A General-Purpose Data Harmonization Framework: Supporting Reproducible and Scalable Data Integration in the RADx Data Hub

Authors: Yu, Jimmy K., Martínez-Romero, Marcos, Horridge, Matthew, Akdogan, Mete U., Musen, Mark A.

Subject Terms: Computer Science - Databases

Access URL: http://arxiv.org/abs/2503.02115

RADx Data Hub: A Cloud Platform for FAIR, Harmonized COVID-19 Data

Authors: Martinez-Romero, Marcos, Horridge, Matthew, Mistry, Nilesh, Weyhmiller, Aubrie, Yu, Jimmy K., Fujimoto, Alissa, Henry, Aria, O'Connor, Martin J., Sier, Ashley, Suber, Stephanie, Akdogan, Mete U., Cao, Yan, Valliappan, Somu, Mieczkowska, Joanna O., team, the RADx Data Hub, Krishnamurthy, Ashok, Keller, Michael A., Musen, Mark A.

Subject Terms: Computer Science - Databases

Access URL: http://arxiv.org/abs/2502.00265

A Change Language for Ontologies and Knowledge Graphs

Authors: Hegde, Harshad, Vendetti, Jennifer, Goutte-Gattat, Damien, Caufield, J Harry, Graybeal, John B, Harris, Nomi L, Karam, Naouel, Kindermann, Christian, Matentzoglu, Nicolas, Overton, James A, Musen, Mark A, Mungall, Christopher J

Source: Database (Oxford). 2025 Jan 22;2025:baae133

Subject Terms: Computer Science - Databases

Access URL: http://arxiv.org/abs/2409.13906

Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets

Authors: O'Connor, Martin J., Hardi, Josef, Martínez-Romero, Marcos, Somasundaram, Sowmya, Honick, Brendan, Fisher, Stephen A., Pillai, Ajay, Musen, Mark A.

Subject Terms: Computer Science - Digital Libraries

Access URL: http://arxiv.org/abs/2409.08897

Use of a Structured Knowledge Base Enhances Metadata Curation by Large Language Models

Authors: Sundaram, Sowmya S., Solomon, Benjamin, Khatri, Avani, Laumas, Anisha, Khatri, Purvesh, Musen, Mark A.

Subject Terms: Computer Science - Artificial Intelligence, Computer Science - Computation and Language, Computer Science - Information Retrieval

Access URL: http://arxiv.org/abs/2404.05893

A Comprehensive Approach to Ensuring Quality in Spreadsheet-Based Metadata

Authors: O'Connor, Martin J., Martínez-Romero, Marcos, Akdogan, Mete Ugur, Hardi, Josef, Musen, Mark A.

Subject Terms: Computer Science - Digital Libraries

Access URL: http://arxiv.org/abs/2312.09107

Making Metadata More FAIR Using Large Language Models

Authors: Sundaram, Sowmya S., Musen, Mark A.

Source: DaMaLOS 2023

Subject Terms: Computer Science - Computation and Language, Computer Science - Artificial Intelligence

Access URL: http://arxiv.org/abs/2307.13085

Modeling community standards for metadata as templates makes data FAIR

Authors: Musen, Mark A., O'Connor, Martin J., Schultes, Erik, Martinez-Romero, Marcos, Hardi, Josef, Graybeal, John

Subject Terms: Computer Science - Digital Libraries

Access URL: http://arxiv.org/abs/2208.02836

Using Ethnographic Methods to Classify the Human Experience in Medicine: A Case Study of the Presence Ontology

Authors: Maitra, Amrapali, Kamdar, Maulik R., Zulman, Donna M., Haverfield, Marie C., Brown-Johnson, Cati, Schwartz, Rachel, Israni, Sonoo Thadaney, Verghese, Abraham, Musen, Mark A.

