A5073479149- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Research Data Management Practices
- Scientific Computing and Data Management
- Service-Oriented Architecture and Web Services
- Data Quality and Management
- Electronic Health Records Systems
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Atmospheric and Environmental Gas Dynamics
- Advanced Text Analysis Techniques
- Healthcare Technology and Patient Monitoring
- Medical Image Segmentation Techniques
- Pharmacogenetics and Drug Metabolism
- Medical Malpractice and Liability Issues
- Pancreatic and Hepatic Oncology Research
- Single-cell and spatial transcriptomics
- Cloud Data Security Solutions
- Cardiovascular Health and Disease Prevention
- Cell Image Analysis Techniques
- Cancer Immunotherapy and Biomarkers
- linguistics and terminology studies
- Natural Language Processing Techniques
- Protein Structure and Dynamics
- Ethics and bioethics in healthcare
Stanford Medicine
2016-2025
Stanford University
2016-2022
Universidade da Coruña
2009-2015
Biomedical researchers use ontologies to annotate their data with ontology terms, enabling better integration and interoperability. However, the number, variety complexity of current biomedical make it cumbersome for determine which ones reuse specific needs. To overcome this problem, in 2010 National Center Ontology (NCBO) released Recommender, is a service that receives text corpus or list keywords suggests appropriate referencing indicated terms. We developed new version NCBO Recommender....
Scientists increasingly recognize the importance of providing rich, standards-adherent metadata to describe their experimental results. Despite availability sophisticated tools assist in process data annotation, investigators generally seem prefer use spreadsheets when supplying metadata, despite limitations ensuring consistency and compliance with formal specifications. In this paper, we an end-to-end approach that supports spreadsheet-based entry while rigorous adherence community-based...
The COVID-19 pandemic highlighted the urgent need for robust systems to enable rapid data collection, integration, and analysis public health responses. Existing approaches often relied on disparate, non-interoperable systems, creating bottlenecks in comprehensive analyses timely decision-making. To address these challenges, U.S. National Institutes of Health (NIH) launched Rapid Acceleration Diagnostics (RADx) initiative 2020, with RADx Data Hub, a centralized repository de-identified...
Abstract It is challenging to determine whether datasets are findable, accessible, interoperable, and reusable (FAIR) because the FAIR Guiding Principles refer highly idiosyncratic criteria regarding metadata used annotate datasets. Specifically, principles require be “rich” adhere “domain-relevant” community standards. Scientific communities should able define their own machine-actionable templates for that encode these “rich,” discipline-specific elements. We have explored this...
Metadata-the machine-readable descriptions of the data-are increasingly seen as crucial for describing vast array biomedical datasets that are currently being deposited in public repositories. While most repositories have firm requirements metadata must accompany submitted datasets, quality those is generally very poor. A key problem typical acquisition process onerous and time consuming, with little interactive guidance or assistance provided to users. Secondary problems include lack...
Physicians in the Intensive Care Unit (ICU) are specially trained to deal constantly with very large and complex quantities of clinical data make quick decisions as they face complications. However, amount information generated way presented may overload cognitive skills even experienced professionals lead inaccurate or erroneous actions that put patients’ lives at risk. In this paper, we present design, development, validation iOSC3, an ontology-based system for intelligent supervision...
Background: The development of diagnostic decision support systems (DDSS) requires having a reliable and consistent knowledge based on diseases their symptoms, signs, tests. Physicians are typically the source this but it is not always possible to obtain all desired information from them. Other valuable sources medical books articles describing diagnosis diseases, again, extracting hard time-consuming task. Objective: In paper we present results our research compare two well-known tools that...
Public biomedical data repositories often provide web-based interfaces to collect experimental metadata. However, these typically reflect the ad hoc metadata specification practices of associated repositories, leading a lack standardization in collected This limits ability source datasets be broadly discovered, reused, and integrated with other datasets. To increase reuse, discoverability, reproducibility described experiments, should appropriately annotated by using agreed-upon terms,...
The adaptation of high-throughput sequencing to the B cell receptor and T has made it possible characterize adaptive immune repertoire (AIRR) at unprecedented depth. These AIRR (AIRR-seq) studies offer tremendous potential increase understanding responses in vaccinology, infectious disease, autoimmunity, cancer. increasingly wide application AIRR-seq is leading a critical mass being deposited public domain, offering possibility novel scientific insights through secondary analyses...
The metadata about scientific experiments are crucial for finding, reproducing, and reusing the data that describe. We present a study of quality stored in BioSample--a repository samples used biomedical managed by U.S. National Center Biomedical Technology Information (NCBI). tested whether 6.6 million BioSample records populated with values fulfill stated requirements such values. Our revealed multiple anomalies analyzed metadata. field names their not standardized or controlled--15%...
The complex information encoded into the element connectivity of a system gives rise to possibility graphical processing divisible systems by using Graph theory. An application in this sense is quantitative characterization molecule topologies drugs, proteins and nucleic acids, order build mathematical models as Quantitative Structure - Activity Relationships between molecules specific biological activity. These types can predict new molecular targets properties structures with an important...