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Journal of Biomedical Informatics

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https://www.readbyqxmd.com/read/28625880/predicting-biomedical-metadata-in-cedar-a-study-of-gene-expression-omnibus-geo
#1
Maryam Panahiazar, Michel Dumontier, Olivier Gevaert
A crucial and limiting factor in data reuse is the lack of accurate, structured, and complete descriptions of data, known as metadata. Towards improving the quantity and quality of metadata, we propose a novel metadata prediction framework to learn associations from existing metadata that can be used to predict metadata values. We evaluate our framework in the context of experimental metadata from the Gene Expression Omnibus (GEO). We applied four rule mining algorithms to the most common structured metadata elements (sample type, molecular type, platform, label type and organism) from over 1,3 million GEO records...
June 15, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28624644/psychiatric-symptom-recognition-without-labeled-data-using-distributional-representations-of-phrases-and-on-line-knowledge
#2
Yaoyun Zhang, Olivia Zhang, Yonghui Wu, Hee-Jin Lee, Jun Xu, Hua Xu, Kirk Roberts
OBJECTIVE: Mental health is becoming an increasingly important topic in healthcare. Psychiatric symptoms, which consist of subjective descriptions of the patient's experience, as well as the nature and severity of mental disorders, are critical to support the phenotypic classification for personalized prevention, diagnosis, and intervention of mental disorders. However, few automated approaches have been proposed to extract psychiatric symptoms from clinical text, mainly due to (a) the lack of annotated corpora, which are time-consuming and costly to build, and (b) the inherent linguistic difficulties that symptoms present as they are not well-defined clinical concepts like diseases...
June 14, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28624643/automated-detection-of-records-in-biological-sequence-databases-that-are-inconsistent-with-the-literature
#3
Mohamed Reda Bouadjenek, Karin Verspoor, Justin Zobel
We investigate and analyse the data quality of nucleotide sequence databases with the objective of automatic detection of data anomalies and suspicious records. Specifically, we demonstrate that the published literature associated with each data record can be used to automatically evaluate its quality, by cross-checking the consistency of the key content of the database record with the referenced publications. Focusing on GenBank, we describe a set of quality indicators based on the relevance paradigm of information retrieval (IR)...
June 14, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28624642/drugsemantics-a-corpus-for-named-entity-recognition-in-spanish-summaries-of-product-characteristics
#4
Isabel Moreno, Ester Boldrini, Paloma Moreda, M Teresa Romá-Ferri
For the healthcare sector, it is critical to exploit the vast amount of textual health-related information. Nevertheless, healthcare providers have difficulties to benefit from such quantity of data during pharmacotherapeutic care. The problem is that such information is stored in different sources and their consultation time is limited. In this context, Natural Language Processing techniques can be applied to efficiently transform textual data into structured information so that it could be used in critical healthcare applications, being of help for physicians in their daily workload, such as: decision support systems, cohort identification, patient management, etc...
June 14, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28624641/text-mining-applied-to-electronic-cardiovascular-procedure-reports-to-identify-patients-with-trileaflet-aortic-stenosis-and-coronary-artery-disease
#5
Aeron M Small, Daniel H Kiss, Yevgeny Zlatsin, David L Birtwell, Heather Williams, Marie A Guerraty, Yuchi Han, Saif Anwaruddin, John H Holmes, Julio A Chirinos, Robert L Wilensky, Jay Giri, Daniel J Rader
BACKGROUND: Interrogation of the electronic health record (EHR) using billing codes as a surrogate for diagnoses of interest has been widely used for clinical research. However, the accuracy of this methodology is variable, as it reflects billing codes rather than severity of disease, and depends on the disease and the accuracy of the coding practitioner. Systematic application of text mining to the EHR has had variable success for the detection of cardiovascular phenotypes. We hypothesize that the application of text mining algorithms to cardiovascular procedure reports may be a superior method to identify patients with cardiovascular conditions of interest...
June 14, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28614702/de-identification-of-psychiatric-intake-records-overview-of-2016-cegs-n-grid-shared-tasks-track-1
#6
Amber Stubbs, Michele Filannino, Özlem Uzuner
The 2016 CEGS N-GRID shared tasks for clinical records contained three tracks. Track 1 focused on de-identification of a new corpus of 1,000 psychiatric intake records. This track tackled de-identification in two sub-tracks: Track 1.A was a "sight unseen" task, where nine teams ran existing de-identification systems, without any modifications or training, on 600 new records in order to gauge how well systems generalize to new data. The best-performing system for this track scored an F1 of 0.799. Track 1.B was a traditional Natural Language Processing (NLP) shared task on de-identification, where 15 teams had two months to train their systems on the new data, then test it on an unannotated test set...
