of biomedical research. Our Center will be truly national in scope, with participation of leading scientific groups from Stanford, Lawrence Berkeley National Laboratory, the Mayo Clinic, SUNY Buffalo, and the University of Victoria. Our objectives are defined by the following seven cores (1) the development of computer science methods for ontology annotation, peer review, alignment, mapping, and management, leading to the creation of a virtual library of Open Biomedical Ontologies and a Web-based BioPortal to allow investigators and intelligent computer programs to access and use the ontology library; (2) the creation of tools to assist biomedical investigators in the use of ontologies accessible through BioPortal to annotate experimental data; to enable scientists to visualize, apply, and store their data and annotations in an online resource also accessible via BioPortal known as Open Biomedical Databases; to ensure that data annotations will change as the underlying ontologies evolve over time; and to facilitate cross-linking among ontologies and data accessed via BioPortal; (3) the promotion of driving biological projects - initially in the areas of (a) interpretation of genomic data in Drosophila (Cambridge, UK); (b) interpretation of genomic data in zebrafish (U. of Oregon); (c) analysis of clinical-trial data for therapy of HIV/AIDS (UCSF) - that can stimulate our research by highlighting the need to use ontologies for data analysis and data annotation; (4) the creation of a computational infrastructure to support our research, development, and dissemination activities; (5) the training of the next generation of biocomputational scientists in the area of biomedical ontology; (6) a set of comprehensive dissemination activities that include the creation of a novel program of workshops led by world-class faculty to assist the biomedical community to create and refine ontologies and to use the Center s technologies to enhance biomedical investigation; and (7) outstanding project administration conducted by a dedicated and talented management group. Our Center will accelerate the transition of biomedicine into the world of e-science, and will provide an essential complement to those National Centers for Biomedical Computation that focus on the development of algorithms.
Keywords: Internet, bioinformatics, computational biology, computer system design /evaluation, computer human interaction, cooperative study, human subject
National Center For Biomedical Ontology
Mark A Musen, Professor
Stanford University Stanford, Ca 94305
Grant 5U54HG004028-02 from National Human Genome Research Institute IRG: ZRG1
Abstract: We propose to create the National Center for Biomedical Ontology (cBIO) that will develop tools and methods for assimilating, archiving, and accessing machine-processable representations of biomedical domain objects, processes, and relations to assist in the management, integration, visualization, analysis, and interpretation of the huge, distributed data sets that are now the hallmark of biomedical research. Our Center will be truly national in scope, with participation of leading scientific groups from Stanford, Lawrence Berkeley National Laboratory, the Mayo Clinic, SUNY Buffalo, and the University of Victoria. Our objectives are defined by the following seven cores (1) the development of computer science methods for ontology annotation, peer review, alignment, mapping, and management, leading to the creation of a virtual library of Open Biomedical Ontologies and a Web-based BioPortal to allow investigators and intelligent computer programs to access and use the ontology library; (2) the creation of tools to assist biomedical investigators in the use of ontologies accessible through BioPortal to annotate experimental data; to enable scientists to visualize, apply, and store their data and annotations in an online resource also accessible via BioPortal known as Open Biomedical Databases; to ensure that data annotations will change as the underlying ontologies evolve over time; and to facilitate cross-linking among ontologies and data accessed via BioPortal; (3) the promotion of driving biological projects - initially in the areas of (a) interpretation of genomic data in Drosophila (Cambridge, UK); (b) interpretation of genomic data in zebrafish (U. of Oregon); (c) analysis of clinical-trial data for therapy of HIV/AIDS (UCSF) - that can stimulate our research by highlighting the need to use ontologies for data analysis and data annotation; (4) the creation of a computational infrastructure to support our research, development, and dissemination activities; (5) the training of the next generation of biocomputational scientists in the area of biomedical ontology; (6) a set of comprehensive dissemination activities that include the creation of a novel program of workshops led by world-class faculty to assist the biomedical community to create and refine ontologies and to use the Center s technologies to enhance biomedical investigation; and (7) outstanding project administration conducted by a dedicated and talented management group. Our Center will accelerate the transition of biomedicine into the world of e-science, and will provide an essential complement to those National Centers for Biomedical Computation that focus on the development of algorithms.
