List of works - Michel Dumontier

3D topography of noncompact zone Golgi tubules in rat spermatids: A computer-assisted serial section reconstruction study

3D topography of noncompact zone Golgi tubules in rat spermatids: a computer-assisted serial section reconstruction study

scientific article published on April 1998

A Novel Ensemble-Based Machine Learning Algorithm to Predict the Conversion From Mild Cognitive Impairment to Alzheimer's Disease Using Socio-Demographic Characteristics, Clinical Information, and Neuropsychological Measures

scientific article published on 16 July 2019

A Privacy-Preserving Infrastructure for Analyzing Personal Health Data in a Vertically Partitioned Scenario

scientific article published on 01 August 2019

A Web API Ecosystem through Feature-Based Reuse

scholarly article by Ruben Verborgh published in May 2018

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

scientific article

A comprehensive comparison of automated FAIRness Evaluation Tools ⬇️

A design framework and exemplar metrics for FAIRness

article published in 2017

A design framework and exemplar metrics for FAIRness

scientific article

A model for capturing provenance of assertions about chemical substances ⬇️

Achieving human and machine accessibility of cited data in scholarly publications

scientific article

Achieving human and machine accessibility of cited data in scholarly publications

article published in 2015

Addendum: The FAIR Guiding Principles for scientific data management and stewardship

article by Mark D Wilkinson et al published 19 March 2019 in Scientific Data

Advancing Discovery Science with FAIR Data Stewardship: Findable, Accessible, Interoperable, Reusable

An Ebola virus-centered knowledge base

scientific article

An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics

scientific article published on January 2013

An evidence-based approach to identify aging-related genes in Caenorhabditis elegans

scientific article

Analysis of In Vitro Aptamer Selection Parameters

scientific article published on 3 November 2015

Annotation of Existing Databases using Semantic Web Technologies: Making Data more FAIR ⬇️

Aptamer Base: a collaborative knowledge base to describe aptamers and SELEX experiments

scientific article (publication date: 2012)

Armadillo: domain boundary prediction by amino acid composition.

scientific article

Author Correction: Evaluating FAIR maturity through a scalable, automated, community-governed framework

scientific article published on 21 October 2019

Authors’ Response to Peer Reviews of “Representing Physician Suicide Claims as Nanopublications: Proof-of-Concept Study Creating Claim Networks”

scientific article published in 2022

Automated Identification of Food Substitutions Using Knowledge Graph Embeddings ⬇️

Automatically exposing OpenLifeData via SADI semantic Web Services

scientific article

Automating Identification of Multiple Chronic Conditions in Clinical Practice Guidelines

scientific article published on 25 March 2015

Bio2RDF Release 2: Improved Coverage, Interoperability and Provenance of Life Science Linked Data

article by Alison Callahan et al published 2013 in Lecture Notes in Computer Science

Bio2RDF Release 3: A larger, more connected network of Linked Data for the Life Sciences

scientific article published in proceedings of the iswc 2014 posters & demonstrations track

BioHackathon 2015: Semantics of data for life sciences and reproducible research

scientific article published on 24 February 2020

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

scientific article (publication date: 5 February 2014)

BioSearch: a semantic search engine for Bio2RDF.

scientific article published in January 2017

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

scientific article

Bioschemas: schema.org for the Life Sciences

scientific article

Biotea, semantics for Pubmed Central

Biotea: semantics for Pubmed Central

scientific article published on 2 January 2018

Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest

scientific article

Building an HIV data mashup using Bio2RDF.

scientific article

CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules

scientific article published on August 2005

Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration

scientific article (publication date: 19 May 2011)

Chemical Knowledge for the Semantic Web

Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata

scientific article published on 18 September 2017

Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud

scientific article (publication date: 7 March 2017)

Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records

article

Comparing Drug-Disease Associations in Clinical Practice Guideline Recommendations and Drug Product Label Indications

scientific article published in January 2015

Computational approaches toward the design of pools for the in vitro selection of complex aptamers

scientific article

Computational methods for predicting protein-protein interactions

scientific article published on January 2008

Considerations for the Conduction and Interpretation of FAIRness Evaluations

Controlled vocabularies and semantics in systems biology

scientific article (publication date: 25 October 2011)

CrowdED 1.0: Statistical Guideline for Designing Optimal Crowdsourcing Experiments ⬇️

scientific article published on 25 June 2024

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

scientific article published on 23 August 2016

Data Science – Methods, infrastructure, and applications

scientific article from 2017

Data2Services: enabling automated conversion of data to services ⬇️

article published in 2018

Decentralized provenance-aware publishing with nanopublications

preprint from 2016

Decentralized provenance-aware publishing with nanopublications

peer-reviewed article from August 2016

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop

scientific article

Development of Small-Molecule Ligands and Inhibitors

article

Discovering associations between adverse drug events using pattern structures and ontologies.

