Biomedical ontologies: what part-of is and isn't.

Abstract:

:Mereological relations such as part-of and its inverse has-part are fundamental to the description of the structure of living organisms. Whereas classical mereology focuses on individual entities, mereological relations in biomedical ontologies are generally asserted between classes of individuals. In general, this practice leaves some basic issues unanswered: type constraints of mereological relations, e.g., concerning artifacts and biological entities, the relation between parthood and time, inferred parts and wholes as well as a delimitation of parthood against spatial inclusion. Furthermore, mereological relations can be asserted not only between physical objects but also between biological processes and medical procedures. We analyze these ambiguities and make suggestions for a standardization of mereological relations in biomedical ontologies.

journal_name

J Biomed Inform

authors

Schulz S,Kumar A,Bittner T

doi

10.1016/j.jbi.2005.11.003

keywords:

subject

Has Abstract

pub_date

2006-06-01 00:00:00

pages

350-61

issue

3

eissn

1532-0464

issn

1532-0480

pii

S1532-0464(05)00113-9

journal_volume

39

pub_type

杂志文章
  • Knowledge-based automated planning system for StereoElectroEncephaloGraphy: A center-based scenario.

    abstract::Surgical planning for StereoElectroEncephaloGraphy (SEEG) is a complex and patient specific task, where the experience and medical workflow of each institution may influence the final planning choices. To account for this variability, we developed a data-based Computer Assisted Planning (CAP) solution able to exploit ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2020.103460

    authors: Scorza D,Rizzi M,De Momi E,Cortés C,Bertelsen Á,Cardinale F

    更新日期:2020-08-01 00:00:00

  • Monitoring Obstructive Sleep Apnea by means of a real-time mobile system based on the automatic extraction of sets of rules through Differential Evolution.

    abstract::Real-time Obstructive Sleep Apnea (OSA) episode detection and monitoring are important for society in terms of an improvement in the health of the general population and of a reduction in mortality and healthcare costs. Currently, to diagnose OSA patients undergo PolySomnoGraphy (PSG), a complicated and invasive test ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2014.02.015

    authors: Sannino G,De Falco I,De Pietro G

    更新日期:2014-06-01 00:00:00

  • Modelling and analysing the dynamics of disease progression from cross-sectional studies.

    abstract::Clinical trials are typically conducted over a population within a defined time period in order to illuminate certain characteristics of a health issue or disease process. These cross-sectional studies give us a 'snapshot' of this disease process over a large number of people but do not allow us to model the temporal ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2012.11.003

    authors: Li Y,Swift S,Tucker A

    更新日期:2013-04-01 00:00:00

  • 3D interactive surgical visualization system using mobile spatial information acquisition and autostereoscopic display.

    abstract::Three-dimensional (3D) visualization of preoperative and intraoperative medical information becomes more and more important in minimally invasive surgery. We develop a 3D interactive surgical visualization system using mobile spatial information acquisition and autostereoscopic display for surgeons to observe surgical...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2017.05.014

    authors: Fan Z,Weng Y,Chen G,Liao H

    更新日期:2017-07-01 00:00:00

  • R.A.P.I.D. (Root Aggregated Prioritized Information Display): A single screen display for efficient digital triaging of medical reports.

    abstract:OBJECTIVE:The timely acknowledgement of critical patient clinical reports is vital for the delivery of safe patient care. With current EHR systems, critical reports reside on different screens. This leads to treatment delays and inefficient work flows. As a remedy, the R.A.P.I.D. (Root Aggregated Prioritized Informatio...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章,随机对照试验

    doi:10.1016/j.jbi.2016.04.001

    authors: Ford JP,Huang L,Richards DS,Ambinder EP,Rosenberger JL

    更新日期:2016-06-01 00:00:00

  • Wisdom of artificial crowds feature selection in untargeted metabolomics: An application to the development of a blood-based diagnostic test for thrombotic myocardial infarction.

    abstract:INTRODUCTION:Heart disease remains a leading cause of global mortality. While acute myocardial infarction (colloquially: heart attack), has multiple proximate causes, proximate etiology cannot be determined by a blood-based diagnostic test. We enrolled a suitable patient cohort and conducted a non-targeted quantificati...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章,多中心研究

    doi:10.1016/j.jbi.2018.03.007

    authors: Trainor PJ,Yampolskiy RV,DeFilippis AP

    更新日期:2018-05-01 00:00:00

  • GLIF3: a representation format for sharable computer-interpretable clinical practice guidelines.

    abstract::The Guideline Interchange Format (GLIF) is a model for representation of sharable computer-interpretable guidelines. The current version of GLIF (GLIF3) is a substantial update and enhancement of the model since the previous version (GLIF2). GLIF3 enables encoding of a guideline at three levels: a conceptual flowchart...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2004.04.002

    authors: Boxwala AA,Peleg M,Tu S,Ogunyemi O,Zeng QT,Wang D,Patel VL,Greenes RA,Shortliffe EH

