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2020 – today
- 2024
[i7]Martin J. O'Connor, Josef Hardi, Marcos Martínez Romero, Sowmya Somasundaram, Brendan Honick, Stephen A. Fisher, Ajay Pillai, Mark A. Musen:
Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets. CoRR abs/2409.08897 (2024)- 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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