scientific article

Disruption of fungal cell wall by antifungal Echinacea extracts

scientific article published in November 2010

Domain-based small molecule binding site annotation

scientific article published on 17 March 2006

Drug-drug Interaction Extraction via Hierarchical RNNs on Sequence and Shortest Dependency Paths

scientific article published on 25 October 2017

Drug-drug interaction data source survey and linking

scientific article

Drug-drug interaction discovery and demystification using Semantic Web technologies

scientific article published on 28 December 2016

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

scientific article published on 10 October 2016

Evaluating FAIR maturity through a scalable, automated, community-governed framework

scientific article published on 20 September 2019

Evaluating FAIR-Compliance Through an Objective, Automated, Community-Governed Framework

Evaluating Scientific Hypotheses Using the SPARQL Inferencing Notation

article

Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction in realistic settings

scientific article published on 18 December 2019

Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction using Linked Open Data ⬇️

Evaluation of research in biomedical ontologies ⬇️

scientific article published on September 8, 2012

Evaluation of the OQuaRE framework for ontology quality

article

Experience: Automated Prediction of Experimental Metadata from Scientific Publications

Exposing Provenance Metadata Using Different RDF Models ⬇️

FAIR Principles for Clinical Practice Guidelines in a Learning Health System

scientific article published on 01 August 2019

FAIR Principles: Interpretations and Implementation Considerations

scholarly article

FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

scientific article published on 13 June 2016

Feasibility of Prioritizing Drug-Drug-Event Associations Found in Electronic Health Records

scientific article

Finding melanoma drugs through a probabilistic knowledge graph

Finding our way through phenotypes

scientific article

Finding the Evidence Base Using Citation Networks: Do 300 to 400 US Physicians Die by Suicide Annually?

scientific article published on 27 May 2020

Formalizing drug indications on the road to therapeutic intent.

scientific article published in November 2017

GFVO: the Genomic Feature and Variation Ontology

scientific article

Genuine semantic publishing

scientific article published on 17 October 2017

Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences.

scientific article published on 27 June 2008

GridCell: a stochastic particle-based biological system simulator

scientific article

Hardware-accelerated protein identification for mass spectrometry

scientific article published in January 2005

HyQue: evaluating hypotheses using Semantic Web technologies ⬇️

scientific article (publication date: 17 May 2011)

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article (publication date: 20 March 2017)

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article

Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics ⬇️

scientific article published on June 17, 2012

Improved Dataset Coverage and Interoperability with Bio2RDF Release 2 ⬇️

In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data

scientific article published on 20 June 2019

Integrating findings of traditional medicine with modern pharmaceutical research: the potential role of linked open data

scientific article (publication date: 17 December 2010)

Integrating systems biology models and biomedical ontologies

scientific article (publication date: 11 August 2011)

Integration and publication of heterogeneous text-mined relationships on the Semantic Web ⬇️

scientific article (publication date: 17 May 2011)

Interoperability and FAIRness through a novel combination of Web technologies ⬇️

scientific article (publication date: 24 April 2017)

Interoperability and FAIRness through a novel combination of Web technologies

Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning

scientific article

Interoperability of text corpus annotations with the semantic web.

scientific article published on 6 August 2015

Is Crowdsourcing Patient-Reported Outcomes the Future of Evidence-Based Medicine? A Case Study of Back Pain

article

Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology

scientific article published on 9 February 2016

Knowledge Graph Completeness: A Systematic Literature Review

LSQ 2.0: A linked dataset of SPARQL query logs ⬇️

scientific article published on 12 January 2024

LUCE: A blockchain-based data sharing platform for monitoring data license accoUntability and CompliancE

scientific article published in 2022

Link Analysis of Life Science Linked Data

article

Linked Data in Drug Discovery

article

Machine Learning Based Drug Indication Prediction Using Linked Open Data ⬇️

scholarly article by Remzi Çelebí et al published 10 January 2018 in Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences

Making Digital Artifacts on the Web Verifiable and Reliable ⬇️

Making Linked Data SPARQL with the InterMine Biological Data Warehouse ⬇️

Mining Electronic Health Records using Linked Data

scientific article

MoSuMo: A Semantic Web service to generate electrostatic potentials across solvent excluded protein surfaces and binding pockets

Modeling and querying graphical representations of statistical data

Modeling tryptic digestion on the Cell BE processor

Mondo: Unifying diseases for the world, by the world

Mouse model phenotypes provide information about human drug targets

scientific article published on 24 October 2013

NBLAST: a cluster variant of BLAST for NxN comparisons

scientific article

Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data ⬇️

article published in 2018

Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data

Nanotate: Semantically annotating experimental protocols with nanopublications ⬇️

