Abstract：
:The centralized and public availability of molecular sequence and clinical trial data presents an opportunity to identify potentially valuable linkages across the bench-to-bedside "T1" translational barrier. In this study, we sought to leverage keyword metadata (Medical Subject Heading [MeSH] descriptors) to infer relationships between molecular sequences and clinical trials, as indexed by GenBank and ClinicalTrials.gov. The results of this feasibility study found that approximately 30% of sequences in GenBank could be linked to trials and over 90% of trials in ClinicalTrials.gov could be linked to sequences through MeSH descriptors. In a cursory evaluation, we were able to consistently identify meaningful linkages between molecular sequences and clinical trials. Based on our findings, there may be promise in subsequent studies aiming to identify linkages across the T1 translational barrier using existing large repositories.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Chen ES,Sarkar INdoi
10.1016/j.jbi.2009.10.003subject
Has Abstractpub_date
2010-06-01 00:00:00pages
442-50issue
3eissn
1532-0464issn
1532-0480pii
S1532-0464(09)00138-5journal_volume
43pub_type
杂志文章abstract：:Social media has been identified as a promising potential source of information for pharmacovigilance. The adoption of social media data has been hindered by the massive and noisy nature of the data. Initial attempts to use social media data have relied on exact text matches to drugs of interest, and therefore suffer ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103307
更新日期：2019-11-01 00:00:00
abstract：:Identifying the symptom clusters (two or more related symptoms) with shared underlying molecular mechanisms has been a vital analysis task to promote the symptom science and precision health. Related studies have applied the clustering algorithms (e.g. k-means, latent class model) to detect the symptom clusters mostly...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2020.103482
更新日期：2020-07-01 00:00:00
abstract：:Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented significant challenges. The variability in data volume results in variable computing and storage requirements, theref...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2014.01.005
更新日期：2014-06-01 00:00:00
abstract：:Previous research on standardization of eligibility criteria and its feasibility has traditionally been conducted on clinical trial protocols from ClinicalTrials.gov (CT). The portability and use of such standardization for full-text industry-standard protocols has not been studied in-depth. Towards this end, in this ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.06.001
更新日期：2013-10-01 00:00:00
abstract：:The rapid expansion of biomedical knowledge, reduction in computing costs, and spread of internet access have created an ocean of electronic data. The decentralized nature of our scientific community and healthcare system, however, has resulted in a patchwork of diverse, or heterogeneous, database implementations, mak...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1006/jbin.2001.1024
更新日期：2001-08-01 00:00:00
abstract：INTRODUCTION:The trend of an ageing and growing world population, particularly in developed countries, is expected to continue for decades to come causing an increase in demand for healthcare resources and services. Consequently, demand is growing faster than rises in funding. The UK government, in partnership with the...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2019.103102
更新日期：2019-02-01 00:00:00
abstract：PURPOSE:Negative life events, such as the death of a family member, an argument with a spouse or the loss of a job, play an important role in triggering depressive episodes. Therefore, it is worthwhile to develop psychiatric services that can automatically identify such events. This study describes the use of associati...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2011.01.006
更新日期：2011-08-01 00:00:00
abstract：:Named entity recognition is an extremely important and fundamental task of biomedical text mining. Biomedical named entities include mentions of proteins, genes, DNA, RNA, etc which often have complex structures, but it is challenging to identify and classify such entities. Machine learning methods like CRF, MEMM and ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2008.12.012
更新日期：2009-10-01 00:00:00
abstract：:To improve the performance of Intensive Care Units (ICUs), the field of bio-statistics has developed scores which try to predict the likelihood of negative outcomes. These help evaluate the effectiveness of treatments and clinical practice, and also help to identify patients with unexpected outcomes. However, they hav...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103269
更新日期：2019-10-01 00:00:00
abstract：BACKGROUND:Identifying key variables such as disorders within the clinical narratives in electronic health records has wide-ranging applications within clinical practice and biomedical research. Previous research has demonstrated reduced performance of disorder named entity recognition (NER) and normalization (or groun...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.07.010
更新日期：2015-10-01 00:00:00
abstract：:Drug target interaction is a prominent research area in the field of drug discovery. It refers to the recognition of interactions between chemical compounds and the protein targets in the human body. Wet lab experiments to identify these interactions are expensive as well as time consuming. The computational methods o...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2019.103159
更新日期：2019-05-01 00:00:00
abstract：OBJECTIVE:Evaluate the quality of clinical order practice patterns machine-learned from clinician cohorts stratified by patient mortality outcomes. MATERIALS AND METHODS:Inpatient electronic health records from 2010 to 2013 were extracted from a tertiary academic hospital. Clinicians (n = 1822) were stratified into lo...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.09.005
更新日期：2018-10-01 00:00:00
abstract：:One of the challenging problems in drug discovery is to identify the novel targets for drugs. Most of the traditional methods for drug targets optimization focused on identifying the particular families of "druggable targets", but ignored their topological properties based on the biological pathways. In this study, we...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.02.007
