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Title: The National Center for Biomedical Ontology: Advancing Biomedicinethrough Structured Organization of Scientific Knowledge

Abstract

The National Center for Biomedical Ontology(http://bioontology.org) is a consortium that comprises leadinginformaticians, biologists, clinicians, and ontologists funded by the NIHRoadmap to develop innovative technology and methods that allowscientists to record, manage, and disseminate biomedical information andknowledge in machine-processable form. The goals of the Center are: (1)to help unify the divergent and isolated efforts in ontology developmentby promoting high quality open-source, standards-based tools to create,manage, and use ontologies, (2) to create new software tools so thatscientists can use ontologies to annotate and analyze biomedical data,(3) to provide a national resource for the ongoing evaluation,integration, and evolution of biomedical ontologies and associated toolsand theories in the context of driving biomedical projects (DBPs), and(4) to disseminate the tools and resources of the Center and to identify,evaluate, and communicate best practices of ontology development to thebiomedical community. The Center is working toward these objectives byproviding tools to develop ontologies and to annotate experimental data,and by developing resources to integrate and relate existing ontologiesas well as by creating repositories of biomedical data that are annotatedusing those ontologies. The Center is providing training workshops inontology design, development, and usage, and is also pursuing research inontology evaluation, quality, and use of ontologies to promote scientificdiscovery. Through themore » research activities within the Center,collaborations with the DBPs, and interactions with the biomedicalcommunity, our goal is to help scientists to work more effectively in thee-science paradigm, enhancing experiment design, experiment execution,data analysis, information synthesis, hypothesis generation and testing,and understand human disease.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
Sponsoring Org.:
USDOE; National Institutes of Health. National Center forBiomedical Ontology Grant U54 HG004028
OSTI Identifier:
890687
Report Number(s):
LBNL-60314
R&D Project: L0324A; BnR: 600305000
DOE Contract Number:
DE-AC02-05CH11231; NIH1-U54-HG004028-01
Resource Type:
Journal Article
Resource Relation:
Journal Name: OMICS: A Journal of Integrative Biology; Journal Volume: 10; Journal Issue: 2; Related Information: Journal Publication Date: Summer 2006
Country of Publication:
United States
Language:
English
Subject:
59; 99; Biomedicine ontologies bioinformatics