Network Ranking Assisted Semantic Data Mining

Ontology-Based Querying with Bio2RDF's Linked Open Data

scientific article (publication date: 15 April 2013)

Overlap in drug-disease associations between clinical practice guidelines and drug structured product label indications

scientific article

Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies

scientific article

Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO).

scientific article published on 15 June 2017

Predicting structured metadata from unstructured metadata

scientific article published on January 2016

Predicting structured metadata from unstructured metadata.

scientific article published on 13 June 2016

Predicting the need for a reduced drug dose, at first prescription

scientific article published in Scientific Reports

Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics

scientific article

Provenance-Centered Dataset of Drug-Drug Interactions

scientific article published at ISWC 2015

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases ⬇️

Article in the Journal of Cheminformatics.

Publishing DisGeNET as Nanopublications

preprint on biorXiv

Publishing DisGeNET as nanopublications

article

Publishing Without Publishers: A Decentralized Approach to Dissemination, Retrieval, and Archiving of Data

article

Putting FAIR Evidence into Practice

article

RKB: a Semantic Web knowledge base for RNA.

scientific article

Ranking adverse drug reactions with crowdsourcing.

scientific article

Relations as patterns: bridging the gap between OBO and OWL

scientific article

Report on semantic web for health care and life sciences workshop

Representing Physician Suicide Claims as Nanopublications: Proof-of-Concept Study Creating Claim Networks

scientific article published in 2022

SIENA: Semi-automatic semantic enhancement of datasets using concept recognition

SPARQL-enabled identifier conversion with Identifiers.org

scientific article

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting

scientific article (publication date: 24 April 2012)

Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting

scientific article (publication date: 15 April 2013)

Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting.

scientific article published on 3 June 2014

Self-organizing ontology of biochemically relevant small molecules

scientific article

Semantic Query Answering with Time-Series Graphs

Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery

article

Semantic Web integration of Cheminformatics resources with the SADI framework

scientific article (publication date: 16 May 2011)

Semantic micro-contributions with decentralized nanopublication services

scientific article

Semantically enabling pharmacogenomic data for the realization of personalized medicine

scientific article (publication date: 2012)

Semantics-Powered Healthcare Engineering and Data Analytics

scientific article published on 26 October 2017

SeqHound: biological sequence and structure database as a platform for bioinformatics research

scientific article

Special issue on bio-ontologies and phenotypes

scientific article

Species-specific protein sequence and fold optimizations

scientific article

State of the art and open challenges in community-driven knowledge curation

Target Profiling of Small Molecules

Ten simple rules for making training materials FAIR

Scientific Article

Ten simple rules for making training materials FAIR

The Biomolecular Interaction Network Database and related tools 2005 update

scientific article

The Chemical Information Ontology: provenance and disambiguation for chemical data on the biological semantic web

scientific article

The FAIR Guiding Principles for scientific data management and stewardship

scientific article (publication date: 15 March 2016)

The Ontology for Biomedical Investigations

scientific article

The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions

scientific article (publication date: 5 April 2013)

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery ⬇️

scientific article published on 6 March 2014

The SmartAPI Ecosystem for Making Web APIs FAIR

scientific article published in proceedings of the iswc 2017 posters & demonstrations and industry tracks

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside ⬇️

scientific article (publication date: 17 May 2011)

The center for expanded data annotation and retrieval

scientific article

The digital revolution in phenotyping

scientific article published on 29 September 2015

The emergence and evolution of the research fronts in HIV/AIDS research

scientific article

The health care and life sciences community profile for dataset descriptions

scientific article (publication date: 2016)

The health care and life sciences community profile for dataset descriptions

article published in 2016

Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop

scientific article published on 12 December 2016

Toward a complete dataset of drug-drug interaction information from publicly available sources

scientific article (publication date: June 2015)

Towards an interoperable information infrastructure providing decision support for genomic medicine

scientific article published on January 1, 2011

Towards pharmacogenomics knowledge discovery with the semantic web.

scientific article published on 24 February 2009

Transformation and Integration of Heterogeneous Health Data in a Privacy-preserving Distributed Learning Infrastructure ⬇️

Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data ⬇️

Using LASSO Regression to Predict Rheumatoid Arthritis Treatment Efficacy

scientific article

List of works by Michel Dumontier

3D topography of noncompact zone Golgi tubules in rat spermatids: A computer-assisted serial section reconstruction study

3D topography of noncompact zone Golgi tubules in rat spermatids: a computer-assisted serial section reconstruction study