Keywords: Internet, bioinformatics, computational biology, computer system design /evaluation, cooperative study, NIH Roadmap Initiative tag, clinical research, human subject
Project start date: 2005-09-23
Project end date: 2010-07-31
5U54HG004028-02 (2006): $3747226
Grants awarded to Mark A Musen
CUSTOM-TAILORED TOOLS FOR PROTOCOL-KNOWLEDGE MANAGEMENT
Mark A Musen, Professor
Medicinestanford University
stanford, Ca 94305
Grant 5R29LM005157-05 from National Library Of Medicine IRG: BLR
Abstract: We propose to develop automated technique to facilitate the creation and maintenance of large electronic knowledge bases of medical treatment plans. These techniques for knowledge-base construction ultimately will aid clinical experts in the design and validation of new treatment protocols. The research will foster dissemination of protocol guidelines in a format that can be incorporated within computer-based systems that physicians will use to obtain patient-specific treatment advice. We will complete development of a computer system, PROTEGE, that will allow users to create protocol-entry tools that are each custom-tailored to a particular medical specialty. These PROTEGE-generated tools will permit expert physicians to describe treatment protocols using simple, graphical notations; the graphical specifications will automatically be converted to an internal format that a special version of the ONCOCIN program will interpret to render patient-specific therapy advice. In the course of our work, we will address issues related both to computer-assisted development and dissemination of clinical protocols, and to the general problem of acquiring and representing medical knowledge for use within computer-based advice systems. Our research plan comprises a four-step process 1. We will implement PROTEGE on a general-purpose computer, developing a new user-interface-management system that will facilitate generation of more flexible protocol-entry tools. 2. We will develop new models of problem solving that will allow PROTEGE users to represent more complex therapy-planning actions. We will postulate new terms and relationships that can be used to describe medical- therapy actions in a domain-independent fashion, and test the effectiveness of these terms and relationships in the specification of new classes of treatment protocols. 3. We will evaluate PROTEGE by creating tools with which physicians will enter new protocols for the therapy of AIDS and of AIDS-related infections. 4. We will develop methods for computer-aided design of new clinical protocols, allowing developers to define libraries of knowledge concerning expected efficacy and expected toxicity of therapeutic agents. We will evaluate these design methods in the area of clinical trials for HIV- related diseases
Project start date: 1990-04-01
Project end date: 1996-03-31
5R29LM005157-05 (1994): $117468
SOFTWARE ARCHITECTURE FOR GUIDELINE DIRECTED THERAPY
Mark A Musen, Professor
Stanford University Stanford, Ca 94305
Grant 5R01LM005708-03 from National Library Of Medicine IRG: SRC
Abstract: We propose to develop a novel computer architecture that will support automated reasoning about protocol-based care. We will build on our previous experience in developing the ONCOCIN and T-HELPER systems to create a highly integrated set of computer programs that will significantly ease the construction of new automated systems that can use knowledge of clinical protocols and guidelines to interpret electronically stored patient data and to monitor patient management. Our approach will allow a wide range of clinical information systems to determine when clinical practice guidelines and protocols may apply to given patients, to recommend therapy in accordance with those guidelines, and to critique patient care that deviates from recommended practice patterns. The goal of our research is to address fundamental deficiencies in existing automated approaches to guideline-directed therapy by developing both new data models that can capture the necessary temporal distinctions in patient data and new problem-solving methods for reasoning about guideline- directed therapy. Our research plan consists of a four-step process that defines our specific aims. (1) We will create a domain model of medical concepts that is sufficient to represent the elements of clinical medicine required for a subset of protocol-based care in three areas of medicine oncology, HIV infection, and hypertension. (2) We will create a temporal data management system that will derive automatically time-related ions from primary clinical data. This system will support a new database query language that will allow software clients to query for the presence of time-related ions in clinical data, in addition to the primary data themselves. (3) We will develop several extensible problem-solving methods for protocol-based care that will be reusable within the three clinical domains that we will explore. These methods will automate the tasks of therapy planning, of determining patient eligibility for protocols and guidelines, and of critiquing provider s management of patients when practice guidelines apply. (4) We will evaluate the applicability of our problem-solving architecture to different classes of clinical protocols. We will reintegrate our architecture into the T-HELPER medical workstation, and will test the architecture s ability to support reasoning about guidelines and protocols in the three clinical application areas that we will explore. At the conclusion of our work, we will have developed a validated software architecture that can support temporal-data management and automated reasoning about complex clinical protocols and guidelines. Because of our commitment to industry standards such as UNIX, C, TCP/IP, and SQL, our system will be usable as an open "server" for temporal-data management within a variety of application programs.
