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Martin J. O'Connor
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2020 – today
- 2023
- [i6]Martin J. O'Connor, Marcos Martínez Romero, Mete Ugur Akdogan, Josef Hardi, Mark A. Musen:
A Comprehensive Approach to Ensuring Quality in Spreadsheet-Based Metadata. CoRR abs/2312.09107 (2023) - 2022
- [i5]Mark A. Musen, Martin J. O'Connor, Erik Schultes, Marcos Martínez Romero, Josef Hardi, John Graybeal:
Modeling community standards for metadata as templates makes data FAIR. CoRR abs/2208.02836 (2022)
2010 – 2019
- 2019
- [j15]Marcos Martínez Romero
, Martin J. O'Connor
, Attila L. Egyedi
, Debra Willrett
, Josef Hardi
, John Graybeal
, Mark A. Musen
:
Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases. Database J. Biol. Databases Curation 2019: baz059 (2019) - [c68]Martin J. O'Connor, Denise B. Warzel, Marcos Martínez Romero, Josef Hardi, Debra Willrett, Aras Efekhari, John Graybeal, Mark A. Musen:
Unleashing the value of Common Data Elements through the CEDAR Workbench. AMIA 2019 - [i4]Marcos Martínez Romero, Martin J. O'Connor, Attila L. Egyedi, Debra Willrett, Josef Hardi, John Graybeal, Mark A. Musen:
Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases. CoRR abs/1903.09270 (2019) - [i3]Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez Romero, Attila L. Egyedi, Debra Willrett, John Graybeal, Mark A. Musen:
The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. CoRR abs/1905.06480 (2019) - 2018
- [j14]Syed Ahmad Chan Bukhari
, Marcos Martínez Romero
, Martin J. O'Connor, Attila L. Egyedi
, Debra Willrett, John Graybeal
, Mark A. Musen, Kei-Hoi Cheung, Steven H. Kleinstein:
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. BMC Bioinform. 19(1): 268:1-268:6 (2018) - [c67]Rafael S. Gonçalves, Csongor I. Nyulas, Marcos Martínez Romero, Martin J. O'Connor, John Graybeal, Mark A. Musen:
Using Ontologies to Drive the Creation of High-Quality Metadata in CEDAR. ISWC (P&D/Industry/BlueSky) 2018 - [c66]Attila L. Egyedi, Martin J. O'Connor, Marcos Martínez Romero, Debra Willrett, Josef Hardi, John Graybeal, Mark A. Musen:
Using semantic technologies to enhance metadata submissions to public repositories in biomedicine. SWAT4LS 2018 - 2017
- [j13]Marcos Martínez Romero
, Clément Jonquet, Martin J. O'Connor, John Graybeal
, Alejandro Pazos
, Mark A. Musen
:
NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. J. Biomed. Semant. 8(1): 21:1-21:22 (2017) - [c65]Marcos Martínez Romero, Martin J. O'Connor, Ravi D. Shankar, Maryam Panahiazar, Debra Willrett, Attila Levente Egyedi, Olivier Gevaert, John Graybeal, Mark A. Musen:
Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. AMIA 2017 - [c64]Marcos Martínez Romero, Martin J. O'Connor, Michael Dorf, Jennifer Vendetti, Debra Willrett, Attila L. Egyedi, John Graybeal, Mark A. Musen:
Supporting Ontology-Based Standardization of Biomedical Metadata in the CEDAR Workbench. ICBO 2017 - [c63]Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez Romero, John Graybeal, Mark A. Musen:
Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies. SemSci@ISWC 2017: 39-46 - [c62]Rafael S. Gonçalves
, Martin J. O'Connor, Marcos Martínez Romero
, Attila L. Egyedi
, Debra Willrett, John Graybeal
, Mark A. Musen
:
The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. ISWC (2) 2017: 103-110 - [c61]Attila L. Egyedi, Martin J. O'Connor, Marcos Martínez Romero, Debra Willrett, Josef Hardi, John Graybeal, Mark A. Musen:
Embracing Semantic Technology for Better Metadata Authoring in Biomedicine. SWAT4LS 2017 - [i2]Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez Romero, John Graybeal, Mark A. Musen:
Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies. CoRR abs/1708.01286 (2017) - 2016
- [c60]Mark A. Musen, Martin J. O'Connor, Marcos Martínez Romero, Attila Levente Egyedi, Debra Willrett, John Graybeal:
CEDAR: Better Data Sharing Through the Authoring of Better Metadata. AMIA 2016 - [c59]Martin J. O'Connor, Marcos Martínez Romero, Attila L. Egyedi, Debra Willrett, John Graybeal
, Mark A. Musen
:
An Open Repository Model for Acquiring Knowledge About Scientific Experiments. EKAW 2016: 762-777 - [i1]Marcos Martínez Romero, Clément Jonquet, Martin J. O'Connor, John Graybeal, Alejandro Pazos, Mark A. Musen:
NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation. CoRR abs/1611.05973 (2016) - 2015
- [j12]Mark A. Musen
, Carol A. Bean, Kei-Hoi Cheung, Michel Dumontier
, Kim A. Durante, Olivier Gevaert
, Alejandra N. González-Beltrán, Purvesh Khatri
, Steven H. Kleinstein, Martin J. O'Connor, Yannick Pouliot, Philippe Rocca-Serra, Susanna-Assunta Sansone
, Jeffrey A. Wiser:
The center for expanded data annotation and retrieval. J. Am. Medical Informatics Assoc. 22(6): 1148-1152 (2015) - 2014
- [j11]Saeed Hassanpour, Martin J. O'Connor, Amar K. Das:
Clustering rule bases using ontology-based similarity measures. J. Web Semant. 25: 1-8 (2014) - 2013
- [j10]Saeed Hassanpour, Martin J. O'Connor, Amar K. Das:
A semantic-based method for extracting concept definitions from scientific publications: evaluation in the autism phenotype domain. J. Biomed. Semant. 4: 14 (2013) - 2012
- [j9]Christophe Gravier, Jacques Fayolle, Jérémy Lardon, Martin J. O'Connor:
Adaptive System for Collaborative Online Laboratories. IEEE Intell. Syst. 27(4): 11-17 (2012) - [c58]João Paulo Orlando, Adriano Rivolli, Saeed Hassanpour, Martin J. O'Connor, Amar K. Das, Dilvan A. Moreira:
SWRL Rule Editor - A Web Application as Rich as Desktop Business Rule Editors. ICEIS (2) 2012: 258-263 - [c57]Martin J. O'Connor, Amar K. Das:
A Pair of OWL 2 RL Reasoners. OWLED 2012 - 2011
- [j8]Philippe Rocca-Serra, Alan Ruttenberg
, Martin J. O'Connor, Patricia L. Whetzel, Daniel Schober
, Jay Greenbaum, Mélanie Courtot
, Ryan Remy Brinkman, Susanna-Assunta Sansone, Richard H. Scheuermann
, Bjoern Peters:
Overcoming the ontology enrichment bottleneck with Quick Term Templates. Appl. Ontology 6(1): 13-22 (2011) - [c56]Martin J. O'Connor, Genaro Hernández, Amar K. Das:
A Rule-Based Method for Specifying and Querying Temporal Abstractions. AIME 2011: 255-259 - [c55]Amanda Richards, Martin J. O'Connor, Susana B. Martins, Michael Uehara-Bingen, Samson W. Tu, Amar K. Das:
Web-Based Querying and Temporal Visualization of Longitudinal Clinical Data. AIME 2011: 260-264 - [c54]Martin J. O'Connor, Amar K. Das:
Acquiring OWL ontologies from XML documents. K-CAP 2011: 17-24 - [c53]Saeed Hassanpour, Martin J. O'Connor, Amar K. Das:
A Framework for the Automatic Extraction of Rules from Online Text. RuleML Europe 2011: 266-280 - [c52]Martin J. O'Connor, Amanda Richards, Susana B. Martins, Mike Bingen, Samson W. Tu, Amar K. Das:
SWEETInfo: a Web-Based System for Visualizing and Querying Temporal Data. RuleML America (2) 2011 - [c51]Martin J. O'Connor, Mike Bingen, Amanda Richards, Samson W. Tu, Amar K. Das:
Web-based Exploration of Temporal Data in Biomedicine. WEBIST 2011: 352-359 - [c50]Tomasz Wiktor Wlodarczyk, Chunming Rong
, Martin J. O'Connor, Mark A. Musen
:
SWRL-F: a fuzzy logic extension of the semantic web rule language. WIMS 2011: 39 - 2010
- [c49]Martin J. O'Connor, Amar K. Das:
A Lightweight Model for Representing and Reasoning with Temporal Information in Biomedical Ontologies. HEALTHINF 2010: 90-97 - [c48]Martin J. O'Connor, Amar K. Das:
A Method for Representing and Querying Temporal Information in OWL. BIOSTEC (Selected Papers) 2010: 97-110 - [c47]Saeed Hassanpour, Martin J. O'Connor, Amar K. Das:
A Software Tool for Visualizing, Managing and Eliciting SWRL Rules. ESWC (2) 2010: 381-385 - [c46]Martin J. O'Connor, Amar K. Das:
Semantic Reasoning with XML-based Biomedical Information Models. MedInfo 2010: 986-990 - [c45]Martin J. O'Connor, Christian Halaschek-Wiener, Mark A. Musen:
M2: A Language for Mapping Spreadsheets to OWL. OWLED 2010 - [c44]Saeed Hassanpour, Martin J. O'Connor, Amar K. Das:
Visualizing Logical Dependencies in SWRL Rule Bases. RuleML 2010: 259-272 - [c43]Tomasz Wiktor Wlodarczyk, Martin J. O'Connor, Chunming Rong, Mark A. Musen:
SWRL-F - A Fuzzy Logic Extension of the Semantic Web Rule Language. URSW 2010: 97-100 - [c42]Martin J. O'Connor, Christian Halaschek-Wiener, Mark A. Musen
:
Mapping Master: A Flexible Approach for Mapping Spreadsheets to OWL. ISWC (2) 2010: 194-208
2000 – 2009
- 2009
- [j7]Martin J. O'Connor, Csongor Nyulas, Samson W. Tu, David L. Buckeridge, Anna Okhmatovskaia, Mark A. Musen
:
Software-engineering challenges of building and deploying reusable problem solvers. Artif. Intell. Eng. Des. Anal. Manuf. 23(4): 339-356 (2009) - [j6]Martin J. O'Connor, Ravi D. Shankar, David B. Parrish, Amar K. Das:
Knowledge-data integration for temporal reasoning in a clinical trial system. Int. J. Medical Informatics 78(Supplement-1): S77-S85 (2009) - [c41]Masoumeh T. Izadi, David L. Buckeridge, Anna Okhmatovskaia, Samson W. Tu, Martin J. O'Connor, Csongor Nyulas, Mark A. Musen:
A Bayesian Network Model for Analysis of Detection Performance in Surveillance Systems. AMIA 2009 - [c40]Mia A. Levy, Martin J. O'Connor, Daniel L. Rubin:
Semantic Reasoning with Image Annotations for Tumor Assessment. AMIA 2009 - [c39]Saeed Hassanpour, Martin J. O'Connor, Amar K. Das:
Exploration of SWRL Rule Bases through Visualization, Paraphrasing, and Categorization of Rules. RuleML 2009: 246-261 - [c38]Saeed Hassanpour, Martin J. O'Connor, Amar K. Das:
A Rule Management and Elicitation Tool for SWRL Rule Bases. RuleML Challenge 2009 - [c37]Saeed Hassanpour, Martin J. O'Connor, Amar K. Das:
Axiomé: A Tool for the Elicitation and Management of SWRL Rules. OWLED 2009 - [c36]Martin J. O'Connor, Amar K. Das:
SQWRL: A Query Language for OWL. OWLED 2009 - 2008
- [j5]David L. Buckeridge, Anna Okhmatovskaia, Samson W. Tu, Martin J. O'Connor, Csongor Nyulas, Mark A. Musen
:
Model Formulation: Understanding Detection Performance in Public Health Surveillance: Modeling Aberrancy-detection Algorithms. J. Am. Medical Informatics Assoc. 15(6): 760-769 (2008) - [c35]Martin J. O'Connor, Ravi D. Shankar, Csongor Nyulas, Samson W. Tu, Amar K. Das:
Developing a Web-Based Application using OWL and SWRL. AAAI Spring Symposium: AI Meets Business Rules and Process Management 2008: 93-98 - [c34]Ravi D. Shankar, Martin J. O'Connor, David B. Parrish, Amar K. Das:
Semantic Integration of Software Systems in Translational Clinical Trials. AAAI Spring Symposium: Semantic Scientific Knowledge Integration 2008: 105-108 - [c33]David L. Buckeridge, Anna Okhmatovskaia, Samson W. Tu, Martin J. O'Connor, Csongor Nyulas, Mark A. Musen:
Predicting Outbreak Detection in Public Health Surveillance: Quantitative Analysis to Enable Evidence-Based Method Selection. AMIA 2008 - [c32]Samson W. Tu, Lakshika Tennakoon, Martin J. O'Connor, Ravi D. Shankar, Amar K. Das:
Using an Integrated Ontology and Information Model for Querying and Reasoning about Phenotypes: The Case of Autism. AMIA 2008 - [c31]Ravi D. Shankar, Susana B. Martins, Martin J. O'Connor, Amar K. Das:
An Ontological Approach to Representing and Reasoning with Temporal Constraints in Clinical Trial Protocols. HEALTHINF (1) 2008: 87-93 - [c30]Ravi D. Shankar, Susana B. Martins, Martin J. O'Connor, David B. Parrish, Amar K. Das:
Representing and Reasoning with Temporal Constraints in Clinical Trials Using Semantic Technologies. BIOSTEC (Selected Papers) 2008: 520-530 - [c29]Csongor Nyulas, Martin J. O'Connor, Samson W. Tu, David L. Buckeridge, Anna Okhmatovskaia, Mark A. Musen
:
An Ontology-Driven Framework for Deploying JADE Agent Systems. IAT 2008: 573-577 - [c28]Martin J. O'Connor, Ravi D. Shankar, Mark A. Musen, Amar K. Das, Csongor Nyulas:
The SWRLAPI: A Development Environment for Working with SWRL Rules. OWLED 2008 - 2007
- [c27]Martin J. O'Connor, Ravi D. Shankar, Samson W. Tu, Csongor Nyulas, Dave Parrish, Mark A. Musen, Amar K. Das:
Using Semantic Web Technologies for Knowledge-Driven Querying of Biomedical Data. AIME 2007: 267-276 - [c26]Rashmi Raj, Martin J. O'Connor, Amar K. Das:
An Ontology-Driven Method for Hierarchical Mining of Temporal Patterns: Application to HIV Drug Resistance Research. AMIA 2007 - [c25]Ravi D. Shankar, Susana B. Martins, Martin J. O'Connor, David B. Parrish, Amar K. Das:
An Ontology-based Architecture for Integration of Clinical Trials Management Applications. AMIA 2007 - [c24]Martin J. O'Connor, Ravi D. Shankar, David B. Parrish, Amar K. Das:
Knowledge-Level Querying of Temporal Patterns in Clinical Research Systems. MedInfo 2007: 311-315 - [c23]Martin J. O'Connor, Ravi D. Shankar, Samson W. Tu, Csongor Nyulas, Amar K. Das, Mark A. Musen:
Efficiently Querying Relational Databases Using OWL and SWRL. RR 2007: 361-363 - [c22]Martin J. O'Connor, Samson W. Tu, Csongor Nyulas, Amar K. Das, Mark A. Musen:
Querying the Semantic Web with SWRL. RuleML 2007: 155-159 - 2006
- [c21]Vijay P. Chauhan, Martin J. O'Connor, Amar K. Das:
A Dynamic Distributed Architecture for Temporal Data Abstraction. AMIA 2006 - [c20]Preetha S. Narayanan, Martin J. O'Connor, Amar K. Das:
Ontology-Driven Mapping of Temporal Data in Biomedical Databases. AMIA 2006 - [c19]Martin J. O'Connor, Ravi D. Shankar, Amar K. Das:
An Ontology-Driven Mediator for Querying Time-Oriented Biomedical Data. CBMS 2006: 264-269 - [c18]Ravi D. Shankar, Susana B. Martins, Martin J. O'Connor, David B. Parrish, Amar K. Das:
Knowledge-Based System for Managing Complex Clinical Trials. CBMS 2006: 270-278 - [c17]Ravi D. Shankar, Susana B. Martins, Martin J. O'Connor, David B. Parrish, Amar K. Das:
Epoch: an ontological framework to support clinical trials management. HIKM 2006: 25-32 - [c16]Ravi D. Shankar, Susana B. Martins, Martin J. O'Connor, David B. Parrish, Amar K. Das:
Towards Semantic Interoperability in a Clinical Trials Management System. ISWC 2006: 901-912 - 2005
- [j4]Monica Crubézy
, Martin J. O'Connor, David L. Buckeridge, Zachary Pincus, Mark A. Musen
:
Ontology-Centered Syndromic Surveillance for Bioterrorism. IEEE Intell. Syst. 20(5): 26-35 (2005) - [c15]Mark A. Musen, Monica Crubézy, Martin J. O'Connor, David L. Buckeridge:
Knowledge-Based Syndromic Surveillance for Bioterrorism. AAAI Spring Symposium: AI Technologies for Homeland Security 2005: 86-90 - [c14]Mohammed I. Rafiq, Martin J. O'Connor, Amar K. Das:
Computational Method for Temporal Pattern Discovery in Biomedical Genomic Databases. CSB 2005: 362-365 - [c13]Martin J. O'Connor, Holger Knublauch, Samson W. Tu, Benjamin N. Grosof, Mike Dean, William E. Grosso, Mark A. Musen
