Micro-kernel support for migration. - Martin J. O'Connor; Brendan Tangney; Vinny Cahill; Neville Harris (Distributed Syst. Eng., 1994)

Integrating a modern knowledge-based system architecture with a legacy VA database: the ATHENA and EON projects at Stanford. - Aneel A. Advani; Samson W. Tu; Martin J. O'Connor; Robert W. Coleman; Mary K. Goldstein; Mark A. Musen (AMIA, 1999)

EON 2.0: Enhanced Middleware for Automation of Protocol-Directed Therapy. - Mark A. Musen; Samson W. Tu; Ravi D. Shankar; Martin J. O'Connor; Aneel A. Advani (AMIA, 1999)

Applying temporal joins to clinical databases. - Martin J. O'Connor; Samson W. Tu; Mark A. Musen (AMIA, 1999)

Implementing clinical practice guidelines while taking account of changing evidence: ATHENA DSS, an easily modifiable decision-support system for managing hypertension in primary care. - 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 (AMIA, 2000)

Representation of temporal indeterminacy in clinical databases. - Martin J. O'Connor; Samson W. Tu; Mark A. Musen (AMIA, 2000)

A Client-Server Framework for Deploying a Decision-support System in a Resource-constrained Environment. - Martin J. O'Connor; Ravi D. Shankar; Samson W. Tu; Aneel A. Advani; Mary K. Goldstein; Robert W. Coleman; Mark A. Musen (AMIA, 2001)

RASTA: A Distributed Temporal Abstraction System to Facilitate Knowledge-Driven Monitoring of Clinical Databases. - Martin J. O'Connor; William E. Grosso; Samson W. Tu; Mark A. Musen (MedInfo, 2001)

Knowledge-based bioterrorism surveillance. - David L. Buckeridge; Justin Graham; Martin J. O'Connor; Michael Choy; Samson W. Tu; Mark A. Musen (AMIA, 2002)

The Chronus II temporal database mediator. - Martin J. O'Connor; Samson W. Tu; Mark A. Musen (AMIA, 2002)

Patient Safety in Guideline-Based Decision Support for Hypertension Management: ATHENA DSS. - 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 (J. Am. Medical Informatics Assoc., 2002)

BioSTORM: A System for Automated Surveillance of Diverse Data Sources. - Martin J. O'Connor; David L. Buckeridge; Michael Choy; Monica Crubézy; Zachary Pincus; Mark A. Musen (AMIA, 2003)

A Knowledge-Based Framework for Deploying Surveillance Problem Solvers. - David L. Buckeridge; Martin J. O'Connor; Haobo Xu; Mark A. Musen (IKE, 2004)

Application of Information Technology: Translating Research into Practice: Organizational Issues in Implementing Automated Decision Support for Hypertension in Three Medical Centers. - 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; et al. (J. Am. Medical Informatics Assoc., 2004)

Knowledge-Based Syndromic Surveillance for Bioterrorism. - Mark A. Musen; Monica Crubézy; Martin J. O'Connor; David L. Buckeridge (AAAI Spring Symposium: AI Technologies for Homeland Security, 2005)

Computational Method for Temporal Pattern Discovery in Biomedical Genomic Databases. - Mohammed I. Rafiq; Martin J. O'Connor; Amar K. Das (CSB, 2005)

Supporting Rule System Interoperability on the Semantic Web with SWRL. - Martin J. O'Connor; Holger Knublauch; Samson W. Tu; Benjamin N. Grosof; Mike Dean; William E. Grosso; Mark A. Musen (ISWC, 2005)

Ontology-Centered Syndromic Surveillance for Bioterrorism. - Monica Crubézy; Martin J. O'Connor; David L. Buckeridge; Zachary Pincus; Mark A. Musen (IEEE Intell. Syst., 2005)

A Dynamic Distributed Architecture for Temporal Data Abstraction. - Vijay P. Chauhan; Martin J. O'Connor; Amar K. Das (AMIA, 2006)

Ontology-Driven Mapping of Temporal Data in Biomedical Databases. - Preetha S. Narayanan; Martin J. O'Connor; Amar K. Das (AMIA, 2006)

An Ontology-Driven Mediator for Querying Time-Oriented Biomedical Data. - Martin J. O'Connor; Ravi D. Shankar; Amar K. Das (CBMS, 2006)

Knowledge-Based System for Managing Complex Clinical Trials. - Ravi D. Shankar; Susana B. Martins; Martin J. O'Connor; David B. Parrish; Amar K. Das (CBMS, 2006)

Epoch: an ontological framework to support clinical trials management. - Ravi D. Shankar; Susana B. Martins; Martin J. O'Connor; David B. Parrish; Amar K. Das (HIKM, 2006)

