114 citations · 456 across the 24 of their papers we have counts for
24 papers
A General-Purpose Data Harmonization Framework: Supporting Reproducible and Scalable Data Integration in the RADx Data Hub
Jimmy K. Yu, Marcos Martínez-Romero, Matthew Horridge +2
In the age of big data, it is important for primary research data to follow the FAIR principles of findability, accessibility, interoperability, and reusability. Data harmonization…
RADx Data Hub: A Cloud Platform for FAIR, Harmonized COVID-19 Data
Marcos Martinez-Romero, Matthew Horridge, Nilesh Mistry +15
The COVID-19 pandemic highlighted the urgent need for robust systems to enable rapid data collection, integration, and analysis for public health responses. Existing approaches oft…
A Change Language for Ontologies and Knowledge Graphs
Harshad Hegde, Jennifer Vendetti, Damien Goutte-Gattat +9
Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information…
Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets
Martin J. O'Connor, Josef Hardi, Marcos Martínez-Romero +5
Scientists increasingly recognize the importance of providing rich, standards-adherent metadata to describe their experimental results. Despite the availability of sophisticated to…
A Comprehensive Approach to Ensuring Quality in Spreadsheet-Based Metadata
Martin J. O'Connor, Marcos Martínez-Romero, Mete Ugur Akdogan +2
While scientists increasingly recognize the importance of metadata in describing their data, spreadsheets remain the preferred tool for supplying this information despite their lim…
Making Metadata More FAIR Using Large Language Models
Sowmya S. Sundaram, Mark A. Musen
With the global increase in experimental data artifacts, harnessing them in a unified fashion leads to a major stumbling block - bad metadata. To bridge this gap, this work present…
Modeling community standards for metadata as templates makes data FAIR
Mark A. Musen, Martin J. O'Connor, Erik Schultes +3
It is challenging to determine whether datasets are findable, accessible, interoperable, and reusable (FAIR) because the FAIR Guiding Principles refer to highly idiosyncratic crite…
Using Ethnographic Methods to Classify the Human Experience in Medicine: A Case Study of the Presence Ontology
Amrapali Maitra, Maulik R. Kamdar, Donna M. Zulman +6
Objective Although social and environmental factors are central to provider patient interactions, the data that reflect these factors can be incomplete, vague, and subjective. We s…
Construction and Usage of a Human Body Common Coordinate Framework Comprising Clinical, Semantic, and Spatial Ontologies
Katy Börner, Ellen M. Quardokus, Bruce W. Herr +14
The National Institutes of Health's (NIH) Human Biomolecular Atlas Program (HuBMAP) aims to create a comprehensive high-resolution atlas of all the cells in the healthy human body.…
An Empirical Meta-analysis of the Life Sciences (Linked?) Open Data on the Web
Maulik R. Kamdar, Mark A. Musen
While the biomedical community has published several "open data" sources in the last decade, most researchers still endure severe logistical and technical challenges to discover, q…
Use of OWL and Semantic Web Technologies at Pinterest
Rafael S. Gonçalves, Matthew Horridge, Rui Li +6
Pinterest is a popular Web application that has over 250 million active users. It is a visual discovery engine for finding ideas for recipes, fashion, weddings, home decoration, an…
The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments
Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez-Romero +4
The Center for Expanded Data Annotation and Retrieval (CEDAR) aims to revolutionize the way that metadata describing scientific experiments are authored. The software we have devel…
Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases
Marcos Martínez-Romero, Martin J. O'Connor, Attila L. Egyedi +4
Metadata-the machine-readable descriptions of the data-are increasingly seen as crucial for describing the vast array of biomedical datasets that are currently being deposited in p…
HopRank: How Semantic Structure Influences Teleportation in PageRank (A Case Study on BioPortal)
Lisette Espín-Noboa, Florian Lemmerich, Simon Walk +2
This paper introduces HopRank, an algorithm for modeling human navigation on semantic networks. HopRank leverages the assumption that users know or can see the whole structure of t…
The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data
P. Wittenburg, H. Pergl Sustkova, A. Montesanti +57
There is a growing acknowledgement in the scientific community of the importance of making experimental data machine findable, accessible, interoperable, and reusable (FAIR). Recog…
WebProtégé: A Cloud-Based Ontology Editor
Matthew Horridge, Rafael S. Gonçalves, Csongor I. Nyulas +2
We present WebProtégé, a tool to develop ontologies represented in the Web Ontology Language (OWL). WebProtégé is a cloud-based application that allows users to collaboratively edi…
Aligning Biomedical Metadata with Ontologies Using Clustering and Embeddings
Rafael S. Gonçalves, Maulik R. Kamdar, Mark A. Musen
The metadata about scientific experiments published in online repositories have been shown to suffer from a high degree of representational heterogeneity---there are often many way…
The variable quality of metadata about biological samples used in biomedical experiments
Rafael S. Gonçalves, Mark A. Musen
We present an analytical study of the quality of metadata about samples used in biomedical experiments. The metadata under analysis are stored in two well-known databases: BioSampl…
Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies
Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez-Romero +2
The metadata about scientific experiments are crucial for finding, reproducing, and reusing the data that the metadata describe. We present a study of the quality of the metadata s…
NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation
Marcos Martinez-Romero, Clement Jonquet, Martin J. O'Connor +3
Biomedical researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability. However, the number, variety and complexity…
How Users Explore Ontologies on the Web: A Study of NCBO's BioPortal Usage Logs
Simon Walk, Lisette Espín-Noboa, Denis Helic +2
Ontologies in the biomedical domain are numerous, highly specialized and very expensive to develop. Thus, a crucial prerequisite for ontology adoption and reuse is effective suppor…
Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains
Simon Walk, Philipp Singer, Markus Strohmaier +3
Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases (ICD) as a taxonomy or the National Cancer Institute Thesaurus as an OWL-…
How to Apply Markov Chains for Modeling Sequential Edit Patterns in Collaborative Ontology-Engineering Projects
Simon Walk, Philipp Singer, Markus Strohmaier +3
With the growing popularity of large-scale collaborative ontology-engineering projects, such as the creation of the 11th revision of the International Classification of Diseases, w…
Graph-Grammar Assistance for Automated Generation of Influence Diagrams
John W. Egar, Mark A. Musen
One of the most difficult aspects of modeling complex dilemmas in decision-analytic terms is composing a diagram of relevance relations from a set of domain concepts. Decision mode…