Subject Terms: Computer Science - Information Theory

Access URL: http://arxiv.org/abs/2105.07238

Making Data FAIR Requires More than Just Principles: We Need Knowledge Technologies

Authors: Musen, Mark

Source: 2019 15th International Conference on eScience (eScience) eScience (eScience), 2019 15th International Conference on. :530-532 Sep, 2019

Relation: 2019 15th International Conference on eScience (eScience)

Construction and Usage of a Human Body Common Coordinate Framework Comprising Clinical, Semantic, and Spatial Ontologies

Authors: Börner, Katy, Quardokus, Ellen M., Herr II, Bruce W., Cross, Leonard E., Record, Elizabeth G., Ju, Yingnan, Bueckle, Andreas D., Sluka, James P., Silverstein, Jonathan C., Browne, Kristen M., Jain, Sanjay, Wasserfall, Clive H., Jorgensen, Marda L., Spraggins, Jeffrey M., Patterson, Nathan H., Musen, Mark A., Weber, Griffin M.

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Computation and Language, Computer Science - Digital Libraries

Access URL: http://arxiv.org/abs/2007.14474

An Empirical Meta-analysis of the Life Sciences (Linked?) Open Data on the Web

Authors: Kamdar, Maulik R., Musen, Mark A.

Subject Terms: Computer Science - Artificial Intelligence

Access URL: http://arxiv.org/abs/2006.04161

Use of OWL and Semantic Web Technologies at Pinterest

Authors: Gonçalves, Rafael S., Horridge, Matthew, Li, Rui, Liu, Yu, Musen, Mark A., Nyulas, Csongor I., Obamos, Evelyn, Shrouty, Dhananjay, Temple, David

Subject Terms: Computer Science - Computation and Language, Computer Science - Computers and Society, Computer Science - Social and Information Networks

Access URL: http://arxiv.org/abs/1907.02106

The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments

Authors: Gonçalves, Rafael S., O'Connor, Martin J., Martínez-Romero, Marcos, Egyedi, Attila L., Willrett, Debra, Graybeal, John, Musen, Mark A.

Subject Terms: Computer Science - Databases, Computer Science - Digital Libraries

Access URL: http://arxiv.org/abs/1905.06480

Episodic skeletal-plan refinement based on temporal data.

Authors: Tu, Samson W., Kahn, Michael G., Musen, Mark A.

Source: Communications of the ACM; December 1989, Vol. 32, p1439-1455, 17p

Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases

Authors: Martínez-Romero, Marcos, O'Connor, Martin J., Egyedi, Attila L., Willrett, Debra, Hardi, Josef, Graybeal, John, Musen, Mark A.

Subject Terms: Computer Science - Databases, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/1903.09270

Aligning Biomedical Metadata with Ontologies Using Clustering and Embeddings

Authors: Gonçalves, Rafael S., Kamdar, Maulik R., Musen, Mark A.

Subject Terms: Computer Science - Computation and Language, Computer Science - Information Retrieval

Access URL: http://arxiv.org/abs/1903.08206

HopRank: How Semantic Structure Influences Teleportation in PageRank (A Case Study on BioPortal)

Authors: Espín-Noboa, Lisette, Lemmerich, Florian, Walk, Simon, Strohmaier, Markus, Musen, Mark A.

Subject Terms: Computer Science - Social and Information Networks

Access URL: http://arxiv.org/abs/1903.05704

WebProt\'eg\'e: A Cloud-Based Ontology Editor

Authors: Horridge, Matthew, Gonçalves, Rafael S., Nyulas, Csongor I., Tudorache, Tania, Musen, Mark A.

Subject Terms: Computer Science - Information Retrieval, Computer Science - Artificial Intelligence

Access URL: http://arxiv.org/abs/1902.08251

Using aggregate taxonomies to summarize SNOMED CT evolution

Authors: Ochs, Christopher, Perl, Yehoshua, Geller, James, Musen, Mark

Source: 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on. :1008-1015 Nov, 2015

Relation: 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)