A5054153288- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Scientific Computing and Data Management
- Research Data Management Practices
- Data Quality and Management
- Clinical practice guidelines implementation
- Electronic Health Records Systems
- Advanced Database Systems and Queries
- Computational Drug Discovery Methods
- Cardiac, Anesthesia and Surgical Outcomes
- Business Process Modeling and Analysis
- Natural Language Processing Techniques
- Health Systems, Economic Evaluations, Quality of Life
- Topic Modeling
- Ethics in Clinical Research
- Delphi Technique in Research
- Safe Handling of Antineoplastic Drugs
- Pharmacogenetics and Drug Metabolism
- Advances in Oncology and Radiotherapy
- Data Management and Algorithms
- Academic Publishing and Open Access
- AI in cancer detection
- Family and Patient Care in Intensive Care Units
- Genomics and Phylogenetic Studies
- Pharmaceutical industry and healthcare
Harvard University
2008-2018
PerkinElmer (United States)
2015-2018
Boston University
2016-2018
Massachusetts General Hospital
2008-2014
University of Delaware
2013
Data61
2013
National Center for Biotechnology Information
2013
Spanish National Cancer Research Centre
2013
Institute of Electrical and Electronics Engineers
2013
Regional Municipality of Niagara
2013
Many groups are developing computer-interpretable clinical guidelines (CIGs) for use during encounters. CIGs "Task-Network Models" representation but differ in their approaches to addressing particular modeling challenges. We have studied similarities and differences between order identify issues that must be resolved before a consensus on set of common components can developed.We compared six models: Asbru, EON, GLIF, GUIDE, PRODIGY, PROforma. Collaborators from created these models...
A vast amount of scientific information is encoded in natural language text, and the quantity such text has become so great that it no longer economically feasible to have a human as first step search process. Natural processing mining tools essential facilitate for extraction from text. This led vigorous research efforts create useful humanly labeled corpora, which can be used improve tools. To encourage combining these into larger, more powerful capable systems, common interchange format...
Abstract Background There is currently a gap between the rich and expressive collection of published biomedical ontologies, natural language expression papers consumed on daily basis by scientific researchers. The purpose this paper to provide an open, shareable structure for dynamic integration domain ontologies with document, in form Annotation Ontology (AO), thus closing enabling application formal directly literature as it emerges. Methods Initial requirements AO were elicited analysis...
Scientific publications are documentary representations of defeasible arguments, supported by data and repeatable methods. They the essential mediating artifacts in ecosystem scientific communications. The institutional "goal" science is publishing results. linear document publication format, dating from 1665, has survived transition to Web. Intractable volumes; difficulty verifying evidence; observed problems evidence citation chains suggest a need for web-friendly machine-tractable model...
Data in the life sciences are extremely diverse and stored a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG pathway or UniProt protein data) to that general-purpose FigShare, Zenodo, Dataverse EUDAT). These have widely different levels sensitivity security considerations. For example, clinical observations about genetic mutations patients highly sensitive, while species diversity generally not. The lack uniformity models one repository...
Provenance is a critical ingredient for establishing trust of published scientific content. This true whether we are considering data set, computational workflow, peer-reviewed publication or simple claim with supportive evidence. Existing vocabularies such as Dublin Core Terms (DC Terms) and the W3C Ontology (PROV-O) domain-independent general-purpose they allow encourage extensions to cover more specific needs. In particular, track authoring versioning information web resources, PROV-O...
The Open Annotation Core Data Model specifies an interoperable framework for creating associations between related resources, called annotations, using a methodology that conforms to the Architecture of World Wide Web. Annotations can easily be shared platforms, with sufficient richness expression satisfy complex requirements while remaining simple enough also allow most common use cases, such as attaching piece text single web resource. This paper presents W3C Community Group specification...
Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of number kinds, using an open representation model.The Domeo Annotation Tool was in tandem with this model, the Ontology (AO). Development both Framework model driven by requirements several different types alpha users, including bench scientists biomedical curators from university research labs, online scientific communities, publishing pharmaceutical companies.Several...
The RDF collections and containers is one of the most used features by technicians practitioners. Although some work has been published in past, there not a standard accepted way for defining within OWL DL frameworks. Here,
Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology a controlled structured vocabulary consisting general terms (such as "cell" or "image" "tissue" "microscope") that form the basis such These are designed to represent types entities in domain reality has been devised capture; provided with logical definitions thereby also supporting reasoning over tagged data.This paper provides survey biomedical imaging ontologies have...
This paper describes the architecture of NewGuide, a guideline management system for handling whole life cycle computerized clinical practice guideline. NewGuide components are organized in distributed architecture: an editor to formalize guidelines, repository store them, inference engine implement guidelines instances multi-user environment, and reporting storing logs order be able completely trace any individual physician guideline-based decision process. There is “central...
The breadth of information resources available to researchers on the Internet continues expand, particularly in light recently implemented data-sharing policies required by funding agencies. However, nature dense, multifaceted neuroscience data and design contemporary search engine systems makes efficient, reliable relevant discovery such a significant challenge. This challenge is specifically pertinent for online databases, whose dynamic content 'hidden' from engines. Neuroscience...
The W3C Open Annotation Data Model provides facilities for annotating content directly on the Web without changing original content. Third-party semantic annotations of are now emerging as first-class objects Web.
Data in the life sciences are extremely diverse and stored a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG pathway or UniProt protein data) to that general-purpose FigShare, Zenodo, EUDat). These have widely different levels sensitivity security considerations. For example, clinical observations about genetic mutations patients highly sensitive, while species diversity generally not. The lack uniformity models one repository another,...
With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well number databases which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies becoming more common. However, rarely available Linked Data, a machine-readable format, or for standardized queries SPARQL. This makes large-scale reuse, integration with other knowledge bases very difficult. To address this challenge, we have developed second...
Guidelines are often based on a mixture of evidence-based and consensus-based recommendations. It is not straightforward that providing series “good” recommendations result in guideline easily applicable, it acting according to such leads an effective efficient clinical practice. In this paper we summarize our experience evaluating both the usability impact for acute/subacute stroke management. A computerised version has been implemented linked electronic patient record....
Most literature searching in biomedicine is now conducted via PubMed, Google Scholar or other web-based bibliographic search mechanisms. Yet until a public, open, interoperable and complete web-adapted information schema for citatio
Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal effort has been invested in development tools which can automate representation recommendations contained within such guidelines, by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based standard terminology systems like UMLS, form one core components models. We have created DAML+OIL-based CTOs for tasks referred to WHO guideline...