Categorizing the world of registries.

Abstract:

:The term registry is widely used to refer to any database storing clinical information collected as a byproduct of patient care. Despite the use of this single characterizing term (registry), these databases exist in various forms and support functions ranging from biomedical informatics and clinical research, to public health, epidemiology and evidence-based clinical practice. This ambiguous terminology impacts the ability to locate and learn about specific types of registries; the goal of this research project was to develop a more useful categorization scheme for registries. We thoroughly analyzed peer-reviewed publications related to registries. From our findings, we created a detailed definition for registries in healthcare (medical data registries, or MDRs) and outlined a set of characteristics common to all such MDRs. This framework, MDR-OK, comprises five distinguishing features of registries, and is intended to provide a clear understanding of MDRs as a functional variety of databases, as well as to provide a framework for evaluation and categorization of registries and other data systems.

journal_name

J Biomed Inform

authors

Drolet BC,Johnson KB

doi

10.1016/j.jbi.2008.01.009

subject

Has Abstract

pub_date

2008-12-01 00:00:00

pages

1009-20

issue

6

eissn

1532-0464

issn

1532-0480

pii

S1532-0464(08)00018-X

journal_volume

41

pub_type

杂志文章
  • Hierarchical data security in a Query-By-Example interface for a shared database.

    abstract::Whenever a shared database resource, containing critical patient data, is created, protecting the contents of the database is a high priority goal. This goal can be achieved by developing a Query-By-Example (QBE) interface, designed to access a shared database, and embedding within the QBE a hierarchical security modu...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/s1532-0464(02)00524-5

    authors: Taylor M

    更新日期:2002-06-01 00:00:00

  • Benchmarking deep learning models on large healthcare datasets.

    abstract::Deep learning models (aka Deep Neural Networks) have revolutionized many fields including computer vision, natural language processing, speech recognition, and is being increasingly used in clinical healthcare applications. However, few works exist which have benchmarked the performance of the deep learning models wit...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2018.04.007

    authors: Purushotham S,Meng C,Che Z,Liu Y

    更新日期:2018-07-01 00:00:00

  • Combining glass box and black box evaluations in the identification of heart disease risk factors and their temporal relations from clinical records.

    abstract:BACKGROUND:The determination of risk factors and their temporal relations in natural language patient records is a complex task which has been addressed in the i2b2/UTHealth 2014 shared task. In this context, in most systems it was broadly decomposed into two sub-tasks implemented by two components: entity detection, a...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.06.014

    authors: Grouin C,Moriceau V,Zweigenbaum P

    更新日期:2015-12-01 00:00:00

  • DEEPEN: A negation detection system for clinical text incorporating dependency relation into NegEx.

    abstract::In Electronic Health Records (EHRs), much of valuable information regarding patients' conditions is embedded in free text format. Natural language processing (NLP) techniques have been developed to extract clinical information from free text. One challenge faced in clinical NLP is that the meaning of clinical entities...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.02.010

    authors: Mehrabi S,Krishnan A,Sohn S,Roch AM,Schmidt H,Kesterson J,Beesley C,Dexter P,Max Schmidt C,Liu H,Palakal M

    更新日期:2015-04-01 00:00:00

  • Visual aggregate analysis of eligibility features of clinical trials.

    abstract:OBJECTIVE:To develop a method for profiling the collective populations targeted for recruitment by multiple clinical studies addressing the same medical condition using one eligibility feature each time. METHODS:Using a previously published database COMPACT as the backend, we designed a scalable method for visual aggr...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.01.005

    authors: He Z,Carini S,Sim I,Weng C

    更新日期:2015-04-01 00:00:00

  • A pilot study of a heuristic algorithm for novel template identification from VA electronic medical record text.

    abstract:RATIONALE:Templates in text notes pose challenges for automated information extraction algorithms. We propose a method that identifies novel templates in plain text medical notes. The identification can then be used to either include or exclude templates when processing notes for information extraction. METHODS:The tw...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.07.019

    authors: Redd AM,Gundlapalli AV,Divita G,Carter ME,Tran LT,Samore MH

    更新日期:2017-07-01 00:00:00

  • Predicting severe clinical events by learning about life-saving actions and outcomes using distant supervision.

