Michel Dumontier

Affiliations:
  • Maastricht University, The Netherlands
  • Carleton University, Ottawa, Canada (former)


According to our database1, Michel Dumontier authored at least 202 papers between 2002 and 2024.

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Bibliography

2024
LSQ 2.0: A linked dataset of SPARQL query logs.
Semantic Web, 2024

2023
ciTIzen-centric DAta pLatform (TIDAL): Sharing distributed personal data in a privacy-preserving manner for health research.
Semantic Web, 2023

Generating synthetic personal health data using conditional generative adversarial networks combining with differential privacy.
J. Biomed. Informatics, 2023

Models towards Risk Behavior Prediction and Analysis: A Netherlands Case study.
CoRR, 2023

FAIR Begins at home: Implementing FAIR via the Community Data Driven Insights.
CoRR, 2023

TAPS Responsibility Matrix: A tool for responsible data science by design.
CoRR, 2023

Evidence From Data Science on the Relationship Between Individual Beliefs/Behaviors Survey During COVID-19 Pandemic and Risk Preference.
Adv. Artif. Intell. Mach. Learn., 2023

Generating Knowledge Graph Based Explanations for Drug Repurposing Predictions.
Proceedings of the 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), 2023

Analyze Decentralized Personal Health Data Using Solid, Digital Consent, and Federated Learning.
Proceedings of the 14th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), 2023

Enhanced GAT: Expanding Receptive Field with Meta Path-Guided RDF Rules for Two-Hop Connectivity.
Proceedings of the Joint Proceedings of Scholarly QALD 2023 and SemREC 2023 co-located with 22nd International Semantic Web Conference ISWC 2023, 2023

Semantically-Informed Deep Neural Networks For Sound Recognition.
Proceedings of the IEEE International Conference on Acoustics, 2023

ACES: Evaluating Automated Audio Captioning Models on the Semantics of Sounds.
Proceedings of the 31st European Signal Processing Conference, 2023

On the Combination of Event Calculus and Empirical Semantic Drifts.
Proceedings of the Joint Proceedings of the ESWC 2023 Workshops and Tutorials co-located with 20th European Semantic Web Conference (ESWC 2023), 2023

2022
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Nucleic Acids Res., 2022

Studying the association of diabetes and healthcare cost on distributed data from the Maastricht Study and Statistics Netherlands using a privacy-preserving federated learning infrastructure.
J. Biomed. Informatics, 2022

A formalization of one of the main claims of "The FAIR Guiding Principles for scientific data management and stewardship" by Wilkinson et al. 20161.
Data Sci., 2022

Improving Correlation Capture in Generating Imbalanced Data using Differentially Private Conditional GANs.
CoRR, 2022

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science.
CoRR, 2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.
CoRR, 2022

LUCE: A Blockchain-based data sharing platform for monitoring data license accountability and compliance.
CoRR, 2022

Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data.
J. Biomed. Semant., 2022

A Comprehensive Comparison of Automated FAIRness Evaluation Tools.
Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2022

Automated Identification of Food Substitutions Using Knowledge Graph Embeddings.
Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2022

Nanotate: Semantically Annotating Experimental Protocols with Nanopublications.
Proceedings of the 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2022

Semantic Correlation Graph Embedding.
Proceedings of the IEEE International Conference on Fuzzy Systems, 2022

2021
Semantic micro-contributions with decentralized nanopublication services.
PeerJ Comput. Sci., 2021

Experience: Automated Prediction of Experimental Metadata from Scientific Publications.
ACM J. Data Inf. Qual., 2021

Relation extraction from DailyMed structured product labels by optimally combining crowd, experts and machines.
J. Biomed. Informatics, 2021

A systematic review on privacy-preserving distributed data mining.
Data Sci., 2021

Privacy preserving distributed learning classifiers - Sequential learning with small sets of data.
Comput. Biol. Medicine, 2021

InContext: curation of medical context for drug indications.
J. Biomed. Semant., 2021