Towards Semantic Interoperability in a Clinical Trials Management System. - Ravi D. Shankar; Susana B. Martins; Martin J. O'Connor; David B. Parrish; Amar K. Das (ISWC, 2006)

Using Semantic Web Technologies for Knowledge-Driven Querying of Biomedical Data. - Martin J. O'Connor; Ravi D. Shankar; Samson W. Tu; Csongor Nyulas; Dave Parrish; Mark A. Musen; Amar K. Das (AIME, 2007)

An Ontology-Driven Method for Hierarchical Mining of Temporal Patterns: Application to HIV Drug Resistance Research. - Rashmi Raj; Martin J. O'Connor; Amar K. Das (AMIA, 2007)

An Ontology-based Architecture for Integration of Clinical Trials Management Applications. - Ravi D. Shankar; Susana B. Martins; Martin J. O'Connor; David B. Parrish; Amar K. Das (AMIA, 2007)

Knowledge-Level Querying of Temporal Patterns in Clinical Research Systems. - Martin J. O'Connor; Ravi D. Shankar; David B. Parrish; Amar K. Das (MedInfo, 2007)

Efficiently Querying Relational Databases Using OWL and SWRL. - Martin J. O'Connor; Ravi D. Shankar; Samson W. Tu; Csongor Nyulas; Amar K. Das; Mark A. Musen (RR, 2007)

Querying the Semantic Web with SWRL. - Martin J. O'Connor; Samson W. Tu; Csongor Nyulas; Amar K. Das; Mark A. Musen (RuleML, 2007)

Developing a Web-Based Application using OWL and SWRL. - Martin J. O'Connor; Ravi D. Shankar; Csongor Nyulas; Samson W. Tu; Amar K. Das (AAAI Spring Symposium: AI Meets Business Rules and Process Management, 2008)

Semantic Integration of Software Systems in Translational Clinical Trials. - Ravi D. Shankar; Martin J. O'Connor; David B. Parrish; Amar K. Das (AAAI Spring Symposium: Semantic Scientific Knowledge Integration, 2008)

Predicting Outbreak Detection in Public Health Surveillance: Quantitative Analysis to Enable Evidence-Based Method Selection. - David L. Buckeridge; Anna Okhmatovskaia; Samson W. Tu; Martin J. O'Connor; Csongor Nyulas; Mark A. Musen (AMIA, 2008)

Using an Integrated Ontology and Information Model for Querying and Reasoning about Phenotypes: The Case of Autism. - Samson W. Tu; Lakshika Tennakoon; Martin J. O'Connor; Ravi D. Shankar; Amar K. Das (AMIA, 2008)

An Ontological Approach to Representing and Reasoning with Temporal Constraints in Clinical Trial Protocols. - Ravi D. Shankar; Susana B. Martins; Martin J. O'Connor; Amar K. Das (HEALTHINF (1), 2008)

Representing and Reasoning with Temporal Constraints in Clinical Trials Using Semantic Technologies. - Ravi D. Shankar; Susana B. Martins; Martin J. O'Connor; David B. Parrish; Amar K. Das (BIOSTEC (Selected Papers), 2008)

An Ontology-Driven Framework for Deploying JADE Agent Systems. - Csongor Nyulas; Martin J. O'Connor; Samson W. Tu; David L. Buckeridge; Anna Okhmatovskaia; Mark A. Musen (IAT, 2008)

The SWRLAPI: A Development Environment for Working with SWRL Rules. - Martin J. O'Connor; Ravi D. Shankar; Mark A. Musen; Amar K. Das; Csongor Nyulas (OWLED, 2008)

Model Formulation: Understanding Detection Performance in Public Health Surveillance: Modeling Aberrancy-detection Algorithms. - David L. Buckeridge; Anna Okhmatovskaia; Samson W. Tu; Martin J. O'Connor; Csongor Nyulas; Mark A. Musen (J. Am. Medical Informatics Assoc., 2008)

A Bayesian Network Model for Analysis of Detection Performance in Surveillance Systems. - Masoumeh T. Izadi; David L. Buckeridge; Anna Okhmatovskaia; Samson W. Tu; Martin J. O'Connor; Csongor Nyulas; Mark A. Musen (AMIA, 2009)

Semantic Reasoning with Image Annotations for Tumor Assessment. - Mia A. Levy; Martin J. O'Connor; Daniel L. Rubin (AMIA, 2009)

Exploration of SWRL Rule Bases through Visualization, Paraphrasing, and Categorization of Rules. - Saeed Hassanpour; Martin J. O'Connor; Amar K. Das (RuleML, 2009)

A Rule Management and Elicitation Tool for SWRL Rule Bases. - Saeed Hassanpour; Martin J. O'Connor; Amar K. Das (RuleML Challenge, 2009)