    abstract::Medical error is a leading cause of patient death in the United States. Among the different types of medical errors, harm to patients caused by doctors missing early signs of deterioration is especially challenging to address due to the heterogeneity of patients' physiological patterns. In this study, we implemented r...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2020.103425

    authors: Lee DH,Yetisgen M,Vanderwende L,Horvitz E

    更新日期:2020-07-01 00:00:00

  • A novel web informatics approach for automated surveillance of cancer mortality trends.

    abstract::Cancer surveillance data are collected every year in the United States via the National Program of Cancer Registries (NPCR) and the Surveillance, Epidemiology and End Results (SEER) Program of the National Cancer Institute (NCI). General trends are closely monitored to measure the nation's progress against cancer. The...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.03.027

    authors: Tourassi G,Yoon HJ,Xu S

    更新日期:2016-06-01 00:00:00

  • Towards an on-demand peer feedback system for a clinical knowledge base: a case study with order sets.

    abstract:OBJECTIVE:We have developed an automated knowledge base peer feedback system as part of an effort to facilitate the creation and refinement of sound clinical knowledge content within an enterprise-wide knowledge base. The program collects clinical data stored in our Clinical Data Repository during usage of a physician ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2007.05.006

    authors: Hulse NC,Del Fiol G,Bradshaw RL,Roemer LK,Rocha RA

    更新日期:2008-02-01 00:00:00

  • The EU-ADR corpus: annotated drugs, diseases, targets, and their relationships.

    abstract::Corpora with specific entities and relationships annotated are essential to train and evaluate text-mining systems that are developed to extract specific structured information from a large corpus. In this paper we describe an approach where a named-entity recognition system produces a first annotation and annotators ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2012.04.004

    authors: van Mulligen EM,Fourrier-Reglat A,Gurwitz D,Molokhia M,Nieto A,Trifiro G,Kors JA,Furlong LI

    更新日期:2012-10-01 00:00:00

  • Evaluation of an Enhanced Role-Based Access Control model to manage information access in collaborative processes for a statewide clinical education program.

    abstract:BACKGROUND:Managing information access in collaborative processes is a critical requirement to team-based biomedical research, clinical education, and patient care. We have previously developed a computation model, Enhanced Role-Based Access Control (EnhancedRBAC), and applied it to coordinate information access in the...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2013.11.007

    authors: Le XH,Doll T,Barbosu M,Luque A,Wang D

    更新日期:2014-08-01 00:00:00

  • PharmActa: Personalized pharmaceutical care eHealth platform for patients and pharmacists.

    abstract::Community pharmacists are critically placed in the patient care chain being an extended frontline within primary healthcare networks across Europe. They are trained to ensure safe and effective medication use, a crucial and responsible role, extending beyond the common misconception limited to just providing timely ac...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2019.103336

    authors: Spanakis M,Sfakianakis S,Kallergis G,Spanakis EG,Sakkalis V

    更新日期:2019-12-01 00:00:00

  • On the reproducibility of results of pathway analysis in genome-wide expression studies of colorectal cancers.

    abstract::One of the major problems in genomics and medicine is the identification of gene networks and pathways deregulated in complex and polygenic diseases, like cancer. In this paper, we address the problem of assessing the variability of results of pathways analysis identified in different and independent genome wide expre...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2009.09.005

    authors: Maglietta R,Distaso A,Piepoli A,Palumbo O,Carella M,D'Addabbo A,Mukherjee S,Ancona N

    更新日期:2010-06-01 00:00:00

  • Learning classification models from multiple experts.

    abstract::Building classification models from clinical data using machine learning methods often relies on labeling of patient examples by human experts. Standard machine learning framework assumes the labels are assigned by a homogeneous process. However, in reality the labels may come from multiple experts and it may be diffi...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2013.08.007

    authors: Valizadegan H,Nguyen Q,Hauskrecht M

    更新日期:2013-12-01 00:00:00

  • Impact of an electronic handoff documentation tool on team shared mental models in pediatric critical care.