SIENA: Semi-automatic semantic enhancement of datasets using concept recognition.
J. Biomed. Semant., 2021

Knowledge Graph Completeness: A Systematic Literature Review.
IEEE Access, 2021

User-friendly Composition of FAIR Workflows in a Notebook Environment.
Proceedings of the K-CAP '21: Knowledge Capture Conference, 2021

Reuse of Design Pattern Measurements for Health Data.
Proceedings of the Joint Ontology Workshops 2021 Episode VII: The Bolzano Summer of Knowledge co-located with the 12th International Conference on Formal Ontology in Information Systems (FOIS 2021), 2021

2020
Ten simple rules for making training materials FAIR.
PLoS Comput. Biol., 2020

Towards FAIR protocols and workflows: the OpenPREDICT use case.
PeerJ Comput. Sci., 2020

BioHackathon 2015: Semantics of data for life sciences and reproducible research.
F1000Research, 2020

FAIR Principles: Interpretations and Implementation Considerations.
Data Intell., 2020

Distributed Analytics on Sensitive Medical Data: The Personal Health Train.
Data Intell., 2020

Considerations for the Conduction and Interpretation of FAIRness Evaluations.
Data Intell., 2020

Introduction - FAIR data, systems and analysis.
Data Sci., 2020

Knowledge Graphs Evolution and Preservation - A Technical Report from ISWS 2019.
CoRR, 2020

Blockchain for Privacy Preserving and Trustworthy Distributed Machine Learning in Multicentric Medical Imaging (C-DistriM).
IEEE Access, 2020

Sleeping Beauties in Case Law.
Proceedings of the Legal Knowledge and Information Systems, 2020

Accelerating Discovery Science with an Internet of FAIR Data and Services.
Proceedings of the CIKM '20: The 29th ACM International Conference on Information and Knowledge Management, 2020

2019
MetaCrowd: Crowdsourcing Biomedical Metadata Quality Assessment.
Hum. Comput., 2019

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services.
F1000Research, 2019

Towards FAIR protocols and workflows: The OpenPREDICT case study.
CoRR, 2019

Privacy-Preserving Generalized Linear Models using Distributed Block Coordinate Descent.
CoRR, 2019

LUCE: A Blockchain Solution for monitoring data License accoUntability and CompliancE.
CoRR, 2019

Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction in realistic settings.
BMC Bioinform., 2019

GrEDeL: A Knowledge Graph Embedding Based Method for Drug Discovery From Biomedical Literatures.
IEEE Access, 2019

Transformation and Integration of Heterogeneous Health Data in a Privacy-preserving Distributed Learning Infrastructure.
Proceedings of the 12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2019

Annotation of Existing Databases using Semantic Web Technologies: Making Data more FAIR.
Proceedings of the 12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 2019

Reflections on: Finding Melanoma Drugs Through a Probabilistic Knowledge Graph.
Proceedings of the Journal Track co-located with the 18th International Semantic Web Conference (ISWC 2019), 2019

A Linked Data Representation for Summary Statistics and Grouping Criteria.
Proceedings of the Joint Proceedings of the International Workshops on Sensors and Actuators on the Web, 2019

A Privacy-Preserving Infrastructure for Analyzing Personal Health Data in a Vertically Partitioned Scenario.
Proceedings of the MEDINFO 2019: Health and Wellbeing e-Networks for All, 2019

FAIR Principles for Clinical Practice Guidelines in a Learning Health System.
Proceedings of the MEDINFO 2019: Health and Wellbeing e-Networks for All, 2019

Similarity and Relevance of Court Decisions: A Computational Study on CJEU Cases.
Proceedings of the Legal Knowledge and Information Systems, 2019

Finding the evidence base using citation networks: Do 300 to 400 U.S. physicians die by suicide annually?
Proceedings of the AMIA 2019, 2019