Keywords: computer assisted medical decision making, computer program /software, computer system design /evaluation, AIDS, hypertension, oncology, problem solving
Project start date: 1995-04-01
Project end date: 1999-03-31
5R01LM005708-03 (1997): $507992
NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY(RMI)
Mark A Musen, Professor
Stanford University, 340 Panama Street, Stanford, Ca 94305-6203
Grant 3U54HG004028-05S1 from Office Of The Director, National Institutes Of Health
Abstract: We propose to create the National Center for Biomedical Ontology (cBIO) that will develop tools and methods for assimilating, archiving, and accessing machine-processable representations of biomedical domain objects, processes, and relations to assist in the management, integration, visualization, analysis, and interpretation of the huge, distributed data sets that are now the hallmark of biomedical research. Our Center will be truly national in scope, with participation of leading scientific groups from Stanford, Lawrence Berkeley National Laboratory, the Mayo Clinic, SUNY Buffalo, and the University of Victoria. Our objectives are defined by the following seven cores (1) the development of computer science methods for ontology annotation, peer review, alignment, mapping, and management, leading to the creation of a virtual library of Open Biomedical Ontologies and a Web-based BioPortal to allow investigators and intelligent computer programs to access and use the ontology library; (2) the creation of tools to assist biomedical investigators in the use of ontologies accessible through BioPortal to annotate experimental data; to enable scientists to visualize, apply, and store their data and annotations in an online resource also accessible via BioPortal known as Open Biomedical Databases; to ensure that data annotations will change as the underlying ontologies evolve over time; and to facilitate cross-linking among ontologies and data accessed via BioPortal; (3) the promotion of driving biological projects - initially in the areas of (a) interpretation of genomic data in Drosophila (Cambridge, UK); (b) interpretation of genomic data in zebrafish (U. of Oregon); (c) analysis of clinical-trial data for therapy of HIV/AIDS (UCSF) - that can stimulate our research by highlighting the need to use ontologies for data analysis and data annotation; (4) the creation of a computational infrastructure to support our research, development, and dissemination activities; (5) the training of the next generation of biocomputational scientists in the area of biomedical ontology; (6) a set of comprehensive dissemination activities that include the creation of a novel program of workshops led by world-class faculty to assist the biomedical community to create and refine ontologies and to use the Center´s technologies to enhance biomedical investigation; and (7) outstanding project administration conducted by a dedicated and talented management group. Our Center will accelerate the transition of biomedicine into the world of e-science, and will provide an essential complement to those National Centers for Biomedical Computation that focus on the development of algorithms
Keywords: AIDS/HIV; AIDS/HIV problem; Algorithms; Analysis, Data; Archives; Area; Automobile Driving; Biological; Biomedical Computing; Biomedical Research; Brachydanio rerio; Buffaloes; Clinic; Clinical Trials; Clinical Trials, Unspecified; Communities; Complement; Complement Proteins; Computer Programs and Programming; Danio rerio; Data; Data Analyses; Data Banks; Data Bases; Data Set; Databank, Electronic; Databanks; Database, Electronic; Databases; Dataset; Development; Development and Research; Drivings, Automobile; Drosophila; Drosophila genus; Educational workshop; Ensure; Faculty; Fruit Fly, Drosophila; Genomics; HIV/AIDS; HIV/AIDS problem; Imagery; Investigation; Investigators; Laboratories; Libraries; Maps; Methods; On-Line Systems; Online Systems; Ontology; Oregon; Peer Review; Process; Programs (PT); Programs [Publication Type]; R & D; R&D; Research; Research Personnel; Research Resources; Researchers; Resources; Scientist; Technology; Time; Training; Universities; Virtual Library; Visualization; Workshop; Zebra Danio; Zebra Fish; Zebrafish; biomedical computation; biomedical ontology; clinical data repository; clinical data warehouse; clinical investigation; cluster computing; computational grid; computer infrastructure; computer program; computer programming; computer science; cross-link; crosslink; data grid; data repository; datagrid; distributed computing; distributed data; driving; e-science; escience; federated computing; federated data; federated database; fruit fly; grid computing; next generation; novel; online computer; programs; relational database; research and development; tool; web based
Project start date: 2005-09-23
Project end date: 2010-07-31
Budget start date: 1-AUG-2009
Budget end date: 31-JUL-2010
PFA/PA: RFA-RM-04-022
3U54HG004028-05S1 (2009): $275000
1U54HG004028-01 (2005): $3758967
Mark A Musen, Professor
Stanford University Stanford, Ca 94305
Grant 1U54HG004028-010001 from National Human Genome Research Institute IRG: ZRG1
Abstract: We propose to create the National Center for Biomedical Ontology (cBIO) that will develop tools and methods for assimilating, archiving, and accessing machine-processable representations of biomedical domain objects, processes, and relations to assist in the management, integration, visualization, analysis, and interpretation of the huge, distributed data sets that are now the hallmark of biomedical research. Our Center will be truly national in scope, with participation of leading scientific groups from Stanford, Lawrence Berkeley National Laboratory, the Mayo Clinic, SUNY Buffalo, and the University of Victoria. Our objectives are defined by the following seven cores (1) the development of computer science methods for ontology annotation, peer review, alignment, mapping, and management, leading to the creation of a virtual library of Open Biomedical Ontologies and a Web-based BioPortal to allow investigators and intelligent computer programs to access and use the ontology library; (2) the creation of tools to assist biomedical investigators in the use of ontologies accessible through BioPortal to annotate experimental data; to enable scientists to visualize, apply, and store their data and annotations in an online resource also accessible via BioPortal known as Open Biomedical Databases; to ensure that data annotations will change as the underlying ontologies evolve over time; and to facilitate cross-linking among ontologies and data accessed via BioPortal; (3) the promotion of driving biological projects - initially in the areas of (a) interpretation of genomic data in Drosophila (Cambridge, UK); (b) interpretation of genomic data in zebrafish (U. of Oregon); (c) analysis of clinical-trial data for therapy of HIV/AIDS (UCSF) - that can stimulate our research by highlighting the need to use ontologies for data analysis and data annotation; (4) the creation of a computational infrastructure to support our research, development, and dissemination activities; (5) the training of the next generation of biocomputational scientists in the area of biomedical ontology; (6) a set of comprehensive dissemination activities that include the creation of a novel program of workshops led by world-class faculty to assist the biomedical community to create and refine ontologies and to use the Center s technologies to enhance biomedical investigation; and (7) outstanding project administration conducted by a dedicated and talented management group. Our Center will accelerate the transition of biomedicine into the world of e-science, and will provide an essential complement to those National Centers for Biomedical Computation that focus on the development of algorithms.
