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Barry Smith

Research Profile

Concepts & Ideas

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United States

Procedures

Biomedical Research

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Publications

TOP 3
Mark A Musen; Natalya F Noy; Nigam Shah; Barry Smith; Margaret-Anne Story; Patricia L Whetzel; Christopher G Chute
The National Center for Biomedical Ontology.
Barry Smith; Richard H Scheuermann
Ontologies for clinical and translational research: Introduction.
Carol Bult; Peter D'Eustachio; Harold Drabkin; Alexei Evsikov; Darren A Natale; Natalia Roberts; Alan Ruttenberg; Barry Smith; Cecilia N Arighi; Judith A Blake; Cathy Wu
The representation of protein complexes in the Protein Ontology (PRO).

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All Publications

2012: Mark A Musen; Natalya F Noy; Nigam Shah; Barry Smith; Margaret-Anne Story; Patricia L Whetzel; Christopher G Chute
The National Center for Biomedical Ontology.
Journal of the American Medical Informatics Association : JAMIA 2012;19(2):190-5.
2011: Barry Smith; Richard H Scheuermann
Ontologies for clinical and translational research: Introduction.
Journal of biomedical informatics 2011;44(1):3-7.
2011: Carol Bult; Peter D'Eustachio; Harold Drabkin; Alexei Evsikov; Darren A Natale; Natalia Roberts; Alan Ruttenberg; Barry Smith; Cecilia N Arighi; Judith A Blake; Cathy Wu
The representation of protein complexes in the Protein Ontology (PRO).
BMC bioinformatics 2011;12():371.
2011: Darren A Natale; Cecilia N Arighi; Winona C Barker; Judith A Blake; Carol Bult; Michael Caudy; Harold J Drabkin; Peter D'Eustachio; Alexei V Evsikov; Hongzhan Huang; Jules Nchoutmboube; Natalia V Roberts; Barry Smith; Jian Zhang; Cathy H Wu
The Protein Ontology: a structured representation of protein forms and complexes.
Nucleic acids research 2011;39(Database issue):D539-45.
2010: werner ceusters; Barry Smith
A unified framework for biomedical terminologies and ontologies.
Studies in health technology and informatics 2010;160(Pt 2):1050-4.
2010: Barry Smith; M Brochhausen
Putting biomedical ontologies to work.
Methods of information in medicine 2010;49(2):135-40.
2009: David Koepsell; Barry Smith
Dealing with socially constructed concepts in an ontology.
Journal of empirical research on human research ethics : JERHRE 2009;4(2):75-6.
2009: David Koepsell; Robert Arp; Jennifer Fostel; Barry Smith
Creating a controlled vocabulary for the ethics of human research: towards a biomedical ethics ontology.
Journal of empirical research on human research ethics : JERHRE 2009;4(1):43-58.
2009: Cecilia N Arighi; Hongfang Liu; Darren A Natale; Winona C Barker; Harold Drabkin; Judith A Blake; Barry Smith; Cathy H Wu
TGF-beta signaling proteins and the Protein Ontology.
BMC bioinformatics 2009;10 Suppl 5():S3.
2009: Daniel Schober; Barry Smith; Suzanna E Lewis; Waclaw Kusnierczyk; Jane Lomax; Chris Mungall; Chris F Taylor; Philippe Rocca-Serra; Susanna-Assunta Sansone
Survey-based naming conventions for use in OBO Foundry ontology development.
BMC bioinformatics 2009;10():125.
2009: Anna Maria Masci; Cecilia N Arighi; Alexander Diehl; Anne E Lieberman; Chris Mungall; Richard Scheuermann; Barry Smith; Lindsay G Cowell
An improved ontological representation of dendritic cells as a paradigm for all cell types.
BMC bioinformatics 2009;10():70.
2008: Christopher Taylor; Dawn Field; Susanna-Assunta Sansone; Jan Aerts; Rolf Apweiler; Michael Ashburner; Catherine A Ball; Pierre-Alain Binz; Molly Bogue; Tim Booth; Alvis Brazma; Ryan R Brinkman; Adam Michael Clark; Eric W Deutsch; Oliver Fiehn; Jennifer Fostel; Peter Ghazal; Frank Gibson; Tanya Gray; Graeme Grimes; John M Hancock; Nigel W Hardy; Henning Hermjakob; Randall K Julian; Matthew Kane; Carsten Kettner; Christopher Kinsinger; Eugene Kolker; Martin Kuiper; Nicolas Le Novère; Jim Leebens-Mack; Suzanna E Lewis; Phillip Lord; Ann-Marie Mallon; Nishanth Marthandan; Hiroshi Masuya; ruth mcnally; Alexander Mehrle; Norman Morrison; Sandra Orchard; John Quackenbush; James Reecy; Donald G Robertson; Philippe Rocca-Serra; Henry Rodriguez; Heiko Rosenfelder; Javier Santoyo-Lopez; Richard Scheuermann; Daniel Schober; Barry Smith; Jason Snape; Christian J Stoeckert; Keith Tipton; Peter Sterk; Andreas Untergasser; Jo Vandesompele; Stefan Wiemann
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
Nature biotechnology 2008;26(8):889-96.
2008: Robert Arp; Barry Smith
Ontologies of cellular networks.
Science signaling 2008;1(50):mr2.
2008: David P Hill; Barry Smith; Monica S McAndrews-Hill; Judith A Blake