A Novel Ensemble-Based Machine Learning Algorithm to Predict the Conversion From Mild Cognitive Impairment to Alzheimer's Disease Using Socio-Demographic Characteristics, Clinical Information, and Neuropsychological Measures

A Privacy-Preserving Infrastructure for Analyzing Personal Health Data in a Vertically Partitioned Scenario

A Web API Ecosystem through Feature-Based Reuse

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

A comprehensive comparison of automated FAIRness Evaluation Tools ⬇️

A design framework and exemplar metrics for FAIRness

A design framework and exemplar metrics for FAIRness

A model for capturing provenance of assertions about chemical substances ⬇️

Achieving human and machine accessibility of cited data in scholarly publications

Achieving human and machine accessibility of cited data in scholarly publications

Achieving human and machine accessibility of cited data in scholarly publications

Achieving human and machine accessibility of cited data in scholarly publications

Achieving human and machine accessibility of cited data in scholarly publications

Achieving human and machine accessibility of cited data in scholarly publications

Addendum: The FAIR Guiding Principles for scientific data management and stewardship

Advancing Discovery Science with FAIR Data Stewardship: Findable, Accessible, Interoperable, Reusable

An Ebola virus-centered knowledge base

An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics

An evidence-based approach to identify aging-related genes in Caenorhabditis elegans

Analysis of In Vitro Aptamer Selection Parameters

Annotation of Existing Databases using Semantic Web Technologies: Making Data more FAIR ⬇️

Aptamer Base: a collaborative knowledge base to describe aptamers and SELEX experiments

Armadillo: domain boundary prediction by amino acid composition.

Author Correction: Evaluating FAIR maturity through a scalable, automated, community-governed framework

Authors’ Response to Peer Reviews of “Representing Physician Suicide Claims as Nanopublications: Proof-of-Concept Study Creating Claim Networks”

Automated Identification of Food Substitutions Using Knowledge Graph Embeddings ⬇️

Automatically exposing OpenLifeData via SADI semantic Web Services

Automating Identification of Multiple Chronic Conditions in Clinical Practice Guidelines

Bio2RDF Release 2: Improved Coverage, Interoperability and Provenance of Life Science Linked Data

Bio2RDF Release 3: A larger, more connected network of Linked Data for the Life Sciences

BioHackathon 2015: Semantics of data for life sciences and reproducible research

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

BioSearch: a semantic search engine for Bio2RDF.

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

Bioschemas: schema.org for the Life Sciences

Biotea, semantics for Pubmed Central

Biotea, semantics for Pubmed Central

Biotea: semantics for Pubmed Central

Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest

Building an HIV data mashup using Bio2RDF.

CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules

Chemical Entity Semantic Specification: Knowledge representation for efficient semantic cheminformatics and facile data integration

Chemical Knowledge for the Semantic Web

Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata

Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud

Columbia Open Health Data, clinical concept prevalence and co-occurrence from electronic health records

Comparing Drug-Disease Associations in Clinical Practice Guideline Recommendations and Drug Product Label Indications

Computational approaches toward the design of pools for the in vitro selection of complex aptamers

Computational methods for predicting protein-protein interactions

Considerations for the Conduction and Interpretation of FAIRness Evaluations

Controlled vocabularies and semantics in systems biology

CrowdED 1.0: Statistical Guideline for Designing Optimal Crowdsourcing Experiments ⬇️

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Data Science – Methods, infrastructure, and applications

Data2Services: enabling automated conversion of data to services ⬇️

Decentralized provenance-aware publishing with nanopublications

Decentralized provenance-aware publishing with nanopublications

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop

Development of Small-Molecule Ligands and Inhibitors

Discovering associations between adverse drug events using pattern structures and ontologies.

Disruption of fungal cell wall by antifungal Echinacea extracts

Domain-based small molecule binding site annotation

Drug-drug Interaction Extraction via Hierarchical RNNs on Sequence and Shortest Dependency Paths

Drug-drug interaction data source survey and linking

Drug-drug interaction discovery and demystification using Semantic Web technologies

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Evaluating FAIR maturity through a scalable, automated, community-governed framework

Evaluating FAIR-Compliance Through an Objective, Automated, Community-Governed Framework

Evaluating Scientific Hypotheses Using the SPARQL Inferencing Notation

Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction in realistic settings

Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction using Linked Open Data ⬇️

Evaluation of research in biomedical ontologies ⬇️

Evaluation of the OQuaRE framework for ontology quality

Experience: Automated Prediction of Experimental Metadata from Scientific Publications

Exposing Provenance Metadata Using Different RDF Models ⬇️

FAIR Principles for Clinical Practice Guidelines in a Learning Health System

FAIR Principles: Interpretations and Implementation Considerations