Keywords: Internet, bioinformatics, computational biology, computer system design /evaluation, computer human interaction, cooperative study, human subject
Project start date: 2005-10-01
Project end date: 2010-07-31
NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY
Mark A Musen
Stanford University, 340 Panama Street, Stanford, Ca 94305-6203
Grant 2U54HG004028-06 from Office Of The Director, National Institutes Of Health
Abstract: We propose to continue the National Center for Biomedical Ontology (NCBO), which develops tools and methods for assimilating, archiving, accessing, and applying machine-processable representations of biomedical domain objects, processes, and relations to assist in the management, integration, visualization, analysis, and interpretation of the huge, distributed data sets that are now the hallmark of biomedical research and clinical care. Our center is truly national in scope, with participation of leading scientific groups at Stanford, Mayo Clinic, University at Buffalo, and the University of Victoria. Our objectives are defined by the following six Cores (1) the development of enhanced computational methods for management of ontologies and controlled terminologies using current Web standards; integration of ontology authoring, publishing, and peer review; creation of a comprehensive ontology-based index of publicly available data resources; development of new analytic methods to summarize and profile biomedical data; (2) the promotion of Driving Biological Projects that can stimulate our research by suggesting new requirements and offering new test beds for deployment-initially involving the Cardiovascular Research Grid, the Rat Genome Database, the caNanoLab nanoparticle database, and the i2b2 National Center for Biomedical Computing, and later engaging the WHO´s development of lCD-11, studies performed by ArrayExpress, and projects that will be selected via open requests for applications; (3) the maintenance of a computational infrastructure to support our research, development, and dissemination activities; provision of user support to the growing number of researchers and clinicians who use our technologies; (4) the training of the next generation of scientists in biomedical ontology; (5) a comprehensive set of dissemination activities, that include workshops, tutorials. Web-based seminars, and a major international conference; and (6) outstanding project administration conducted by a dedicated and talented management team. The NCBO will accelerate the transition of biomedicine into the world of e-science, facilitate the creation of a National Health Information Infrastructure, and extend a network of collaboration through its interactions with other NCBCs, with other research consortia, and with the biomedical community at large
Relevance: RELEVANCE (See instructions): The NCBO supports a burgeoning user community that is using ontologies to enhance biomedical research and to improve patient care. It supports bench scientists, clinician researchers, and workers in informatics in data annnotation, data integration, information retrieval, natural-language processing, electronic patient record systems, and decision-support systems. It is a primary source of semantic-technology infrastructure and expertise for biomedical research and the development of advanced clinical information svstems
Project start date: 2005-09-23
Project end date: 2015-07-31
Budget start date: 27-SEP-2010
Budget end date: 31-JUL-2011
PFA/PA: RFA-RM-09-002
2U54HG004028-06 (2010): $3698211
Mark A Musen
Stanford University, 340 Panama Street, Stanford, Ca 94305-6203
Abstract: The NCBO encompasses numerous activities, projects, and sites. Our Center allocates substantial resources to scholarly and technical research and development as well as to collaborative Driving Biological Projects (DBPs), training, and dissemination activities. Consequently, the NCBO requires a comprehensive management structure that efficiently copes with complex administrative task of running a unified and interactive center
Keywords: Automobile Driving; Biological; Collaborations; Complex; Computational Biology; Development and Research; Drivings, Automobile; Funding Opportunities; Future; Goals; Individual; Infrastructure; Investigators; Monitor; NIH; National Institutes of Health; National Institutes of Health (U.S.); Process; R & D; R&D; Research Infrastructure; Research Personnel; Research Resources; Researchers; Resources; Running; Site; Structure; United States National Institutes of Health; biomed informatics; biomedical informatics; coping; driving; research and development; training project
Project start date: 2010-09-01
Project end date: 2015-08-31
Budget start date: 27-SEP-2010
Budget end date: 31-JUL-2011
PFA/PA: RFA-RM-09-002
2U54HG004028-06_8465 (2010): $344759
Mark A Musen
Stanford University, 340 Panama Street, Stanford, Ca 94305-6203
Abstract: The NCBO creates tools and services that provide the ontological backbone for a broad range of scientific disciplines. We are producing a scalable, distributed infrastructure for publishing, managing, and evaluating ontologies. We are also creating ontology-based annotations of biomedical data sources to advance biomedical, clinical, and translational research. In the next five years, we will continue to grow the BioPortal library and services that will enable scientists to custom-tailor library components and to embed these components directly in their applications. The first generation of BioPortal focused on the content and services for the bio-ontology community. The next generation will provide additional content and services for the broader community of biomedical, clinical, and translational researchers, with an emphasis on generalizability and wide-scale adoption. In many cases, the ontology needs of a research area evolve quickly and researchers must be able to add new ontology terms and to