更新日期：2015-04-01 00:00:00
abstract：:Computational identification of missing enzymes plays a significant role in accurate and complete reconstruction of metabolic network for both newly sequenced and well-studied organisms. For a metabolic reaction, given a set of candidate enzymes identified according to certain biological evidences, a powerful mathemat...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2007.09.002
更新日期：2008-04-01 00:00:00
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
更新日期：2016-06-01 00:00:00
abstract：:The Foundational Model of Anatomy (FMA), initially developed as an enhancement of the anatomical content of UMLS, is a domain ontology of the concepts and relationships that pertain to the structural organization of the human body. It encompasses the material objects from the molecular to the macroscopic levels that c...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2003.11.007
更新日期：2003-12-01 00:00:00
abstract：:Proper understanding of textual data requires the exploitation and integration of unstructured and heterogeneous clinical sources, healthcare records or scientific literature, which are fundamental aspects in clinical and translational research. The determination of semantic similarity between word pairs is an importa...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2010.09.002
更新日期：2011-02-01 00:00:00
abstract：BACKGROUND:The realization of the potential benefits of health information exchange systems (HIEs) for emergency departments (EDs) depends on the way these systems are actually used. The attributes of volume of information and duration of information processing are important for the study of HIE use patterns in the ED,...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.05.007
更新日期：2017-07-01 00:00:00
abstract：:Linkage analysis uses information from family pedigrees to map genes and locate disease genes on particular chromosomes. A recombination fraction denoted as theta is estimated as a measure of crossing over between two loci. Genetic linkage calculations are very time-consuming particularly for large family pedigrees, a...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1006/jbin.2002.1031
更新日期：2001-12-01 00:00:00
abstract：:In this paper, a Hidden Semi-Markov Model (HSMM) based approach is proposed to evaluate and monitor body motion during a rehabilitation training program. The approach extracts clinically relevant motion features from skeleton joint trajectories, acquired by the RGB-D camera, and provides a score for the subject's perf...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.12.012
更新日期：2018-02-01 00:00:00
abstract：:Game-based interventions (GBI) have been used to promote health-related outcomes, including cognitive functions. Criteria for game-elements (GE) selection are insufficiently characterized in terms of their adequacy to patients' clinical conditions or targeted cognitive outcomes. This study aimed to identify GE applied...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103287
更新日期：2019-10-01 00:00:00
abstract：:Human musculoskeletal system resources of the human body are valuable for the learning and medical purposes. Internet-based information from conventional search engines such as Google or Yahoo cannot response to the need of useful, accurate, reliable and good-quality human musculoskeletal resources related to medical ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2012.11.001
更新日期：2013-02-01 00:00:00
abstract：:The aim of this study is to explore the word sense disambiguation (WSD) problem across two biomedical domains-biomedical literature and clinical notes. A supervised machine learning technique was used for the WSD task. One of the challenges addressed is the creation of a suitable clinical corpus with manual sense anno...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2008.02.003
更新日期：2008-12-01 00:00:00
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
更新日期：2015-08-01 00:00:00
abstract：:We designed and implemented a generic search engine (Vaidurya), as part of our Digital clinical-Guideline Library (DeGeL) framework. Two search methods were implemented in addition to full-text search: (1) concept-based search, which relies on pre-indexing the guidelines in a clinically meaningful fashion, and (2) con...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2008.07.003
更新日期：2009-02-01 00:00:00
abstract：:Patient monitoring algorithms that analyze multiple features from physiological signals can produce an index that serves as a predictive or prognostic measure for a specific critical health event or physiological instability. Classical detection metrics such as sensitivity and positive predictive value are often used ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.09.008
更新日期：2017-11-01 00:00:00
abstract：:Bioinformatics research relies heavily on the ability to discover and correlate data from various sources. The specialization of life sciences over the past decade, coupled with an increasing number of biomedical datasets available through standardized interfaces, has created opportunities towards new methods in biome...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.10.001
更新日期：2014-02-01 00:00:00
abstract：OBJECTIVE:Clinical care guidelines recommend that newly diagnosed prostate cancer patients at high risk for metastatic spread receive a bone scan prior to treatment and that low risk patients not receive it. The objective was to develop an automated pipeline to interrogate heterogeneous data to evaluate the use of bone...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103184
更新日期：2019-06-01 00:00:00
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
更新日期：2005-08-01 00:00:00
abstract：:Stomach cancer is one of the leading causes of cancer-related deaths worldwide. More than 80% diagnosis of this cancer occur at later stages leading to low 5-year survival rate. This emphasizes the need to have better prognostic techniques for stomach cancer. In this regard, the Next-Generation Sequencing of whole gen...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103254
更新日期：2019-09-01 00:00:00