Citation Formats

Rubin, Daniel L., Lewis, Suzanna E., Mungall, Chris J., Misra,Sima, Westerfield, Monte, Ashburner, Michael, Sim, Ida, Chute,Christopher G., Solbrig, Harold, Storey, Margaret-Anne, Smith, Barry, Day-Richter, John, Noy, Natalya F., and Musen, Mark A. The National Center for Biomedical Ontology: Advancing Biomedicinethrough Structured Organization of Scientific Knowledge. United States: N. p., 2006. Web. doi:10.1089/omi.2006.10.185.
Rubin, Daniel L., Lewis, Suzanna E., Mungall, Chris J., Misra,Sima, Westerfield, Monte, Ashburner, Michael, Sim, Ida, Chute,Christopher G., Solbrig, Harold, Storey, Margaret-Anne, Smith, Barry, Day-Richter, John, Noy, Natalya F., & Musen, Mark A. The National Center for Biomedical Ontology: Advancing Biomedicinethrough Structured Organization of Scientific Knowledge. United States. doi:10.1089/omi.2006.10.185.
Rubin, Daniel L., Lewis, Suzanna E., Mungall, Chris J., Misra,Sima, Westerfield, Monte, Ashburner, Michael, Sim, Ida, Chute,Christopher G., Solbrig, Harold, Storey, Margaret-Anne, Smith, Barry, Day-Richter, John, Noy, Natalya F., and Musen, Mark A. Mon . "The National Center for Biomedical Ontology: Advancing Biomedicinethrough Structured Organization of Scientific Knowledge". United States. doi:10.1089/omi.2006.10.185.
@article{osti_890687,
title = {The National Center for Biomedical Ontology: Advancing Biomedicinethrough Structured Organization of Scientific Knowledge},
author = {Rubin, Daniel L. and Lewis, Suzanna E. and Mungall, Chris J. and Misra,Sima and Westerfield, Monte and Ashburner, Michael and Sim, Ida and Chute,Christopher G. and Solbrig, Harold and Storey, Margaret-Anne and Smith, Barry and Day-Richter, John and Noy, Natalya F. and Musen, Mark A.},
abstractNote = {The National Center for Biomedical Ontology(http://bioontology.org) is a consortium that comprises leadinginformaticians, biologists, clinicians, and ontologists funded by the NIHRoadmap to develop innovative technology and methods that allowscientists to record, manage, and disseminate biomedical information andknowledge in machine-processable form. The goals of the Center are: (1)to help unify the divergent and isolated efforts in ontology developmentby promoting high quality open-source, standards-based tools to create,manage, and use ontologies, (2) to create new software tools so thatscientists can use ontologies to annotate and analyze biomedical data,(3) to provide a national resource for the ongoing evaluation,integration, and evolution of biomedical ontologies and associated toolsand theories in the context of driving biomedical projects (DBPs), and(4) to disseminate the tools and resources of the Center and to identify,evaluate, and communicate best practices of ontology development to thebiomedical community. The Center is working toward these objectives byproviding tools to develop ontologies and to annotate experimental data,and by developing resources to integrate and relate existing ontologiesas well as by creating repositories of biomedical data that are annotatedusing those ontologies. The Center is providing training workshops inontology design, development, and usage, and is also pursuing research inontology evaluation, quality, and use of ontologies to promote scientificdiscovery. Through the research activities within the Center,collaborations with the DBPs, and interactions with the biomedicalcommunity, our goal is to help scientists to work more effectively in thee-science paradigm, enhancing experiment design, experiment execution,data analysis, information synthesis, hypothesis generation and testing,and understand human disease.},
doi = {10.1089/omi.2006.10.185},
journal = {OMICS: A Journal of Integrative Biology},
number = 2,
volume = 10,
place = {United States},
year = {Mon Jan 23 00:00:00 EST 2006},
month = {Mon Jan 23 00:00:00 EST 2006}
}
  • The National Center for Biomedical Ontology (http://bioontology.org) is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists funded by the NIH Roadmap to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are: (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource formore » the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. The Center is working toward these objectives by providing tools to develop ontologies and to annotate experimental data, and by developing resources to integrate and relate existing ontologies as well as by creating repositories of biomedical data that are annotated using those ontologies. The Center is providing training workshops in ontology design, development, and usage, and is also pursuing research in ontology evaluation, quality, and use of ontologies to promote scientific discovery. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease.« less
  • The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of human disease. DO is a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology. The content of DO has had 192 revisions since 2012, including the addition of 760 terms. Thirty-two percent of all terms now include definitions. DO has expanded the number and diversity of research communities and community members by 50+ during the past two years.more » These community members actively submit term requests, coordinate biomedical resource disease representation and provide expert curation guidance. Since the DO 2012 NAR paper, there have been hundreds of term requests and a steady increase in the number of DO listserv members, twitter followers and DO website usage. DO is moving to a multi-editor model utilizing Protégé to curate DO in web ontology language. In conclusion, this will enable closer collaboration with the Human Phenotype Ontology, EBI's Ontology Working Group, Mouse Genome Informatics and the Monarch Initiative among others, and enhance DO's current asserted view and multiple inferred views through reasoning.« less
  • National Energy Research Scientific Computing Center (NERSC) provides researchers with high-performance computing tools to tackle science`s biggest and most challenging problems. Founded in 1974 by DOE/ER, the Controlled Thermonuclear Research Computer Center was the first unclassified supercomputer center and was the model for those that followed. Over the years the center`s name was changed to the National Magnetic Fusion Energy Computer Center and then to NERSC; it was relocated to LBNL. NERSC, one of the largest unclassified scientific computing resources in the world, is the principal provider of general-purpose computing services to DOE/ER programs: Magnetic Fusion Energy, High Energy andmore » Nuclear Physics, Basic Energy Sciences, Health and Environmental Research, and the Office of Computational and Technology Research. NERSC users are a diverse community located throughout US and in several foreign countries. This brochure describes: the NERSC advantage, its computational resources and services, future technologies, scientific resources, and computational science of scale (interdisciplinary research over a decade or longer; examples: combustion in engines, waste management chemistry, global climate change modeling).« less