Literature DB >> 22081220

The National Center for Biomedical Ontology.

Mark A Musen1, Natalya F Noy, Nigam H Shah, Patricia L Whetzel, Christopher G Chute, Margaret-Anne Story, Barry Smith.   

Abstract

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data.

Mesh:

Year:  2011        PMID: 22081220      PMCID: PMC3277625          DOI: 10.1136/amiajnl-2011-000523

Source DB:  PubMed          Journal:  J Am Med Inform Assoc        ISSN: 1067-5027            Impact factor:   4.497


  19 in total

1.  The Unified Medical Language System (UMLS): integrating biomedical terminology.

Authors:  Olivier Bodenreider
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  OBO-Edit--an ontology editor for biologists.

Authors:  John Day-Richter; Midori A Harris; Melissa Haendel; Suzanna Lewis
Journal:  Bioinformatics       Date:  2007-06-01       Impact factor: 6.937

3.  An ontology-neutral framework for enrichment analysis.

Authors:  Rob Tirrell; Uday Evani; Ari E Berman; Sean D Mooney; Mark A Musen; Nigam H Shah
Journal:  AMIA Annu Symp Proc       Date:  2010-11-13

4.  The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies.

Authors:  Gautam K Parai; Clement Jonquet; Rong Xu; Mark A Musen; Nigam H Shah
Journal:  AMIA Annu Symp Proc       Date:  2010-11-13

5.  Leveraging biomedical ontologies and annotation services to organize microbiome data from Mammalian hosts.

Authors:  Indra Neil Sarkar
Journal:  AMIA Annu Symp Proc       Date:  2010-11-13

6.  The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research.

Authors:  Jessica D Tenenbaum; Patricia L Whetzel; Kent Anderson; Charles D Borromeo; Ivo D Dinov; Davera Gabriel; Beth Kirschner; Barbara Mirel; Tim Morris; Natasha Noy; Csongor Nyulas; David Rubenson; Paul R Saxman; Harpreet Singh; Nancy Whelan; Zach Wright; Brian D Athey; Michael J Becich; Geoffrey S Ginsburg; Mark A Musen; Kevin A Smith; Alice F Tarantal; Daniel L Rubin; Peter Lyster
Journal:  J Biomed Inform       Date:  2010-10-16       Impact factor: 6.317

7.  In silico functional profiling of human disease-associated and polymorphic amino acid substitutions.

Authors:  Matthew Mort; Uday S Evani; Vidhya G Krishnan; Kishore K Kamati; Peter H Baenziger; Angshuman Bagchi; Brandon J Peters; Rakesh Sathyesh; Biao Li; Yanan Sun; Bin Xue; Nigam H Shah; Maricel G Kann; David N Cooper; Predrag Radivojac; Sean D Mooney
Journal:  Hum Mutat       Date:  2010-03       Impact factor: 4.878

8.  BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Authors:  Patricia L Whetzel; Natalya F Noy; Nigam H Shah; Paul R Alexander; Csongor Nyulas; Tania Tudorache; Mark A Musen
Journal:  Nucleic Acids Res       Date:  2011-06-14       Impact factor: 16.971

9.  Comparison of concept recognizers for building the Open Biomedical Annotator.

Authors:  Nigam H Shah; Nipun Bhatia; Clement Jonquet; Daniel Rubin; Annie P Chiang; Mark A Musen
Journal:  BMC Bioinformatics       Date:  2009-09-17       Impact factor: 3.169

10.  Ontology quality assurance through analysis of term transformations.

Authors:  Karin Verspoor; Daniel Dvorkin; K Bretonnel Cohen; Lawrence Hunter
Journal:  Bioinformatics       Date:  2009-06-15       Impact factor: 6.937

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  66 in total

1.  National Centers for Biomedical Computing: from the BISTI report to the future.

Authors:  Jeremy M Berg
Journal:  J Am Med Inform Assoc       Date:  2012-01-18       Impact factor: 4.497

2.  Trends in biomedical informatics: automated topic analysis of JAMIA articles.

Authors:  Dong Han; Shuang Wang; Chao Jiang; Xiaoqian Jiang; Hyeon-Eui Kim; Jimeng Sun; Lucila Ohno-Machado
Journal:  J Am Med Inform Assoc       Date:  2015-11       Impact factor: 4.497

3.  Developing predictive molecular maps of human disease through community-based modeling.

Authors:  Jonathan M J Derry; Lara M Mangravite; Christine Suver; Matthew D Furia; David Henderson; Xavier Schildwachter; Brian Bot; Jonathan Izant; Solveig K Sieberts; Michael R Kellen; Stephen H Friend
Journal:  Nat Genet       Date:  2012-01-27       Impact factor: 38.330

4.  Scientific Reproducibility in Biomedical Research: Provenance Metadata Ontology for Semantic Annotation of Study Description.

Authors:  Satya S Sahoo; Joshua Valdez; Michael Rueschman
Journal:  AMIA Annu Symp Proc       Date:  2017-02-10

5.  The Ontology of Clinical Research (OCRe): an informatics foundation for the science of clinical research.

Authors:  Ida Sim; Samson W Tu; Simona Carini; Harold P Lehmann; Brad H Pollock; Mor Peleg; Knut M Wittkowski
Journal:  J Biomed Inform       Date:  2013-11-13       Impact factor: 6.317

6.  Mining Electronic Health Records to Extract Patient-Centered Outcomes Following Prostate Cancer Treatment.

Authors:  Tina Hernandez-Boussard; Panagiotis D Kourdis; Tina Seto; Michelle Ferrari; Douglas W Blayney; Daniel Rubin; James D Brooks
Journal:  AMIA Annu Symp Proc       Date:  2018-04-16

Review 7.  The ontology of craniofacial development and malformation for translational craniofacial research.

Authors:  J F Brinkley; C Borromeo; M Clarkson; T C Cox; M J Cunningham; L T Detwiler; C L Heike; H Hochheiser; J L V Mejino; R S Travillian; L G Shapiro
Journal:  Am J Med Genet C Semin Med Genet       Date:  2013-10-04       Impact factor: 3.908

8.  Speeding up Batch Alignment of Large Ontologies Using MapReduce.

Authors:  Uthayasanker Thayasivam; Prashant Doshi
Journal:  Proc IEEE Int Conf Semant Comput       Date:  2013-09

9.  BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration.

Authors:  Martin Ringwald; Chunlei Wu; Andrew I Su
Journal:  Mamm Genome       Date:  2012-07-31       Impact factor: 2.957

10.  A gene ontology inferred from molecular networks.

Authors:  Janusz Dutkowski; Michael Kramer; Michal A Surma; Rama Balakrishnan; J Michael Cherry; Nevan J Krogan; Trey Ideker
Journal:  Nat Biotechnol       Date:  2013-01       Impact factor: 54.908

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