    更新日期:2004-06-01 00:00:00

  • Evaluation of relational and NoSQL database architectures to manage genomic annotations.

    abstract::While the adoption of next generation sequencing has rapidly expanded, the informatics infrastructure used to manage the data generated by this technology has not kept pace. Historically, relational databases have provided much of the framework for data storage and retrieval. Newer technologies based on NoSQL architec...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.10.015

    authors: Schulz WL,Nelson BG,Felker DK,Durant TJS,Torres R

    更新日期:2016-12-01 00:00:00

  • Consensus and Meta-analysis regulatory networks for combining multiple microarray gene expression datasets.

    abstract::Microarray data is a key source of experimental data for modelling gene regulatory interactions from expression levels. With the rapid increase of publicly available microarray data comes the opportunity to produce regulatory network models based on multiple datasets. Such models are potentially more robust with great...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章,meta分析

    doi:10.1016/j.jbi.2008.01.011

    authors: Steele E,Tucker A

    更新日期:2008-12-01 00:00:00

  • Quality assurance of chemical ingredient classification for the National Drug File - Reference Terminology.

    abstract::The National Drug File - Reference Terminology (NDF-RT) is a large and complex drug terminology consisting of several classification hierarchies on top of an extensive collection of drug concepts. These hierarchies provide important information about clinical drugs, e.g., their chemical ingredients, mechanisms of acti...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2017.07.013

    authors: Zheng L,Yumak H,Chen L,Ochs C,Geller J,Kapusnik-Uner J,Perl Y

    更新日期:2017-09-01 00:00:00

  • Algorithms for rapid outbreak detection: a research synthesis.

    abstract::The threat of bioterrorism has stimulated interest in enhancing public health surveillance to detect disease outbreaks more rapidly than is currently possible. To advance research on improving the timeliness of outbreak detection, the Defense Advanced Research Project Agency sponsored the Bio-event Advanced Leading In...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2004.11.007

    authors: Buckeridge DL,Burkom H,Campbell M,Hogan WR,Moore AW

    更新日期:2005-04-01 00:00:00

  • Multi-faceted informatics system for digitising and streamlining the reablement care model.

    abstract::Reablement is new paradigm to increase independence in the home amongst the ageing population. And it remains a challenge to design an optimal electronic system to streamline and integrate reablement into current healthcare infrastructure. Furthermore, given reablement requires collaboration with a range of organisati...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.05.008

    authors: Bond RR,Mulvenna MD,Finlay DD,Martin S

    更新日期:2015-08-01 00:00:00

  • Prediction of influenza vaccination outcome by neural networks and logistic regression.

    abstract::The major challenge in influenza vaccination is to predict vaccine efficacy. The purpose of this study was to design a model to enable successful prediction of the outcome of influenza vaccination based on real historical medical data. A non-linear neural network approach was used, and its performance compared to logi...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2010.04.011

    authors: Trtica-Majnaric L,Zekic-Susac M,Sarlija N,Vitale B

    更新日期:2010-10-01 00:00:00

  • Game-based interventions for neuropsychological assessment, training and rehabilitation: Which game-elements to use? A systematic review.

    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

    authors: Ferreira-Brito F,Fialho M,Virgolino A,Neves I,Miranda AC,Sousa-Santos N,Caneiras C,Carriço L,Verdelho A,Santos O

    更新日期:2019-10-01 00:00:00

  • Facilitating pre-operative assessment guidelines representation using SNOMED CT.

    abstract:OBJECTIVE:To investigate whether SNOMED CT covers the terms used in pre-operative assessment guidelines, and if necessary, how the measured content coverage can be improved. METHODS:Pre-operative assessment guidelines were retrieved from the websites of (inter)national anesthesia-related societies. The recommendations...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2010.07.009

    authors: Ahmadian L,Cornet R,de Keizer NF

    更新日期:2010-12-01 00:00:00

  • Induction of comprehensible models for gene expression datasets by subgroup discovery methodology.

    abstract::Finding disease markers (classifiers) from gene expression data by machine learning algorithms is characterized by a high risk of overfitting the data due the abundance of attributes (simultaneously measured gene expression values) and shortage of available examples (observations). To avoid this pitfall and achieve pr...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2004.07.007

    authors: Gamberger D,Lavrac N,Zelezný F,Tolar J

    更新日期:2004-08-01 00:00:00

  • MACE prediction of acute coronary syndrome via boosted resampling classification using electronic medical records.

    abstract:OBJECTIVES:Major adverse cardiac events (MACE) of acute coronary syndrome (ACS) often occur suddenly resulting in high mortality and morbidity. Recently, the rapid development of electronic medical records (EMR) provides the opportunity to utilize the potential of EMR to improve the performance of MACE prediction. In t...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2017.01.001

    authors: Huang Z,Chan TM,Dong W

    更新日期:2017-02-01 00:00:00

  • Exploring the associations between drug side-effects and therapeutic indications.