Gene Ontology annotations: what they mean and where they come from.
BMC bioinformatics 2008;9 Suppl 5():S2.
2008: Barry Smith; Mathias Brochhausen
Establishing and harmonizing ontologies in an interdisciplinary health care clinical research environment.
Studies in health technology and informatics 2008;134():219-33.
2007: werner ceusters; Peter Elkin; Barry Smith
Negative findings in electronic health records and biomedical ontologies: a realist approach.
International journal of medical informatics 2007;76 Suppl 3():S326-33.
2007: Barry Smith; Michael Ashburner; Cornelius Rosse; Jonathan Bard; William Bug; werner ceusters; Louis J Goldberg; Karen Eilbeck; Amelia Ireland; Chris Mungall; Neocles Leontis; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; Richard Scheuermann; Nigam Shah; Patricia L Whetzel; Suzanna Lewis
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.
Nature biotechnology 2007;25(11):1251-5.
2007: Olivier Bodenreider; Barry Smith; Anand Kumar; Anita Burgun
Investigating subsumption in SNOMED CT: an exploration into large description logic-based biomedical terminologies.
Artificial intelligence in medicine 2007;39(3):183-95.
2007: Lee Sam; Tara Borlawsky; Ying Tao; Jianrong Li; Carol Friedman; Barry Smith; Yves lussier
Information-theoretic classification of SNOMED improves the organization of context-sensitive excerpts from Cochrane reviews.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2007;():1100.
2007: Ron Rudnicki; werner ceusters; Shahid Manzoor; Barry Smith
What particulars are referred to in Electronic Health Record data? A case study in integrating Referent Tracking into an EHR application.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2007;():630-4.
2007: Werner M Ceusters; Kent A Spackman; Barry Smith
Would SNOMED CT benefit from realism-based ontology evolution?
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2007;():105-9.
2007: Darren A Natale; Cecilia N Arighi; Winona C Barker; Judith Blake; Ti-Cheng Chang; Zhangzhi Hu; Hongfang Liu; Barry Smith; Cathy H Wu
Framework for a protein ontology.
BMC bioinformatics 2007;8 Suppl 9():S1.
2007: Thaddeus H Grasela; Jill Fiedler-Kelly; Brenda B Cirincione; Darcy Hitchcock; Kathleen Reitz; Susanne Sardella; Barry Smith
Informatics: the fuel for pharmacometric analysis.
The AAPS journal 2007;9(1):E84-91.
2006: Anand Kumar; Yum Yip; Barry Smith; Pierre Grenon
Bridging the gap between medical and bioinformatics: an ontological case study in colon carcinoma.
Computers in biology and medicine 2006;36(7-8):694-711.
2006: Christiane Fellbaum; Udo Hahn; Barry Smith
Towards new information resources for public health--from WordNet to MedicalWordNet.
Journal of biomedical informatics 2006;39(3):321-32.
2006: Barry Smith
From concepts to clinical reality: an essay on the benchmarking of biomedical terminologies.
Journal of biomedical informatics 2006;39(3):288-98.
2006: werner ceusters; Barry Smith
Strategies for referent tracking in electronic health records.
Journal of biomedical informatics 2006;39(3):362-78.
2006: Jonathan Simon; Mariana Dos Santos; James Fielding; Barry Smith
Formal ontology for natural language processing and the integration of biomedical databases.
International journal of medical informatics 2006;75(3-4):224-31.
2006: werner ceusters; Barry Smith
A realism-based approach to the evolution of biomedical ontologies.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2006;():121-5.
2006: werner ceusters; Peter Elkin; Barry Smith
Referent tracking: the problem of negative findings.
Studies in health technology and informatics 2006;124():741-6.
2006: Barry Smith; werner ceusters
HL7 RIM: an incoherent standard.
Studies in health technology and informatics 2006;124():133-8.
2006: Patricia L Whetzel; Ryan R Brinkman; Helen C Causton; Liju Fan; Dawn Field; Jennifer Fostel; Gilberto Fragoso; Tanya Gray; Mervi Heiskanen; Tina Hernandez-Boussard; Norman Morrison; Helen Parkinson; Philippe Rocca-Serra; Susanna-Assunta Sansone; Daniel Schober; Barry Smith; Robert Stevens; Christian J Stoeckert; Chris Taylor; Joe White; Andrew Wood
Development of FuGO: an ontology for functional genomics investigations.
Omics : a journal of integrative biology 2006;10(2):199-204.
2006: Daniel L Rubin; Suzanna E Lewis; Chris Mungall; Sima Misra; Monte Westerfield; Michael Ashburner; Ida Sim; Christopher G Chute; Harold Solbrig; Margaret-Anne Storey; Barry Smith; John Day-Richter; Natalya F Noy; Mark Musen
National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge.
Omics : a journal of integrative biology 2006;10(2):185-98.