refine and extend existing ones in order to meet community and institutional requirements. Our goal is to enable "agile ontology development"¿the incremental, user-guided, needs-driven evolution of ontologies. To accomplish this goal, we will integrate the infrastructure for ontology publishing, review, and application with the ontology-revision process, to create a common infrastructure for user feedback, change proposals, and updates by developers. We will use the annotation tools that we have already developed to annotate automatically a large set of public biomedical resources, creating a comprehensive index of ontology-based annotations for enabling translational discoveries. Finally, we will develop analytic methods to profile biomedical data sets for enrichment against the background of these annotations. As a result, just as biologists use the Gene Ontology to determine biological processes over-represented (or enriched) in a set of differentially expressed genes, clinical and translational investigators will be able to determine enrichment of terms representing diseases (or class of diseases), drugs, or other controlled terms in data sets of their choice
Keywords: Address; Adoption; Area; Biological Function; Biological Process; Clinical; Communities; Computer Programs; Computer software; Custom; Data Banks; Data Bases; Data Set; Data Sources; Databank, Electronic; Databanks; Database, Electronic; Databases; Dataset; Development; Discipline; Disease; Disorder; Drugs; Evolution; Feedback; Generations; Genes; Goals; Infrastructure; Investigators; Libraries; Library Services; Maps; Medication; Methods; Nucleic Acids; Ontology; Peer Review; Pharmaceutic Preparations; Pharmaceutical Preparations; Process; Publishing; Publishing Peer Reviews; Records; Research; Research Infrastructure; Research Personnel; Research Resources; Researchers; Resources; Scientist; Services; Software; Spinal Column; Spine; Translational Research; Translational Research Enterprise; Translational Science; Update; Vertebral column; Work; backbone; base; biomedical ontology; biomedical resource; clinical data repository; clinical data warehouse; computer program/software; data format; data repository; disease/disorder; drug/agent; indexing; meetings; next generation; relational database; tool; translation research enterprise
Project start date: 2010-09-01
Project end date: 2015-08-31
Budget start date: 1-SEP-2010
Budget end date: 31-JUL-2011
PFA/PA: RFA-RM-09-002
2U54HG004028-06_8460 (2010): $1803820
Mark A Musen
Stanford University, 340 Panama Street, Stanford, Ca 94305-6203
Abstract: The institutions comprising the NCBO have a long tradition of training tomorrow´s investigators. Stanford University has had more than 25 years of continual support from the National Library of Medicine for its training program in biomedical informatics and is widely recognized as providing a model for graduate education in this discipline. The Mayo Clinic, the University at Buffalo, and the University of Victoria all have long and distinguished track records in training students and postdoctoral fellows in disciplines related to our Center´s work. The NCBO will collaborate with these existing programs to advance training in biomedical ontology as it applies to practical problems in biomedicine. As a national center, we also seek to improve ontology training across the biomedical research community. Taken together, our Education and Training activities will create an interactive community of graduate students, post-doctoral fellows, visiting scholars, and other scientists who understand the critical role of biomedical ontology and are positioned to communicate that role to the larger biomedical research community
Keywords: Biomedical Research; Buffaloes; Clinic; Clinical; Communities; Discipline; Education; Educational aspects; Educational workshop; Graduate Education; Institution; International; Investigators; Link; Modeling; NCI Scholars Program; National Library of Medicine; National Library of Medicine (U.S.); National Medical Library; Ontology; Position; Positioning Attribute; Postdoc; Postdoctoral Fellow; Programs (PT); Programs [Publication Type]; Records; Recruitment Activity; Research Associate; Research Personnel; Researchers; Role; Scholars Program; Scientist; Students; Training; Training Activity; Training Programs; Translational Research; Translational Research Enterprise; Translational Science; United States National Library of Medicine; Universities; Visit; Work; Workshop; biomed informatics; biomedical informatics; biomedical ontology; computer science; graduate student; improved; meetings; performance site; post-doc; post-doctoral; programs; recruit; social role; translation research enterprise
Project start date: 2010-09-01
Project end date: 2015-08-31
Budget start date: 27-SEP-2010
Budget end date: 31-JUL-2011
PFA/PA: RFA-RM-09-002
2U54HG004028-06_8463 (2010): $439990
COLLABORATIVE DEVELOPMENT OF BIOMEDICAL ONTOLOGIES AND TERMINOLOGIES
Mark A Musen, Professor
Stanford University, 340 Panama Street, Stanford, Ca 94305-6203
Grant 5R01GM086587-02 from National Institute Of General Medical Sciences