    abstract::Drug therapeutic indications and side-effects are both measurable patient phenotype changes in response to the treatment. Inferring potential drug therapeutic indications and identifying clinically interesting drug side-effects are both important and challenging tasks. Previous studies have utilized either chemical st...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2014.03.014

    authors: Wang F,Zhang P,Cao N,Hu J,Sorrentino R

    更新日期:2014-10-01 00:00:00

  • Development of the nursing problem list subset of SNOMED CT®.

    abstract:OBJECTIVE:To create an interoperable set of nursing diagnoses for use in the patient problem list in the EHR to support interoperability. DESIGN:Queries for nursing diagnostic concepts were executed against the UMLS Metathesaurus to retrieve all nursing diagnoses across four nursing terminologies where the concept was...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2011.12.003

    authors: Matney SA,Warren JJ,Evans JL,Kim TY,Coenen A,Auld VA

    更新日期:2012-08-01 00:00:00

  • Comparison between passive vision-based system and a wearable inertial-based system for estimating temporal gait parameters related to the GAITRite electronic walkway.

    abstract::Quantitative gait analysis allows clinicians to assess the inherent gait variability over time which is a functional marker to aid in the diagnosis of disabilities or diseases such as frailty, the onset of cognitive decline and neurodegenerative diseases, among others. However, despite the accuracy achieved by the cur...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.07.009

    authors: González I,López-Nava IH,Fontecha J,Muñoz-Meléndez A,Pérez-SanPablo AI,Quiñones-Urióstegui I

    更新日期:2016-08-01 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

  • TRAK ontology: defining standard care for the rehabilitation of knee conditions.

    abstract::In this paper we discuss the design and development of TRAK (Taxonomy for RehAbilitation of Knee conditions), an ontology that formally models information relevant for the rehabilitation of knee conditions. TRAK provides the framework that can be used to collect coded data in sufficient detail to support epidemiologic...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2013.04.009

    authors: Button K,van Deursen RW,Soldatova L,Spasić I

    更新日期:2013-08-01 00:00:00

  • Comparison of reversible-jump Markov-chain-Monte-Carlo learning approach with other methods for missing enzyme identification.

    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

    authors: Geng B,Zhou X,Zhu J,Hung YS,Wong ST

    更新日期:2008-04-01 00:00:00

  • A term extraction tool for expanding content in the domain of functioning, disability, and health: proof of concept.

    abstract::Among the challenges in developing terminology systems is providing complete content coverage of specialized subject fields. This paper reports on a term extraction tool designed for the development and expansion of terminology systems concerned with functioning, disability, and health. Content relevant to this domain...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2003.09.005

    authors: Harris MR,Savova GK,Johnson TM,Chute CG

    更新日期:2003-08-01 00:00:00

  • Information extraction from biomedical text.

    abstract::Information extraction is the process of scanning text for information relevant to some interest, including extracting entities, relations, and events. It requires deeper analysis than key word searches, but its aims fall short of the very hard and long-term problem of full text understanding. Information extraction r...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/s1532-0464(03)00015-7

    authors: Hobbs JR

    更新日期:2002-08-01 00:00:00

  • A method and software framework for enriching private biomedical sources with data from public online repositories.

    abstract::Modern biomedical research relies on the semantic integration of heterogeneous data sources to find data correlations. Researchers access multiple datasets of disparate origin, and identify elements-e.g. genes, compounds, pathways-that lead to interesting correlations. Normally, they must refer to additional public da...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.02.004

    authors: Anguita A,García-Remesal M,Graf N,Maojo V

    更新日期:2016-04-01 00:00:00

  • Health information technology adoption: Understanding research protocols and outcome measurements for IT interventions in health care.

    abstract:OBJECTIVE:To classify and characterize the variables commonly used to measure the impact of Information Technology (IT) adoption in health care, as well as settings and IT interventions tested, and to guide future research. MATERIALS AND METHODS:We conducted a descriptive study screening a sample of 236 studies from a...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.07.018

    authors: Colicchio TK,Facelli JC,Del Fiol G,Scammon DL,Bowes WA 3rd,Narus SP

    更新日期:2016-10-01 00:00:00

  • Lexical patterns, features and knowledge resources for coreference resolution in clinical notes.

    abstract::Generation of entity coreference chains provides a means to extract linked narrative events from clinical notes, but despite being a well-researched topic in natural language processing, general-purpose coreference tools perform poorly on clinical texts. This paper presents a knowledge-centric and pattern-based approa...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2012.02.012

    authors: Gooch P,Roudsari A

    更新日期:2012-10-01 00:00:00

  • Quantifying semantic similarity of clinical evidence in the biomedical literature to facilitate related evidence synthesis.

    abstract:OBJECTIVE:Published clinical trials and high quality peer reviewed medical publications are considered as the main sources of evidence used for synthesizing systematic reviews or practicing Evidence Based Medicine (EBM). Finding all relevant published evidence for a particular medical case is a time and labour intensiv...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2019.103321

    authors: Hassanzadeh H,Nguyen A,Verspoor K

    更新日期:2019-12-01 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