June 11, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28606870/a-deep-learning-approach-for-predicting-the-quality-of-online-health-expert-question-answering-services
#7
Ze Hu, Zhan Zhang, Haiqin Yang, Qing Chen, Decheng Zuo
Recently, online health expert question-answering (HQA) services (systems) have attracted more and more health consumers to ask health-related questions everywhere at any time due to the convenience and effectiveness. However, the quality of answers in existing HQA systems varies in different situations. It is significant to provide effective tools to automatically determine the quality of the answers. Two main characteristics in HQA systems raise the difficulties of classification: 1) physicians' answers in an HQA system are usually written in short text, which yields the data sparsity issue; 2) HQA systems apply the quality control mechanism, which shield the wisdom of crowd...
June 9, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28606869/predicting-mental-conditions-based-on-history-of-present-illness-in-psychiatric-notes-with-deep-neural-networks
#8
Tung Tran, Ramakanth Kavuluru
BACKGROUND: Applications of natural language processing to mental health notes are not common given the sensitive nature of the associated narratives. The CEGS N-GRID 2016 Shared Task in Clinical Natural Language Processing (NLP) changed this scenario by providing the first set of neuropsychiatric notes to participants. This study summarizes our efforts and results in proposing a novel data use case for this dataset as part of the third track in this shared task. OBJECTIVE: We explore the feasibility and effectiveness of predicting a set of common mental conditions a patient has based on the short textual description of patient's history of present illness typically occurring in the beginning of a psychiatric initial evaluation note...
June 9, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28603041/modeling-the-mind-how-do-we-design-effective-decision-support
#9
EDITORIAL
Michael Rubin, Mathew Samore, Charlene R Weir, Jonathan Nebeker
No abstract text is available yet for this article.
June 8, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28602908/learning-to-identify-protected-health-information-by-integrating-knowledge-and-data-driven-algorithms-a-case-study-on-psychiatric-evaluation-notes
#10
Azad Dehghan, Aleksandar Kovacevic, George Karystianis, John A Keane, Goran Nenadic
De-identification of clinical narratives is one of the main obstacles to making healthcare free text available for research. In this paper we describe our experience in expanding and tailoring two existing tools as part of the 2016 CEGS N-GRID Shared Tasks Track 1, which evaluated de-identification methods on a set of psychiatric evaluation notes for up to 25 different types of Protected Health Information (PHI). The methods we used rely on machine learning on either a large or small feature space, with additional strategies, including two-pass tagging and multi-class models, which both proved to be beneficial...
June 7, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28602907/an-efficient-architecture-to-support-digital-pathology-in-standard-medical-imaging-repositories
#11
Tiago Marques Godinho, Rui Lebre, Luís Bastião Silva, Carlos Costa
In the past decade, digital pathology and whole-slide imaging (WSI) have been gaining momentum with the proliferation of digital scanners from different manufacturers. The literature reports significant advantages associated with the adoption of digital images in pathology, namely, improvements in diagnostic accuracy and better support for telepathology. Moreover, it also offers new clinical and research applications. However, numerous barriers have been slowing the adoption of WSI, among which the most important are performance issues associated with storage and distribution of huge volumes of data, and lack of interoperability with other hospital information systems, most notably Picture Archive and Communications Systems (PACS) based on the DICOM standard...
June 7, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28602906/counting-trees-in-random-forests-predicting-symptom-severity-in-psychiatric-intake-reports
#12
Elyne Scheurwegs, Madhumita Sushil, Stéphan Tulkens, Walter Daelemans, Kim Luyckx
The CEGS N-GRID 2016 Shared Task (Filannino, Stubbs, Uzuner (2017)) in Clinical Natural Language Processing introduces the assignment of a severity score to a psychiatric symptom, based on a psychiatric intake report. We present a method that employs the inherent interview-like structure of the report to extract relevant information from the report and generate a representation. The representation consists of a restricted set of psychiatric concepts (and the context they occur in), identified using medical concepts defined in UMLS that are directly related to the psychiatric diagnoses present in the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV) ontology...
June 7, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28602905/special-issue-on-cognitive-informatics-methods-for-interactive-clinical-systems
#13
EDITORIAL
Thomas G Kannampallil, Vimla L Patel
No abstract text is available yet for this article.
June 7, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28602904/a-hybrid-approach-to-automatic-de-identification-of-psychiatric-notes
#14
Hee-Jin Lee, Yonghui Wu, Yaoyun Zhang, Jun Xu, Hua Xu, Kirk Roberts
De-identification, or identifying and removing protected health information (PHI) from clinical data, is a critical step in making clinical data available for clinical applications and research. This paper presents a natural language processing system for automatic de-identification of psychiatric notes, which was designed to participate in the 2016 CEGS N-GRID shared task Track 1. The system has a hybrid structure that combines machine leaning techniques and rule-based approaches. The rule-based components exploit the structure of the psychiatric notes as well as characteristic surface patterns of PHI mentions...