Abstract: The development of ontologies that define entities and the relationships among them has become essential for modern work in biomedicine. Ontologies help both humans and computers to manage the burgeoning data that are pervasive in biology and medicine. The need to annotate, retrieve, and integrate high-throughput data sets, to process natural language, and to build systems for decision support has set many communities of investigators to work building large ontologies. To date, these groups of ontology developers have been limited by the lack of methods and tools that facilitate distributed, collaborative engineering of large-scale ontologies and vocabularies. In this proposal, we outline three specific aims. First, we will explore basic computational methods that are essential for collaborative ontology engineering. We will investigate methods for representing diverse collaborative workflows, information about changes and concept history, trust, and provenance, and for recording decision making and design rationale. Empirical analysis of existing ontology-development projects will inform our construction of models for collaborative development workflows that will guide the processes of authoring, reviewing, and curating biomedical ontologies. Second, we will use the results from our first specific aim to build cProtigi, a set of robust, customizable, interactive tools to support distributed users in their collaborative work to build and edit terminologies and ontologies. Third, we will evaluate our work in the context of real-world, large-scale ontology-engineering projects, including the autism ontology of the National Database for Autism Research; the 11th revision of the WHO´s International Classification of Diseases; the Ontology for Biomedical Investigations, under development by a wide range of NIH-supported researchers; and BiomedGT, under development by NCI. It is no longer feasible to imagine that investigators can create biomedical ontologies working independently. The collaborative methods that we will study and the tools that we will build will lead to expanded opportunities to support the diverse data- and knowledge-intensive activities that pervade BISTI, the CTSAs, the NCBCs, and myriad biomedical initiatives that require robust, scaleable ontologies. The knowledge-based nature of modern medicine requires the use of ontologies and terminologies to process and integrate data. Ontology development itself becomes a collaborative process, with members of the larger research community contributing to and commenting on emerging ontologies. We plan to extend the Protigi ontology editor-the most widely used ontology editor today, with almost 100,000 registered users-to support collaborative development of ontologies and to evaluate the new tools by deploying them at the World Health Organization for the development of ICD-11 and in other settings
Keywords: Adopted; Autism; Autism, Early Infantile; Autism, Infantile; Autistic Disorder; Beds; Bio-Informatics; Bioinformatics; Biology; Collaborations; Comment; Comment (PT); Comment [Publication Type]; Commentary; Commentary (PT); Communities; Computer Systems Development; Computers; Computing Methodologies; Conflict; Conflict (Psychology); Consensus; Data; Data Banks; Data Bases; Data Set; Databank, Electronic; Databanks; Database, Electronic; Databases; Dataset; Decision Making; Decision Support Systems; Development; Development, Computer Systems; Drugs, Nonproprietary; Editorial Comment; Editorial Comment (PT); Educational Mainstreaming; Engineering; Engineerings; Evaluation; Generic Drugs; Goals; History; Human; Human, General; Industry; Institutes; International Classification of Diseases; International Statistical Classification of Diseases and Related Health Problems; Internet; Investigation; Investigators; Kanner`s Syndrome; Knowledge; Lead; Life; Mainstream Education, achievement; Mainstreaming; Mainstreaming (Education); Maintenance; Maintenances; Man (Taxonomy); Man, Modern; Medicine; Metadata; Methods; Modeling; Modern Medicine; NCI Thesaurus; NIH; NIH Program Announcements; National Institutes of Health; National Institutes of Health (U.S.); Natural Language Processing; Nature; On-Line Systems; Online Systems; Ontology; Outsourcing; Pb element; Process; Processings, Natural Language; Program Announcement; Program Development; Programs (PT); Programs [Publication Type]; Published Comment; Recording of previous events; Research; Research Personnel; Researchers; Resolution; Science of Medicine; Scientist; Source; Staging; Systems Development; Terminology; Testing; Trust; United States National Institutes of Health; Viewpoint; Viewpoint (PT); Vocabulary; Vocabulary Words; WHO; WWW; Work; World Health Organization; biomedical ontology; biomedical scientist; caBIG; cancer Biomedical Informatics Grid; clinical data repository; clinical data warehouse; computational methodology; computational methods; computer methods; data repository; design; designing; experience; experiment; experimental research; experimental study; flexibility; forging; generic; heavy metal Pb; heavy metal lead; knowledge base; member; natural language understanding; online computer; open source; programs; public health relevance; relational database; research study; response; tool; usability; web; web based; world wide web
Project start date: 2009-03-01
Project end date: 2013-02-28
Budget start date: 1-MAR-2010
Budget end date: 28-FEB-2011
PFA/PA: PAR-07-344
5R01GM086587-02 (2010): $525262
Sponsored Links Excellgen http://Excellgen.com
Mark A Musen
Stanford University, 340 Panama Street, Stanford, Ca 94305-6203
Abstract: Our Center´s effectiveness will be measured by the ability of the biomedical community to access ontologies, ontology metadata, and ontology-based annotations of biomedical data sets; to develop. new ontology-aware tools and applications; and to incorporate methods that ensure conformance with knowledge-representation standards in the creation of new content. The achievement of these goals depends on a substantial infrastructure to allow access to the Center´s services and to support the Center´s own research and development activities. The Stanford Center for Biomedical Informatics Research has more than 35 years of experience in the management of wide-ranging computational resources and in providing outstanding infrastructure to support advanced research and development in biomedical informatics. Over the past four years, we have developed a. flexible and scalable infrastructure to host the NCBO resources and to support our collaborators and users, including mechanisms to serve ontology content created by biomedical researchers from around the world. Most of this infrastructure is already adequate to support the projected capacity and scope of the Center. We will build on this infrastructure to provide a new generation of NCBO services and tools, addressing the key challenges of data management, and fast and reliable access to our content
