Publications by authors named "M Musen"
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 systems. Most of these structures change over time, incorporating new knowledge or information that was previously missing. Managing these changes is a challenge, both in terms of communicating changes to users and providing mechanisms to make it easier for multiple stakeholders to contribute.
View Article and Find Full Text PDFThe Human Reference Atlas (HRA) for the healthy, adult body is developed by a team of international, interdisciplinary experts across 20+ consortia. It provides standard terminologies and data structures for describing specimens, biological structures, and spatial positions of experimental datasets and ontology-linked reference anatomical structures (AS), cell types (CT), and biomarkers (B). We introduce the HRA Knowledge Graph (KG) as central data resource for HRA v2.
View Article and Find Full Text PDFArticle Synopsis
- The use of well-structured ontologies and ontology-aware tools enhances data and analyses to be FAIR (Findable, Accessible, Interoperable, Reusable), supporting effective lexical searches and biologically meaningful annotation grouping.
- Researchers face challenges in adopting ontologies, primarily due to their complexity and the tendency to create simplified hierarchies that may misuse relationship types, leading to ineffective organization.
- A suite of validation tools is introduced to help users align their hierarchies with established ontology structures, providing graphical reports and tailored views for various atlases like the HuBMAP Human Reference Atlas and the Human Developmental Cell Atlas.
The Human Reference Atlas (HRA) is defined as a comprehensive, three-dimensional (3D) atlas of all the cells in the healthy human body. It is compiled by an international team of experts who develop standard terminologies that they link to 3D reference objects, describing anatomical structures. The third HRA release (v1.
View Article and Find Full Text PDFMotivation: Knowledge graphs (KGs) are being adopted in industry, commerce and academia. Biomedical KG presents a challenge due to the complexity, size and heterogeneity of the underlying information.
Results: In this work, we present the Scalable Precision Medicine Open Knowledge Engine (SPOKE), a biomedical KG connecting millions of concepts via semantically meaningful relationships.