2018
A Web API Ecosystem through Feature-Based Reuse.
IEEE Internet Comput., 2018

Analyzing Partitioned FAIR Health Data Responsibly.
CoRR, 2018

Drug-drug interaction extraction via hierarchical RNNs on sequence and shortest dependency paths.
Bioinform., 2018

CrowdED: Guideline for Optimal Crowdsourcing Experimental Design.
Proceedings of the Companion of the The Web Conference 2018 on The Web Conference 2018, 2018

A model for capturing provenance of assertions about chemical substances.
Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018

Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings.
Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018

Data2Services: enabling automated conversion of data to services.
Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018

Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction using Linked Open Data.
Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, 2018

Using the Personal Health Train for Automated and Privacy-Preserving Analytics on Vertically Partitioned Data.
Proceedings of the Building Continents of Knowledge in Oceans of Data: The Future of Co-Created eHealth, 2018

Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data.
Proceedings of the 14th IEEE International Conference on e-Science, 2018

2017
Interoperability and FAIRness through a novel combination of Web technologies.
PeerJ Comput. Sci., 2017

Finding melanoma drugs through a probabilistic knowledge graph.
PeerJ Comput. Sci., 2017

Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO).
J. Biomed. Informatics, 2017

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop.
J. Biomed. Informatics, 2017

Drug-drug interaction discovery and demystification using Semantic Web technologies.
J. Am. Medical Informatics Assoc., 2017

Formalizing drug indications on the road to therapeutic intent.
J. Am. Medical Informatics Assoc., 2017

Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud.
Inf. Serv. Use, 2017

Genuine semantic publishing.
Data Sci., 2017

Data Science - Methods, infrastructure, and applications.
Data Sci., 2017

Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata.
BMC Bioinform., 2017

Discovering associations between adverse drug events using pattern structures and ontologies.
J. Biomed. Semant., 2017

Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data.
J. Biomed. Semant., 2017

BioSearch: a semantic search engine for Bio2RDF.
Database J. Biol. Databases Curation, 2017

Machine Learning Based Drug Indication Prediction Using Linked Open Data.
Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), 2017

Bioschemas: schema.org for the Life Sciences.
Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017), 2017

The SmartAPI Ecosystem for Making Web APIs FAIR.
Proceedings of the ISWC 2017 Posters & Demonstrations and Industry Tracks co-located with 16th International Semantic Web Conference (ISWC 2017), Vienna, Austria, October 23rd - to, 2017

smartAPI: Towards a More Intelligent Network of Web APIs.
Proceedings of the Semantic Web - 14th International Conference, 2017

Is Crowdsourcing Patient-Reported Outcomes the Future of Evidence-Based Medicine? A Case Study of Back Pain.
Proceedings of the Artificial Intelligence in Medicine, 2017

2016
Publishing DisGeNET as nanopublications.
Semantic Web, 2016

Interoperability and FAIRness through a novel combination of Web technologies.
PeerJ Prepr., 2016

Decentralized provenance-aware publishing with nanopublications.
PeerJ Comput. Sci., 2016

Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology.
J. Biomed. Informatics, 2016

The structure and dynamics of the research fronts in HIV/AIDS research: part-whole and adaptive specialization.
CoRR, 2016

Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop.
J. Biomed. Semant., 2016

Overlap in drug-disease associations between clinical practice guidelines and drug structured product label indications.
J. Biomed. Semant., 2016

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.
J. Biomed. Semant., 2016

Predicting structured metadata from unstructured metadata.
Database J. Biol. Databases Curation, 2016

The digital revolution in phenotyping.
Briefings Bioinform., 2016

Making Linked Data SPARQL with the InterMine Biological Data Warehouse.
Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 2016

Ontology Mapping for Life Science Linked Data.
Proceedings of the First International Workshop on Biomedical Data Integration and Discovery (BMDID 2016) co-located with The 15th International Semantic Web Conference (ISWC 2016), 2016

Semantic Research Platform for Model Organisms.
Proceedings of the First International Workshop on Biomedical Data Integration and Discovery (BMDID 2016) co-located with The 15th International Semantic Web Conference (ISWC 2016), 2016