Keywords: Achievement; Achievement Attainment; Address; Architecture; Collaborations; Communities; Computer Programs; Computer software; Data Set; Dataset; Development and Research; Effectiveness; Engineering / Architecture; Ensure; Generations; Goals; Infrastructure; Investigators; Link; Measures; Metadata; Methods; Ontology; Performance; Procedures; R & D; R&D; Research; Research Infrastructure; Research Personnel; Research Resources; Researchers; Resources; Services; Software; System; System, LOINC Axis 4; base; biomed informatics; biomedical informatics; computer program/software; computer-based representation; computing resources; data management; experience; flexibility; frame-based representation; information organization; knowledge representation; quality assurance; research and development; tool
Project start date: 2010-09-01
Project end date: 2015-08-31
Budget start date: 27-SEP-2010
Budget end date: 31-JUL-2011
PFA/PA: RFA-RM-09-002
2U54HG004028-06_8462 (2010): $276817
A RESOURCE FOR BIOMEDICAL ONTOLOGIES AND KNOWLEDGE BASES
Mark A Musen, Professor
Stanford University, 340 Panama Street, Stanford, Ca 94305-6203
Grant 5P41LM007885-08 from National Library Of Medicine
Abstract: For more than two decades, our laboratory has been studying technology to develop, manage, and use formal descriptions of biomedical concepts. The result of this work is Protege, a workbench that allows users to edit and apply controlled terminologies, ontologies, and knowledge bases to a wide range of information-management problems. To date, more than 50,000 people have registered as users of the system. Many diverse projects in biomedicine-supported by nearly every institute and center at NIH-have become critically dependent on this software and the knowledge-engineering principles that it supports. This P41 competing renewal application seeks to continue support for Protege, as a biomedical informatics resource that will benefit the system´s entire user community. We propose technology research and development to expand the capabilities of the Protege system to meet the current and anticipated needs of the user community. We will re-engineer Protege with a service-oriented architecture that can adapt to the requirements of new ontology languages, large ontology repositories, and cutting-edge ontology-management-services, such as reasoning, alignment, and evolution. We will create support for collaborative ontology development, in the context of both large, centralized projects and open, decentralized efforts. We also will develop advanced support for using ontologies in application software development and as integral parts of software systems. As a biomedical informatics resource, we will expand our collaborative research projects with other Prot¿g¿ users. We will provide service to the Protege user community through enhanced technical support, user documentation, tutorials, and workshops. These activities will serve to disseminate information about the resource and will aid research and development in many aspects of biomedical informatics both in the United States and internationally
Project start date: 2003-06-01
Project end date: 2011-12-31
Budget start date: 1-JUL-2010
Budget end date: 31-DEC-2011
PFA/PA: PAR-04-142
5P41LM007885-08 (2010): $956625
5P41LM007885-07 (2009): $688362
2P41LM007885-05 (2007): $693808
5P41LM007885-04 (2006): $783054
5P41LM007885-03 (2005): $769698
5P41LM007885-02 (2004): $754794
1P41LM007885-01 (2003): $723380
SOFTWARE ARCHITECTURE FOR GUIDELINE DIRECTED THERAPY
Mark A Musen, Professor
Medicinestanford University
stanford, Ca 94305
Grant 3R01LM005708-06S2 from National Library Of Medicine IRG: BLR
Abstract: EON is a modern, component-based architecture that developers can use to build robust decision-support systems that reason about guideline- directed care. The system comprises a number of modules, including (1) problem solvers that plan medical therapy and determine whether patients are eligible for particular protocols, (2) a database mediator that handles all queries posed by the problem solvers to return point patient data or temporal ions of those data in a transparent fashion, and (3) a shared knowledge based of clinical guidelines and basic medical knowledge. EON is not a standalone program, but rather constitutes middleware that is intended to be embedded within a given clinical information system. In this competing renewal application, we propose to develop and evaluate new computational methods to improve the EON architecture in a variety of ways to make the components more useful, explainable, and maintainable. Our specific aims include (1) creation of a set of interactive interfaces that will allow clinicians to visualize the behavior of the EON components and the data that they process, (2) extension of the capabilities of the EON database mediator to answer more complex time-dependent queries, (3) reformulation of the knowledge bases on which the EON components operate as CORBA-compliant servers, and (4) extensions to the problem-solving components that automate specific tasks related to guideline-directed therapy. In particular, we will develop CORBA-based mapping objects that allow problem solvers and knowledge bases of clinical protocols to interoperate over the Internet. We will evaluate the usability of the new EON components both within our laboratory and at another clinical site outside of Stanford. We will use EON to encode and execute protocols for breast cancer, AIDS, hypertension, and diabetes. Our goals are to develop EON into a set of middleware components that are sufficiently robust to handle the complexities of an extremely wide range of clinical protocols and guidelines, to demonstrate the effectiveness of a comprehensive decision-support system that is compatible with modern component-based software architectures, to provide better insight into the basis for EON´s therapy recommendations, and to refine EON´s knowledge-acquisition methodology so that clinicians can author and maintain electronic knowledge bases of protocols and guidelines more confidently and independently