    abstract:OBJECTIVE:To examine the impact of the implementation of an electronic handoff tool (the Handoff Tool) on shared mental models (SMM) within patient care teams as measured by content overlap and discrepancies in verbal handoff presentations given by different clinicians caring for the same patient. MATERIALS AND METHOD...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2017.03.004

    authors: Jiang SY,Murphy A,Heitkemper EM,Hum RS,Kaufman DR,Mamykina L

    更新日期:2017-05-01 00:00:00

  • An image score inference system for RNAi genome-wide screening based on fuzzy mixture regression modeling.

    abstract::With recent advances in fluorescence microscopy imaging techniques and methods of gene knock down by RNA interference (RNAi), genome-scale high-content screening (HCS) has emerged as a powerful approach to systematically identify all parts of complex biological processes. However, a critical barrier preventing fulfill...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2008.04.007

    authors: Wang J,Zhou X,Li F,Bradley PL,Chang SF,Perrimon N,Wong ST

    更新日期:2009-02-01 00:00:00

  • A framework for modeling health behavior protocols and their linkage to behavioral theory.

    abstract::With the rise in chronic, behavior-related disease, computerized behavioral protocols (CBPs) that help individuals improve behaviors have the potential to play an increasing role in the future health of society. To be effective and widely used CBPs should be based on accepted behavioral theory. However, designing CBPs...

    journal_title:Journal of biomedical informatics

    pub_type: 临床试验,杂志文章

    doi:10.1016/j.jbi.2004.12.001

    authors: Lenert L,Norman GJ,Mailhot M,Patrick K

    更新日期:2005-08-01 00:00:00

  • Neural network-based approaches for biomedical relation classification: A review.

    abstract::The explosive growth of biomedical literature has created a rich source of knowledge, such as that on protein-protein interactions (PPIs) and drug-drug interactions (DDIs), locked in unstructured free text. Biomedical relation classification aims to automatically detect and classify biomedical relations, which has gre...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章,评审

    doi:10.1016/j.jbi.2019.103294

    authors: Zhang Y,Lin H,Yang Z,Wang J,Sun Y,Xu B,Zhao Z

    更新日期:2019-11-01 00:00:00

  • Learning hidden patterns from patient multivariate time series data using convolutional neural networks: A case study of healthcare cost prediction.

    abstract:OBJECTIVE:To develop an effective and scalable individual-level patient cost prediction method by automatically learning hidden temporal patterns from multivariate time series data in patient insurance claims using a convolutional neural network (CNN) architecture. METHODS:We used three years of medical and pharmacy c...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2020.103565

    authors: Morid MA,Sheng ORL,Kawamoto K,Abdelrahman S

    更新日期:2020-11-01 00:00:00

  • A controlled greedy supervised approach for co-reference resolution on clinical text.

    abstract::Identification of co-referent entity mentions inside text has significant importance for other natural language processing (NLP) tasks (e.g. event linking). However, this task, known as co-reference resolution, remains a complex problem, partly because of the confusion over different evaluation metrics and partly beca...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2013.03.007

    authors: Chowdhury MF,Zweigenbaum P

    更新日期:2013-06-01 00:00:00

  • Automatic detection of protected health information from clinic narratives.

    abstract::This paper presents a natural language processing (NLP) system that was designed to participate in the 2014 i2b2 de-identification challenge. The challenge task aims to identify and classify seven main Protected Health Information (PHI) categories and 25 associated sub-categories. A hybrid model was proposed which com...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.06.015

    authors: Yang H,Garibaldi JM

    更新日期:2015-12-01 00:00:00

  • A cascaded approach for Chinese clinical text de-identification with less annotation effort.