Network Ranking Assisted Semantic Data Mining.
Proceedings of the Bioinformatics and Biomedical Engineering, 2016

Using LASSO Regression to Predict Rheumatoid Arthritis Treatment Efficacy.
Proceedings of the Summit on Clinical Research Informatics, 2016

2015
Making Digital Artifacts on the Web Verifiable and Reliable.
IEEE Trans. Knowl. Data Eng., 2015

Achieving human and machine accessibility of cited data in scholarly publications.
PeerJ Comput. Sci., 2015

Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies.
BMC Medical Informatics Decis. Mak., 2015

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases.
J. Cheminformatics, 2015

Toward a complete dataset of drug-drug interaction information from publicly available sources.
J. Biomed. Informatics, 2015

The center for expanded data annotation and retrieval.
J. Am. Medical Informatics Assoc., 2015

On Reasoning with RDF Statements about Statements using Singleton Property Triples.
CoRR, 2015

An evidence-based approach to identify aging-related genes in Caenorhabditis elegans.
BMC Bioinform., 2015

Special issue on bio-ontologies and phenotypes.
J. Biomed. Semant., 2015

SPARQL-enabled identifier conversion with Identifiers.org.
Bioinform., 2015

An Ebola virus-centered knowledge base.
Database J. Biol. Databases Curation, 2015

Exposing Provenance Metadata Using Different RDF Models.
Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

Publishing Without Publishers: A Decentralized Approach to Dissemination, Retrieval, and Archiving of Data.
Proceedings of the Semantic Web - ISWC 2015, 2015

Link Analysis of Life Science Linked Data.
Proceedings of the Semantic Web - ISWC 2015, 2015

Provenance-Centered Dataset of Drug-Drug Interactions.
Proceedings of the Semantic Web - ISWC 2015, 2015

Comparing Drug-Disease Associations in Clinical Practice Guideline Recommendations and Drug Product Label Indications.
Proceedings of the MEDINFO 2015: eHealth-enabled Health, 2015

A Preliminary Investigation into SPARQL Query Complexity and Federation in Bio2RDF.
Proceedings of the 9th Alberto Mendelzon International Workshop on Foundations of Data Management, Lima, Peru, May 6, 2015

Drug-Disease Associations in Guidelines, Drug Labels, and Practice.
Proceedings of the AMIA 2015, 2015

2014
Special issue on Linked Data for Health Care and the Life Sciences.
Semantic Web, 2014

Hash-URIs for Verifiable, Immutable, and Permanent Digital Artifacts.
CoRR, 2014

Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting.
J. Biomed. Semant., 2014

Automatically exposing OpenLifeData via SADI semantic Web Services.
J. Biomed. Semant., 2014

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.
J. Biomed. Semant., 2014

Mouse model phenotypes provide information about human drug targets.
Bioinform., 2014

Bio2RDF Release 3: A larger, more connected network of Linked Data for the Life Sciences.
Proceedings of the ISWC 2014 Posters & Demonstrations Track a track within the 13th International Semantic Web Conference, 2014

A Nanopublication Framework for Biological Networks using Cytoscape.js.
Proceedings of the 5th International Conference on Biomedical Ontology, 2014

Erratum: Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data.
Proceedings of the Semantic Web: Trends and Challenges - 11th International Conference, 2014

Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data.
Proceedings of the Semantic Web: Trends and Challenges - 11th International Conference, 2014

Automating Identification of Multiple Chronic Conditions in Clinical Practice Guidelines.
Proceedings of the AMIA 2014, 2014

2013
1st Semantic Web Technologies for Libraries and Readers (STLR 2011).
Bull. IEEE Tech. Comm. Digit. Libr., 2013

State of the art and open challenges in community-driven knowledge curation.
J. Biomed. Informatics, 2013

Evaluation of the OQuaRE framework for ontology quality.
Expert Syst. Appl., 2013