Keywords: computer assisted medical decision making, computer program /software, computer system design /evaluation AIDS, hypertension, oncology, problem solving human data
Project start date: 1995-04-01
Project end date: 2003-03-31
3R01LM005708-06S2 (2002): $680964
Sponsored Links Excellgen http://Excellgen.com
3R01LM005708-06S1 (2001): $142894
5R01LM005708-06 (2000): $561890
5R01LM005708-05 (1999): $546864
2R01LM005708-04 (1998): $537276
Mark A Musen
Stanford University, 340 Panama Street, Stanford, Ca 94305-6203
Abstract: Education of trainees and dissemination to the broader biomedical community are highly interrelated tasks. Our dissemination goal is to educate our colleagues in the biomedical community about the use of ontology-oriented tools in general and about the Center´s technology in particular. NCBO differs from other current NCBCs because our computational technology is only as useful as the ontological content that our technology supports. NCBO thus has a special obligation to promote the construction of useful, reliable, scalable, and easily maintainable ontologies, which are at the same time biologically accurate. The NCBO seeks to transform the work of developing and using biomedical ontologies into an enterprise that is supported by computational tools that allow biomedical researchers to capture the benefits of instantaneous global collaboration made possible through the Web. Our dissemination efforts thus concentrate both on making technology available in ways that allow users to gain access to ontologies and to other formal representations of biomedical knowledge, and on assisting the community in building ontologies that are well-structured, coherently integrated, and useful to biomedical researchers. The latter is achieved by promoting maximally effective retrieval, integration, and exploitation of data and information
Keywords: Area; Clinical; Collaborations; Communities; Computer Programs; Computer software; Data; Development; Education; Educational Materials; Educational aspects; Educational workshop; Ensure; Evaluation; Funding Agency; Funding Source; Future; Goals; Government; International; Internet; Investigators; Knowledge; Laboratories; Libraries; NIH; National Institutes of Health; National Institutes of Health (U.S.); Ontology; Research Personnel; Research Resources; Researchers; Resources; Retrieval; Scientist; Societies; Software; Structure; Technology; Time; Translational Research; Translational Research Enterprise; Translational Science; United States National Institutes of Health; WWW; Work; Workshop; biomedical ontology; computational tools; computer program/software; computerized tools; conference; innovate; innovation; innovative; member; open source; symposium; tool; translation research enterprise; web; world wide web
Project start date: 2010-09-01
Project end date: 2015-08-31
Budget start date: 27-SEP-2010
Budget end date: 31-JUL-2011
PFA/PA: RFA-RM-09-002
2U54HG004028-06_8464 (2010): $552925
Mark A Musen
Stanford University, 340 Panama Street, Stanford, Ca 94305-6203
Abstract: 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
Keywords: Advertising; Automobile Driving; Back; Biological; Biomedical Computing; Biomedical Research; Cancers; Candidate Disease Gene; Candidate Gene; Cardiovascular; Cardiovascular Body System; Cardiovascular system; Cardiovascular system (all sites); Clinical Informatics; Data; Data Banks; Data Bases; Data Sources; Databank, Electronic; Databanks; Database, Electronic; Databases; Development; Dorsum; Drivings, Automobile; Engineering; Engineerings; Evaluation; Feedback; Funding; Grafting, Kidney; Grant; International Classification of Diseases; International Statistical Classification of Diseases and Related Health Problems; Kidney Transplantation; Kidney Transplants; Learning; Malignant Neoplasms; Malignant Tumor; Nanoscale Science; Nanotechnology; Ontology; Organ System, Cardiovascular; Outcome; Renal Transplantation; Renal Transplants; Research; Risk Factors; Series; Services; Shapes; Technology; Terminology; Time; TimeLine; Translational Research; Translational Research Enterprise; Translational Science; Transplant Recipients; Vascular, Heart; Work; base; biomedical computation; circulatory system; clinical data repository; clinical data warehouse; data repository; design; designing; driving; experiment; experimental research; experimental study; gene discovery; indexing; knowledge base; malignancy; nano particle; nano scale Science; nano tech; nano technology; nanoparticle; nanotech; neoplasm/cancer; network models; relational database; research study; technology development; translation research enterprise; transplant patient
Project start date: 2010-09-27
Project end date: 2015-07-31
Budget start date: 27-SEP-2010
Budget end date: 31-JUL-2011
PFA/PA: RFA-RM-09-002
2U54HG004028-06_8461 (2010): $279900
A Resource For Biomedical Ontologies And Knowledge Bases
Mark A Musen, Professor
Medicinestanford University
stanford, Ca 94305
Grant 3P41LM007885-05S1 from National Library Of Medicine IRG: BLR
Project start date: 2003-06-01
Project end date: 2010-06-30
3P41LM007885-05S1 (2007): $160000
SOFTWARE ARCHITECTURE FOR GUIDELINE DIRECTED THERAPY
Mark A Musen, Professor
Stanford University Stanford, Ca 94305
Grant 5R01LM005708-02 from National Library Of Medicine IRG: SRC
Project start date: 1995-04-01
Project end date: 1998-03-31
5R01LM005708-02 (1996): $479180