Axiomé: A Tool for the Elicitation and Management of SWRL Rules. - Saeed Hassanpour; Martin J. O'Connor; Amar K. Das (OWLED, 2009)

SQWRL: A Query Language for OWL. - Martin J. O'Connor; Amar K. Das (OWLED, 2009)

Software-engineering challenges of building and deploying reusable problem solvers. - Martin J. O'Connor; Csongor Nyulas; Samson W. Tu; David L. Buckeridge; Anna Okhmatovskaia; Mark A. Musen (Artif. Intell. Eng. Des. Anal. Manuf., 2009)

Knowledge-data integration for temporal reasoning in a clinical trial system. - Martin J. O'Connor; Ravi D. Shankar; David B. Parrish; Amar K. Das (Int. J. Medical Informatics, 2009)

A Lightweight Model for Representing and Reasoning with Temporal Information in Biomedical Ontologies. - Martin J. O'Connor; Amar K. Das (HEALTHINF, 2010)

A Method for Representing and Querying Temporal Information in OWL. - Martin J. O'Connor; Amar K. Das (BIOSTEC (Selected Papers), 2010)

A Software Tool for Visualizing, Managing and Eliciting SWRL Rules. - Saeed Hassanpour; Martin J. O'Connor; Amar K. Das (ESWC (2), 2010)

Semantic Reasoning with XML-based Biomedical Information Models. - Martin J. O'Connor; Amar K. Das (MedInfo, 2010)

M2: A Language for Mapping Spreadsheets to OWL. - Martin J. O'Connor; Christian Halaschek-Wiener; Mark A. Musen (OWLED, 2010)

Visualizing Logical Dependencies in SWRL Rule Bases. - Saeed Hassanpour; Martin J. O'Connor; Amar K. Das (RuleML, 2010)

Mapping Master: A Flexible Approach for Mapping Spreadsheets to OWL. - Martin J. O'Connor; Christian Halaschek-Wiener; Mark A. Musen (ISWC (2), 2010)

SWRL-F - A Fuzzy Logic Extension of the Semantic Web Rule Language. - Tomasz Wiktor Wlodarczyk; Martin J. O'Connor; Chunming Rong; Mark A. Musen (URSW, 2010)

A Rule-Based Method for Specifying and Querying Temporal Abstractions. - Martin J. O'Connor; Genaro Hernández; Amar K. Das (AIME, 2011)

Web-Based Querying and Temporal Visualization of Longitudinal Clinical Data. - Amanda Richards; Martin J. O'Connor; Susana B. Martins; Michael Uehara-Bingen; Samson W. Tu; Amar K. Das (AIME, 2011)

Acquiring OWL ontologies from XML documents. - Martin J. O'Connor; Amar K. Das (K-CAP, 2011)

A Framework for the Automatic Extraction of Rules from Online Text. - Saeed Hassanpour; Martin J. O'Connor; Amar K. Das (RuleML Europe, 2011)

SWEETInfo: a Web-Based System for Visualizing and Querying Temporal Data. - Martin J. O'Connor; Amanda Richards; Susana B. Martins; Mike Bingen; Samson W. Tu; Amar K. Das (RuleML America (2), 2011)

Web-based Exploration of Temporal Data in Biomedicine. - Martin J. O'Connor; Mike Bingen; Amanda Richards; Samson W. Tu; Amar K. Das (WEBIST, 2011)

Overcoming the ontology enrichment bottleneck with Quick Term Templates. - 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 (Appl. Ontology, 2011)

SWRL Rule Editor - A Web Application as Rich as Desktop Business Rule Editors. - João Paulo Orlando; Adriano Rivolli; Saeed Hassanpour; Martin J. O'Connor; Amar K. Das; Dilvan A. Moreira (ICEIS (2), 2012)

A Pair of OWL 2 RL Reasoners. - Martin J. O'Connor; Amar K. Das (OWLED, 2012)

Adaptive System for Collaborative Online Laboratories. - Christophe Gravier; Jacques Fayolle; Jérémy Lardon; Martin J. O'Connor (IEEE Intell. Syst., 2012)

A semantic-based method for extracting concept definitions from scientific publications: evaluation in the autism phenotype domain. - Saeed Hassanpour; Martin J. O'Connor; Amar K. Das (J. Biomed. Semant., 2013)

Clustering rule bases using ontology-based similarity measures. - Saeed Hassanpour; Martin J. O'Connor; Amar K. Das (J. Web Semant., 2014)

The center for expanded data annotation and retrieval. - 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; et al. (J. Am. Medical Informatics Assoc., 2015)