:
Supporting Rule System Interoperability on the Semantic Web with SWRL. ISWC 2005: 974-986 - 2004
- [j3]Mary K. Goldstein, Robert W. Coleman, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Mark A. Musen
, Susana B. Martins, Philip W. Lavori, Michael G. Shlipak, Eugene Oddone, Aneel A. Advani, Parisa Gholami, Brian B. Hoffman:
Application of Information Technology: Translating Research into Practice: Organizational Issues in Implementing Automated Decision Support for Hypertension in Three Medical Centers. J. Am. Medical Informatics Assoc. 11(5): 368-376 (2004) - [c12]David L. Buckeridge, Martin J. O'Connor, Haobo Xu, Mark A. Musen:
A Knowledge-Based Framework for Deploying Surveillance Problem Solvers. IKE 2004: 28-32 - 2003
- [c11]Martin J. O'Connor, David L. Buckeridge, Michael Choy, Monica Crubézy, Zachary Pincus, Mark A. Musen:
BioSTORM: A System for Automated Surveillance of Diverse Data Sources. AMIA 2003 - 2002
- [j2]Mary K. Goldstein, Brian B. Hoffman, Robert W. Coleman, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Susana B. Martins, Aneel A. Advani, Mark A. Musen
:
Patient Safety in Guideline-Based Decision Support for Hypertension Management: ATHENA DSS. J. Am. Medical Informatics Assoc. 9(Supplement): 11-16 (2002) - [c10]David L. Buckeridge, Justin Graham, Martin J. O'Connor, Michael Choy, Samson W. Tu, Mark A. Musen:
Knowledge-based bioterrorism surveillance. AMIA 2002 - [c9]Martin J. O'Connor, Samson W. Tu, Mark A. Musen:
The Chronus II temporal database mediator. AMIA 2002 - 2001
- [c8]Mary K. Goldstein, Brian B. Hoffman, Robert W. Coleman, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Susana B. Martins, Aneel A. Advani, Mark A. Musen:
Patient safety in guideline-based decision support for hypertension management: ATHENA DSS. AMIA 2001 - [c7]Martin J. O'Connor, Ravi D. Shankar, Samson W. Tu, Aneel A. Advani, Mary K. Goldstein, Robert W. Coleman, Mark A. Musen:
A Client-Server Framework for Deploying a Decision-support System in a Resource-constrained Environment. AMIA 2001 - [c6]Martin J. O'Connor, William E. Grosso, Samson W. Tu, Mark A. Musen
:
RASTA: A Distributed Temporal Abstraction System to Facilitate Knowledge-Driven Monitoring of Clinical Databases. MedInfo 2001: 508-512 - 2000
- [c5]Mary K. Goldstein, Brian B. Hoffman, Robert W. Coleman, Mark A. Musen, Samson W. Tu, Aneel A. Advani, Ravi D. Shankar, Martin J. O'Connor:
Implementing clinical practice guidelines while taking account of changing evidence: ATHENA DSS, an easily modifiable decision-support system for managing hypertension in primary care. AMIA 2000 - [c4]Martin J. O'Connor, Samson W. Tu, Mark A. Musen:
Representation of temporal indeterminacy in clinical databases. AMIA 2000
1990 – 1999
- 1999
- [c3]Aneel A. Advani, Samson W. Tu, Martin J. O'Connor, Robert W. Coleman, Mary K. Goldstein, Mark A. Musen:
Integrating a modern knowledge-based system architecture with a legacy VA database: the ATHENA and EON projects at Stanford. AMIA 1999 - [c2]Mark A. Musen, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Aneel A. Advani:
EON 2.0: Enhanced Middleware for Automation of Protocol-Directed Therapy. AMIA 1999 - [c1]Martin J. O'Connor, Samson W. Tu, Mark A. Musen:
Applying temporal joins to clinical databases. AMIA 1999 - 1994
- [j1]Martin J. O'Connor, Brendan Tangney
, Vinny Cahill, Neville Harris:
Micro-kernel support for migration. Distributed Syst. Eng. 1(4): 212-223 (1994)
Coauthor Index
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