June 7, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28600026/metabolitepredict-a-de-novo-human-metabolomics-prediction-system-and-its-applications-in-rheumatoid-arthritis
#15
QuanQiu Wang, Rong Xu
Human metabolomics has great potential in disease mechanism understanding, early diagnosis, and therapy. Existing metabolomics studies are often based on profiling patient biofluids and tissue samples and are difficult owing to the challenges of sample collection and data processing. Here, we report an alternative approach and developed a computation-based prediction system, MetabolitePredict, for disease metabolomics biomarker prediction. We applied MetabolitePredict to identify metabolite biomarkers and metabolite targeting therapies for rheumatoid arthritis (RA), a last-lasting complex disease with multiple genetic and environmental factors involved...
June 6, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28600025/creating-a-sustainable-collaborative-consumer-health-application-for-chronic-disease-self-management
#16
Constance M Johnson, Steve McIlwain, Oliver Gray, Bradley Willson, Allison Vorderstrasse
As the prevalence of chronic diseases increase, there is a need for consumer-centric health informatics applications that assist individuals with disease self-management skills. However, due to the cost of development of these applications, there is also a need to build a disease agnostic architecture so that they could be reused for any chronic disease. This paper describes the architecture of a collaborative virtual environment (VE) platform, LIVE©, that was developed to teach self-management skills and provide social support to those individuals with type 2 diabetes...
June 6, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28587890/spectral-dynamic-representation-of-dna-sequences
#17
Dorota Bielińska-Wa Ż, Piotr Wa Ż
A graphical representation of DNA sequences in which the distribution of a particular base B=A,C,G,T is represented by a set of discrete lines has been formulated. The methodology of this approach has been borrowed from two areas of physics: spectroscopy and dynamics. Consequently, the set of discrete lines is referred to as the B-spectrum. Next, the B-spectrum is transformed to a rigid body composed of material points. In this way a dynamic representation of the DNA sequence has been obtained. The centers of mass of these rigid bodies, divided by their moments of inertia, have been taken as the descriptors of the spectra and, thus, of the DNA sequences...
June 3, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28583809/an-empirical-analysis-of-ontology-reuse-in-bioportal
#18
Christopher Ochs, Yehoshua Perl, James Geller, Sivaram Arabandi, Tania Tudorache, Mark A Musen
Biomedical ontologies often reuse content (i.e., classes and properties) from other ontologies. Content reuse enables a consistent representation of a domain and reusing content can save an ontology author significant time and effort. Prior studies have investigated the existence of reused terms among the ontologies in the NCBO BioPortal, but as of yet there has not been a study investigating how the ontologies in BioPortal utilize reused content in the modeling of their own content. In this study we investigate how 355 ontologies hosted in the NCBO BioPortal reuse content from other ontologies for the purposes of creating new ontology content...
June 2, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28579533/de-identification-of-clinical-notes-via-recurrent-neural-network-and-conditional-random-field
#19
Zengjian Liu, Buzhou Tang, Xiaolong Wang, Qingcai Chen
De-identification, identifying information from data, such as protected health information (PHI) present in clinical data, is a critical step to enable data to be shared or published. The 2016 Centers of Excellence in Genomic Science (CEGS) Neuropsychiatric Genome-scale and RDOC Individualized Domains (N-GRID) clinical natural language processing (NLP) challenge contains a de-identification track in de-identifying electronic medical records (EMRs) (i.e., track 1). The challenge organizers provide 1000 annotated mental health records for this track, 600 out of which are used as a training set and 400 as a test set...
June 1, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28579532/dashboard-visualizations-supporting-real-time-throughput-decision-making
#20
Amy Franklin, Swaroop Gantela, Salsawit Shifarraw, Todd R Johnson, David J Robinson, Brent R King, Amit M Mehta, Charles L Maddow, Nathan R Hoot, Vickie Nguyen, Adriana Stanley, Jiajie Zhang, Nnaemeka G Okafor
Providing timely and effective care in the emergency department (ED) requires the management of individual patients as well as the flow and demands of the entire department. Strategic changes to work processes, such as adding a flow coordination nurse or a physician in triage, have demonstrated improvements in throughput times. However, such global strategic changes do not address the real-time, often opportunistic workflow decisions of individual clinicians in the ED. We believe that real-time representation of the status of the entire emergency department and each patient within it through information visualizations will better support clinical decision-making in-the-moment and provide for rapid intervention to improve ED flow...
June 1, 2017: Journal of Biomedical Informatics
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