CEDAR: Better Data Sharing Through the Authoring of Better Metadata. - Mark A. Musen; Martin J. O'Connor; Marcos Martínez Romero; Attila Levente Egyedi; Debra Willrett; John B. Graybeal (AMIA, 2016)

An Open Repository Model for Acquiring Knowledge About Scientific Experiments. - Martin J. O'Connor; Marcos Martínez Romero; Attila L. Egyedi; Debra Willrett; John B. Graybeal; Mark A. Musen (EKAW, 2016)

Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. - Marcos Martínez Romero; Martin J. O'Connor; Ravi D. Shankar; Maryam Panahiazar; Debra Willrett; Attila Levente Egyedi; Olivier Gevaert; John B. Graybeal; Mark A. Musen (AMIA, 2017)

Supporting Ontology-Based Standardization of Biomedical Metadata in the CEDAR Workbench. - Marcos Martínez Romero; Martin J. O'Connor; Michael Dorf; Jennifer Vendetti; Debra Willrett; Attila L. Egyedi; John B. Graybeal; Mark A. Musen (ICBO, 2017)

The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. - Rafael S. Gonçalves 001; Martin J. O'Connor; Marcos Martínez Romero; Attila L. Egyedi; Debra Willrett; John B. Graybeal; Mark A. Musen (ISWC (2), 2017)

Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies. - Rafael S. Gonçalves 001; Martin J. O'Connor; Marcos Martínez Romero; John B. Graybeal; Mark A. Musen (SemSci@ISWC, 2017)

Embracing Semantic Technology for Better Metadata Authoring in Biomedicine. - Attila L. Egyedi; Martin J. O'Connor; Marcos Martínez Romero; Debra Willrett; Josef Hardi; John B. Graybeal; Mark A. Musen (SWAT4LS, 2017)

NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. - Marcos Martínez Romero; Clément Jonquet; Martin J. O'Connor; John B. Graybeal; Alejandro Pazos; Mark A. Musen (J. Biomed. Semant., 2017)

Using Ontologies to Drive the Creation of High-Quality Metadata in CEDAR. - Rafael S. Gonçalves 001; Csongor I. Nyulas; Marcos Martínez Romero; Martin J. O'Connor; John B. Graybeal; Mark A. Musen (ISWC (P&D/Industry/BlueSky), 2018)

Using semantic technologies to enhance metadata submissions to public repositories in biomedicine. - Attila L. Egyedi; Martin J. O'Connor; Marcos Martínez Romero; Debra Willrett; Josef Hardi; John B. Graybeal; Mark A. Musen (SWAT4LS, 2018)

CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. - Syed Ahmad Chan Bukhari; Marcos Martínez Romero; Martin J. O'Connor; Attila L. Egyedi; Debra Willrett; John B. Graybeal; Mark A. Musen; Kei-Hoi Cheung; Steven H. Kleinstein (BMC Bioinform., 2018)

Unleashing the value of Common Data Elements through the CEDAR Workbench. - Martin J. O'Connor; Denise B. Warzel; Marcos Martínez Romero; Josef Hardi; Debra Willrett; Aras Efekhari; John B. Graybeal; Mark A. Musen (AMIA, 2019)

Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases. - Marcos Martínez Romero; Martin J. O'Connor; Attila L. Egyedi; Debra Willrett; Josef Hardi; John B. Graybeal; Mark A. Musen (Database J. Biol. Databases Curation, 2019)

Modeling community standards for metadata as templates makes data FAIR. - Mark A. Musen; Martin J. O'Connor; Erik Schultes; Marcos Martínez Romero; Josef Hardi; John B. Graybeal (CoRR, 2022)

A Comprehensive Approach to Ensuring Quality in Spreadsheet-Based Metadata. - Martin J. O'Connor; Marcos Martínez Romero; Mete Ugur Akdogan; Josef Hardi; Mark A. Musen (CoRR, 2023)

Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets. - Martin J. O'Connor; Josef Hardi; Marcos Martínez Romero; Sowmya Somasundaram; Brendan Honick; Stephen A. Fisher; Ajay Pillai; Mark A. Musen (CoRR, 2024)

RADx Data Hub: A Cloud Platform for FAIR, Harmonized COVID-19 Data. - Marcos Martínez Romero; Matthew Horridge; Nilesh Mistry; Aubrie Weyhmiller; Jimmy K. Yu; Alissa Fujimoto; Aria Henry; Martin J. O'Connor; Ashley Sier; Stephanie Suber; Mete Ugur Akdogan; Yan Cao; et al. (CoRR, 2025)

Knowledge engineering for open science: Building and deploying knowledge bases for metadata standards. - Mark A. Musen; Martin J. O'Connor; Josef Hardi; Marcos Martínez Romero (CoRR, 2025)