2006: Jacob Köhler; Katherine Munn; Alexander Rüegg; Andre Skusa; Barry Smith
Quality control for terms and definitions in ontologies and taxonomies.
BMC bioinformatics 2006;7():212.
2006: Anand Kumar; Barry Smith; Domenico Pisanelli; Aldo Gangemi; Mario Stefanelli
Clinical guidelines as plans--an ontological theory.
Methods of information in medicine 2006;45(2):204-10.
2006: Mark Musen; Suzanna Lewis; Barry Smith
Wrestling with SUMO and bio-ontologies.
Nature biotechnology 2006;24(1):21; author reply 23.
2005: Barry Smith; Anand Kumar; werner ceusters; Cornelius Rosse
On carcinomas and other pathological entities.
Comparative and functional genomics 2005;6(7-8):379-87.
2005: Barry Smith; werner ceusters
An ontology-based methodology for the migration of biomedical terminologies to electronic health records.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2005;():704-8.
2005: Stefan Schulz; Philipp Daumke; Barry Smith; Udo Hahn
How to distinguish parthood from location in bioontologies.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2005;():669-73.
2005: Cornelius Rosse; Anand Kumar; José L V Mejino; Daniel L Cook; Landon T Detwiler; Barry Smith
A strategy for improving and integrating biomedical ontologies.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2005;():639-43.
2005: werner ceusters; Barry Smith; L Goldberg
A terminological and ontological analysis of the NCI Thesaurus.
Methods of information in medicine 2005;44(4):498-507.
2005: Ingvar Johansson; Barry Smith; Katherine Munn; Nikoloz Tsikolia; Kathleen Elsner; Dominikus Ernst; Dirk Siebert
Functional anatomy: a taxonomic proposal.
Acta biotheoretica 2005;53(3):153-66.
2005: Louis J Goldberg; werner ceusters; John Eisner; Barry Smith
The Significance of SNODENT.
Studies in health technology and informatics 2005;116():737-42.
2005: Barry Smith; werner ceusters; Rita Temmerman
Wüsteria.
Studies in health technology and informatics 2005;116():647-52.
2005: Anand Kumar; Yum Yip; Barry Smith; Dirk Marwede; Daniel Novotny
An ontology for carcinoma classification for clinical bioinformatics.
Studies in health technology and informatics 2005;116():635-40.
2005: werner ceusters; Barry Smith
Tracking referents in electronic health records.
Studies in health technology and informatics 2005;116():71-6.
2005: Barry Smith; werner ceusters; Bert Klagges; Jacob Köhler; Anand Kumar; Jane Lomax; Chris Mungall; Fabian Neuhaus; Alan L Rector; Cornelius Rosse
Relations in biomedical ontologies.
Genome biology 2005;6(5):R46.
2004: Anand Kumar; Barry Smith; Daniel D Novotny
Biomedical informatics and granularity.
Comparative and functional genomics 2004;5(6-7):501-8.
2004: werner ceusters; Barry Smith; Anand Kumar; Christoffel Dhaen
Mistakes in medical ontologies: where do they come from and how can they be detected?
Studies in health technology and informatics 2004;102():145-63.
2004: Anand Kumar; Barry Smith; Domenico Pisanelli; Aldo Gangemi; Mario Stefanelli
An ontological framework for the implementation of clinical guidelines in health care organizations.
Studies in health technology and informatics 2004;102():95-107.
2004: Anand Kumar; Paolo Ciccarese; Barry Smith; Matteo Piazza
Context-based task ontologies for clinical guidelines.
Studies in health technology and informatics 2004;102():81-94.
2004: Barry Smith; Katherine Munn; Igor Papakin
Bodily systems and the spatial-functional structure of the human body.
Studies in health technology and informatics 2004;102():39-63.
2004: Pierre Grenon; Barry Smith; Louis Goldberg
Biodynamic ontology: applying BFO in the biomedical domain.
Studies in health technology and informatics 2004;102():20-38.
2004: werner ceusters; Barry Smith; Anand Kumar; Christoffel Dhaen
Ontology-based error detection in SNOMED-CT.
Studies in health technology and informatics 2004;107(Pt 1):482-6.
2004: Barry Smith; Cornelius Rosse
The role of foundational relations in the alignment of biomedical ontologies.
Studies in health technology and informatics 2004;107(Pt 1):444-8.
2003: Barry Smith; Berit Brogaard
Sixteen days.
The Journal of medicine and philosophy 2003;28(1):45-78.
2003: Barry Smith; Jennifer Williams; Steffen Schulze-Kremer
The ontology of the gene ontology.
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2003;():609-13.
2003: werner ceusters; Ignace Desimpel; Barry Smith; Stefan Schulz
Using cross-lingual information to cope with underspecification in formal ontologies.
Studies in health technology and informatics 2003;95():391-6.

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