A5009128820- Semantic Web and Ontologies
- Biomedical Text Mining and Ontologies
- Service-Oriented Architecture and Web Services
- Advanced Database Systems and Queries
- Electronic Health Records Systems
- Scientific Computing and Data Management
- Bioinformatics and Genomic Networks
- AI-based Problem Solving and Planning
- Natural Language Processing Techniques
- Clinical practice guidelines implementation
- Research Data Management Practices
- Data Quality and Management
- Data-Driven Disease Surveillance
- Business Process Modeling and Analysis
- Topic Modeling
- linguistics and terminology studies
- Data Management and Algorithms
- Genomics and Rare Diseases
- Constraint Satisfaction and Optimization
- Wikis in Education and Collaboration
- Machine Learning in Healthcare
- Bayesian Modeling and Causal Inference
- Bacillus and Francisella bacterial research
- Artificial Intelligence in Healthcare
- Software Engineering Research
Stanford University
2016-2025
Stanford Medicine
2010-2025
Translational Research Informatics Center (Japan)
2010-2020
University of Notre Dame
2017
Center for Open Science
2017
Association of Research Libraries
2017
Centre for Life
2017
Leiden University Medical Center
2017
Pennsylvania State University
2017
The Nature Conservancy
2009
research-article Share on The protégé project: a look back and forward Author: Mark A. Musen Stanford University UniversityView Profile Authors Info & Claims AI MattersVolume 1Issue 4June 2015 pp 4–12https://doi.org/10.1145/2757001.2757003Published:16 June 2015Publication History 583citation1,035DownloadsMetricsTotal Citations583Total Downloads1,035Last 12 Months264Last 6 weeks54 Get Citation AlertsNew Alert added!This alert has been successfully added will be sent to:You notified whenever...
Functional brain networks detected in task-free ("resting-state") functional magnetic resonance imaging (fMRI) have a small-world architecture that reflects robust organization of the brain. Here, we examined whether this is disrupted Alzheimer's disease (AD). Task-free fMRI data from 21 AD subjects and 18 age-matched controls were obtained. Wavelet analysis was applied to compute frequency-dependent correlation matrices. Correlation matrices thresholded create 90-node undirected-graphs...
As researchers continue to create new languages in the hope of developing a Semantic Web, they still lack consensus on standard. The authors describe how Protege-2000, tool for ontology development and knowledge acquisition, can be adapted editing models different Web languages.
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, annotation, natural-language processing and decision support. BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical that provides access via Web services browsers developed in OWL, RDF, OBO format Protégé frames. functionality includes the ability browse, search visualize ontologies. The interface also facilitates community-based participation evaluation...
The ontogeny of large-scale functional organization the human brain is not well understood. Here we use network analysis intrinsic connectivity to characterize networks in 23 children (ages 7-9 y) and 22 young-adults 19-22 y). Comparison properties, including path-length, clustering-coefficient, hierarchy, regional connectivity, revealed that although young-adults' brains have similar "small-world" at global level, they differ significantly hierarchical interregional connectivity. We found...
The National Center for Biomedical Ontology (NCBO) is one of the Centers Computing funded under NIH Roadmap Initiative. Contributing to national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access library biomedical ontologies and terminologies ( http://bioportal.bioontology.org ) via Web services. BioPortal enables community participation in evaluation evolution ontology content by providing features add mappings between terms, comments linked specific...
Abstract Objective The capability to share data, and harness its potential generate knowledge rapidly inform decisions, can have transformative effects that improve health. infrastructure achieve this goal at scale—marrying technology, process, policy—is commonly referred as the Learning Health System (LHS). Achieving an LHS raises numerous scientific challenges. Materials methods National Science Foundation convened invitational workshop identify fundamental engineering research challenges...
The National Center for Biomedical Ontology is now in its seventh year. goals of this Computing are to: create and maintain a repository biomedical ontologies terminologies; build tools web services to enable the use terminologies clinical translational research; educate their trainees scientific community broadly about ontology ontology-based technology best practices; collaborate with variety groups who develop biomedicine. centerpiece web-based resource known as BioPortal. BioPortal makes...
The AMIA biomedical informatics (BMI) core competencies have been designed to support and guide graduate education in BMI, the scientific discipline underlying breadth of field's research, practice, education. definition BMI adopted by specifies that is ‘the interdisciplinary field studies pursues effective uses data, information, knowledge for inquiry, problem solving decision making, motivated efforts improve human health.’ Application areas range from bioinformatics clinical public health...
Abstract Motivation Knowledge graphs (KGs) are being adopted in industry, commerce and academia. Biomedical KG presents a challenge due to the complexity, size heterogeneity of underlying information. Results In this work, we present Scalable Precision Medicine Open Engine (SPOKE), biomedical connecting millions concepts via semantically meaningful relationships. SPOKE contains 27 million nodes 21 different types 53 edges 55 downloaded from 41 databases. The graph is built on framework 11...
Provision of automated support for planning protocol-directed therapy requires a computer program to take as input clinical data stored in an electronic patient-record system and generate output recommendations therapeutic interventions laboratory testing that are defined by applicable protocols. This paper presents synthesis research carried out at Stanford University model the therapy-planning task demonstrate component-based architecture building protocol-based decision-support systems.
We have defined a knowledge-based framework for the creation of abstract, interval-based concepts from time-stamped clinical data, temporal-abstraction (KBTA) method. The KBTA method decomposes its task into five subtasks; each subtask we propose formal solving mechanism. Our emphasizes explicit representation knowledge required abstraction time-oriented and facilitates acquisition, maintenance, reuse sharing. RÉSUMÉ system implements tested in several clinical-monitoring domains, including...
As ontology development becomes a more ubiquitous and collaborative process, the developers face problem of maintaining versions ontologies akin to software code in large projects. Versioning systems for provide mechanisms tracking versions, checking out editing, comparing different so on. We can directly reuse many these versioning. However, version comparison is based on text files--an approach that does not work ontologies. Two be identical but have representation. developed PROMPTDIFF...