Ovopub: Modular data publication with minimal provenance
CoRR, 2013

Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting.
J. Biomed. Semant., 2013

Ontology-Based Querying with Bio2RDF's Linked Open Data.
J. Biomed. Semant., 2013

Evaluation of research in biomedical ontologies.
Briefings Bioinform., 2013

A Large-scale Gene-centric Semantic Web Knowledge Base for Molecular Biology.
Proceedings of the Informal Proceedings of the 2nd International Workshop on OWL Reasoner Evaluation (ORE-2013), 2013

An RDF/OWL Knowledge Base for Query Answering and Decision Support in Clinical Pharmacogenetics.
Proceedings of the MEDINFO 2013, 2013

The Web as a Distributed Biochemical Reactor: Semantically Enabled Metabolic Fate Prediction.
Proceedings of the 4th International Conference on Biomedical Ontology, 2013

HyQue: A Semantic Web tool for evaluating scientific hypotheses.
Proceedings of the 4th International Conference on Biomedical Ontology, 2013

Bio2RDF Release 2: Improved Coverage, Interoperability and Provenance of Life Science Linked Data.
Proceedings of the Semantic Web: Semantics and Big Data, 10th International Conference, 2013

Looking into Reactome through Biopax Lens.
Proceedings of the 4th Canadian Semantic Web Symposium part of the Semantic Trilogy 2013, 2013

2012
Linked Data in Drug Discovery.
IEEE Internet Comput., 2012

Towards quantitative measures in applied ontology
CoRR, 2012

Self-organizing ontology of biochemically relevant small molecules.
BMC Bioinform., 2012

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting.
J. Biomed. Semant., 2012

Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics.
Bioinform., 2012

Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments.
Database J. Biol. Databases Curation, 2012

Building an HIV data mashup using Bio2RDF.
Briefings Bioinform., 2012

YummyData: Measuring the "Sparkliness" of Biomedical Sparql Endpoints.
Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012

Improved Dataset Coverage and Interoperability with Bio2RDF Release 2.
Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2012

Molecular Symmetry and Specialization of Atomic Connectivity by Class-based Reasoning of Chemical Structure.
Proceedings of OWL: Experiences and Directions Workshop 2012, 2012

Role-based representation and inference of biochemical processes.
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

Evaluating Scientific Hypotheses Using the SPARQL Inferencing Notation.
Proceedings of the Semantic Web: Research and Applications, 2012

2011
Taking flight with OWL2.
Semantic Web, 2011

Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration.
J. Cheminformatics, 2011

Semantic Web integration of Cheminformatics resources with the SADI framework.
J. Cheminformatics, 2011

MoSuMo: A Semantic Web service to generate electrostatic potentials across solvent excluded protein surfaces and binding pockets.
Comput. Graph., 2011

Integrating systems biology models and biomedical ontologies.
BMC Syst. Biol., 2011

Prototype Semantic Infrastructure for Automated Small Molecule Classification and Annotation in Lipidomics.
BMC Bioinform., 2011

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside.
J. Biomed. Semant., 2011

Integration and publication of heterogeneous text-mined relationships on the Semantic Web.
J. Biomed. Semant., 2011

HyQue: evaluating hypotheses using Semantic Web technologies.
J. Biomed. Semant., 2011

A common layer of interoperability for biomedical ontologies based on OWL EL.
Bioinform., 2011

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data.
Appl. Ontology, 2011

Chemical Hazard Estimation and Method Comparison with OWL-Encoded Toxicity Decision Trees.
Proceedings of the 8th International Workshop on OWL: Experiences and Directions (OWLED 2011), 2011

Towards an Interoperable Information Infrastructure Providing Decision Support for Genomic Medicine.
Proceedings of the User Centered Networked Health Care - Proceedings of MIE 2011, 2011

SADI for GMOD: Semantic Web Services for Model Organism Databases.
Proceedings of the 3rd Canadian Semantic Web Symposium (CSWS2011), 2011