    abstract::With rapid adoption of Electronic Health Records (EHR) in China, an increasing amount of clinical data has been available to support clinical research. Clinical data secondary use usually requires de-identification of personal information to protect patient privacy. Since manually de-identification of free clinical te...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2017.07.017

    authors: Jian Z,Guo X,Liu S,Ma H,Zhang S,Zhang R,Lei J

    更新日期:2017-09-01 00:00:00

  • Development of a clinician reputation metric to identify appropriate problem-medication pairs in a crowdsourced knowledge base.

    abstract:BACKGROUND:Correlation of data within electronic health records is necessary for implementation of various clinical decision support functions, including patient summarization. A key type of correlation is linking medications to clinical problems; while some databases of problem-medication links are available, they are...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2013.11.010

    authors: McCoy AB,Wright A,Rogith D,Fathiamini S,Ottenbacher AJ,Sittig DF

    更新日期:2014-04-01 00:00:00

  • MeSHy: Mining unanticipated PubMed information using frequencies of occurrences and concurrences of MeSH terms.

    abstract:MOTIVATION:PubMed is the most widely used database of biomedical literature. To the detriment of the user though, the ranking of the documents retrieved for a query is not content-based, and important semantic information in the form of assigned Medical Subject Headings (MeSH) terms is not readily presented or producti...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2011.05.009

    authors: Theodosiou T,Vizirianakis IS,Angelis L,Tsaftaris A,Darzentas N

    更新日期:2011-12-01 00:00:00

  • Intradialytic blood pressure pattern recognition based on density peak clustering.

    abstract::End-stage renal disease (ESRD) is the final stage of chronic kidney disease (CKD) and requires hemodialysis (HD) for survival. Intradialytic blood pressure (IBP) measurements are necessary to ensure patient safety during HD treatments and have critical clinical and prognostic significance. Studies on IBP measurements,...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2018.05.013

    authors: Wang F,Zhou JY,Tian Y,Wang Y,Zhang P,Chen JH,Li JS

    更新日期:2018-07-01 00:00:00

  • Inductive creation of an annotation schema for manually indexing clinical conditions from emergency department reports.

    abstract::Evaluating automated indexing applications requires comparing automatically indexed terms against manual reference standard annotations. However, there are no standard guidelines for determining which words from a textual document to include in manual annotations, and the vague task can result in substantial variation...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2005.06.004

    authors: Chapman WW,Dowling JN

    更新日期:2006-04-01 00:00:00

  • Reflective Random Indexing and indirect inference: a scalable method for discovery of implicit connections.

    abstract::The discovery of implicit connections between terms that do not occur together in any scientific document underlies the model of literature-based knowledge discovery first proposed by Swanson. Corpus-derived statistical models of semantic distance such as Latent Semantic Analysis (LSA) have been evaluated previously a...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2009.09.003

    authors: Cohen T,Schvaneveldt R,Widdows D

    更新日期:2010-04-01 00:00:00

  • Research-IQ: development and evaluation of an ontology-anchored integrative query tool.

    abstract::Investigators in the translational research and systems medicine domains require highly usable, efficient and integrative tools and methods that allow for the navigation of and reasoning over emerging large-scale data sets. Such resources must cover a spectrum of granularity from bio-molecules to population phenotypes...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2011.07.006

    authors: Borlawsky TB,Lele O,Payne PR

    更新日期:2011-12-01 00:00:00

  • Comparing image search behaviour in the ARRS GoldMiner search engine and a clinical PACS/RIS.

    abstract::Information search has changed the way we manage knowledge and the ubiquity of information access has made search a frequent activity, whether via Internet search engines or increasingly via mobile devices. Medical information search is in this respect no different and much research has been devoted to analyzing the w...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.04.013

    authors: De-Arteaga M,Eggel I,Do B,Rubin D,Kahn CE Jr,Müller H

    更新日期:2015-08-01 00:00:00

  • Classification models for the prediction of clinicians' information needs.

    abstract:OBJECTIVE:Clinicians face numerous information needs during patient care activities and most of these needs are not met. Infobuttons are information retrieval tools that help clinicians to fulfill their information needs by providing links to on-line health information resources from within an electronic medical record...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2008.07.001

    authors: Del Fiol G,Haug PJ

    更新日期:2009-02-01 00:00:00