2010
Modeling and querying graphical representations of statistical data.
J. Web Semant., 2010

Building an effective Semantic Web for health care and the life sciences.
Semantic Web, 2010

Relations as patterns: bridging the gap between OBO and OWL.
BMC Bioinform., 2010

RKB: a Semantic Web knowledge base for RNA.
J. Biomed. Semant., 2010

Relational Patterns in OWL and Their Application to OBO.
Proceedings of the 7th International Workshop on OWL: Experiences and Directions (OWLED 2010), 2010

Representing Chemicals Using OWL, Description Graphs and Rules.
Proceedings of the 7th International Workshop on OWL: Experiences and Directions (OWLED 2010), 2010

Realism for scientific ontologies.
Proceedings of the Formal Ontology in Information Systems, 2010

2009
Towards pharmacogenomics knowledge discovery with the semantic web.
Briefings Bioinform., 2009

Conjunctive Query Answering in Distributed Ontology Systems for Ontologies with Large OWL ABoxes.
Proceedings of the 5th International Workshop on OWL: Experiences and Directions (OWLED 2009), 2009

A Platform for Reasoning with OWL-EL Knowledge Bases in a Peer-to-Peer Environment.
Proceedings of the 5th International Workshop on OWL: Experiences and Directions (OWLED 2009), 2009

PDB2RDF - Exposing Molecular and Experimental Knowledge on the Semantic Web.
Proceedings of the 5th International Conference on Semantic Systems, 2009

Modeling tryptic digestion on the Cell BE processor.
Proceedings of the 22nd Canadian Conference on Electrical and Computer Engineering, 2009

2008
yOWL: An ontology-driven knowledge base for yeast biologists.
J. Biomed. Informatics, 2008

GridCell: a stochastic particle-based biological system simulator.
BMC Syst. Biol., 2008

Report on semantic web for health care and life sciences workshop.
Proceedings of the 17th International Conference on World Wide Web, 2008

Modeling Life Science Knowledge with OWL 1.1.
Proceedings of the Fourth OWLED Workshop on OWL: Experiences and Directions, 2008

Situational Modeling: Defining Molecular Roles in Biochemical Pathways and Reactions.
Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions, 2008

Publishing OWL Ontologies with Presto.
Proceedings of the Fourth OWLED Workshop on OWL: Experiences and Directions, 2008

Semantic Annotation and Question Answering of Statistical Graphs.
Proceedings of the MICAI 2008: Advances in Artificial Intelligence, 2008

Chemical Knowledge for the Semantic Web.
Proceedings of the Data Integration in the Life Sciences, 5th International Workshop, 2008

2007
SMART: A Web-Based, Ontology-Driven, Semantic Web Query Answering Application.
Proceedings of the Semantic Web Challenge 2007 co-located with ISWC 2007 + ASWC 2007, 2007

A stochastic particle-based biological system simulator.
Proceedings of the 2007 Summer Computer Simulation Conference, 2007

Describing Chemical Functional Groups in OWL-DL for the Classification of Chemical Compounds.
Proceedings of the OWLED 2007 Workshop on OWL: Experiences and Directions, 2007

Three-Layer OWL Ontology Design.
Proceedings of the 2nd International Workshop on Modular Ontologies, WoMO 2007, 2007

Semantic Query Answering with Time-Series Graphs.
Proceedings of the Workshops Proceedings of the 11th International IEEE Enterprise Distributed Object Computing Conference, 2007

2006
Domain-based small molecule binding site annotation.
BMC Bioinform., 2006

2005
The Biomolecular Interaction Network Database and related tools 2005 update.
Nucleic Acids Res., 2005

2002
SeqHound: biological sequence and structure database as a platform for bioinformatics research.
BMC Bioinform., 2002

Species-specific protein sequence and fold optimizations.
BMC Bioinform., 2002

NBLAST: a cluster variant of BLAST for NxN comparisons.
BMC Bioinform., 2002


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