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The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications
2013
Journal of Biomedical Semantics
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The Clinical Measurement Ontology (CMO), Measurement Method Ontology (MMO), and Experimental Condition Ontology (XCO) were originally developed at the Rat Genome Database (RGD) to standardize quantitative ...
These ontologies provide the framework for presenting what was measured, how it was measured, and under what conditions it was measured. ...
Acknowledgements This project was supported by grants HL064541 (RGD) and HL094271 (PhenoMiner) from the National Heart, Lung, and Blood Institute on behalf of the National Institutes of Health. ...
doi:10.1186/2041-1480-4-26
pmid:24103152
pmcid:PMC3882879
fatcat:nszdruvaffer5mms66nucddxpe
Ontology Summit 2016 Communique: Ontologies within semantic interoperability ecosystems
2017
Applied Ontology
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(what functionality do they offer consuming applications/ecosystem participants), ⋅ characterization of semantic interoperability ecosystems as a whole, ⋅ measures of appropriate SI, and ⋅ conditions ...
Integration across an expanse of datasets and local domains can be accomplished by careful and consistent application of ODPs. ...
doi:10.3233/ao-170181
fatcat:v7gurhorhre37fvugolrar2uzm
Ontology-based semantic clustering
2011
AI Communications
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On having consulted this thesis you're accepting the following use conditions: Spreading this thesis by the TDX (www.tesisenxarxa.net) service has been authorized by the titular of the intellectual property ...
Reproduction with lucrative aims is not authorized neither its spreading and availability from a site foreign to the TDX service. ...
Acknowledgements This work has been partially supported by the Spanish Ministry of Science and Innovation (DAMASK project, Data mining algorithms with semantic knowledge, TIN2009-11005) and the Spanish ...
doi:10.3233/aic-2011-0501
fatcat:anuhrvzepfezre6qkx5ryh3mam
Improved characterisation of clinical text through ontology-based vocabulary expansion
[article]
2020
biorxiv/medrxiv
pre-print
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Conclusions: Inter-ontology synonym expansion can lead to a vast increase in the scale of vocabulary available for text mining applications. ...
Linking these definitions to make use of their combined metadata could lead to improved performance in ontology-based information retrieval, extraction, and analysis tasks. ...
We would also like to thank Syed Ali Raza for work on the AberOWL platform, and the creators of MIMIC-III for making their data available for public use. ...
doi:10.1101/2020.07.10.197541
fatcat:6w6ir4qgqnbjjdncebelvh7fpm
Improved characterisation of clinical text through ontology-based vocabulary expansion
2021
Journal of Biomedical Semantics
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Conclusions Inter-ontology synonym expansion can lead to a vast increase in the scale of vocabulary available for text mining applications. ...
Linking these definitions to make use of their combined metadata could lead to improved performance in ontology-based information retrieval, extraction, and analysis tasks. ...
We would also like to thank Syed Ali Raza for work on the AberOWL platform, and the creators of MIMIC-III for making their data available for public use. ...
doi:10.1186/s13326-021-00241-5
pmid:33845909
fatcat:au5zlj3mjrh4xebjqiqoqswzve
Constructing Ontology-Based Cancer Treatment Decision Support System with Case-Based Reasoning
[article]
2018
arXiv
pre-print
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Disease Ontology (DO) that pertains to cancer's clinical stages and their corresponding information components is utilized to improve the reasoning ability of a decision support system (DSS). ...
The problem of natural language applications is that they lack formality and the interpretation is not consistent. ...
Since new clinical knowledge cannot be applied automatically without clinical verification, a hierarchy expansion is implemented for incorporating new input data, which should be supported by clinical ...
arXiv:1812.01891v1
fatcat:ybhqgcjgnbfozeedwhlirk4geq
Novelty Indicator for Enhanced Prioritization of Predicted Gene Ontology Annotations
2018
IEEE/ACM Transactions on Computational Biology & Bioinformatics
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To limit the possibility that these techniques predict obvious and trivial high-level features, and to help prioritizing their results, we introduce here a new element that can improve the accuracy and ...
We propose a novelty indicator able to state the level of "newness" (or "originality") of the annotations predicted for a specific gene to Gene Ontology terms, and to help prioritizing the most novel and ...
A concrete application of our methods, that we hope may improve and quicken the discovery of new cures, new therapies, and new knowledge about gene functions. ...
doi:10.1109/tcbb.2017.2695459
pmid:28436884
fatcat:l75ibw3ewzgu7buxeyauejsihy
Cognitive ontologies for neuropsychiatric phenomics research
2009
Cognitive Neuropsychiatry
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of cognitive ontologies (Phenowiki and the Cognitive Atlas). ...
Several free web applications are available already to support examination and visualization of cognitive concepts in the literature (PubGraph, PubAtlas, PubBrain) and to aid collaborative development ...
(Freimer), RL1LM009833 (Parker, Chu, Fox), and The Cognitive Atlas (R01MH082795; Poldrack, Kalar). ...
doi:10.1080/13546800902787180
pmid:19634038
pmcid:PMC2752634
fatcat:a5vbymyahzhqjobdmo6gqi4wqi
Ontology for fMRI as a Biomedical Informatics Method
2008
Magnetic Resonance in Medical Sciences
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purposes, imaging protocol, analyzing methods, and data structure; semantic gaps that remain among the modalities will be bridged as ontology develops. ...
In developing clinical functional neuroimaging, which requires the integration of heterogeneous information derived from multimodal measurement of the brain, these features will be indispensable. ...
description (scan protocols, task design) Experimental data (personal, behavioral, and run data) Machine (types of magnetic resonance [MR] system and radiofrequency [RF] coils) Measurement (display measurement ...
doi:10.2463/mrms.7.141
pmid:18827457
fatcat:z4qijfvlqzfojllunm47furzkq
Annotating breast cancer microarray samples using ontologies
2008
AMIA Annual Symposium Proceedings
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However, the high dimensionality of microarray experiments and public access of data from many experiments have caused inconsistencies which initiated the development of controlled terminologies and ontologies ...
that allows the retrieval of microarray data based on the ontology annotations. ...
Acknowledgements This project is partially supported by the following grants NSF/IIS-0639062, NIH/R01-CA096483 and DOD/BCRP BC030280. ...
pmid:18999108
pmcid:PMC2655965
fatcat:w5ujbqpahbafpl2rzdmwffwmyq
Tackling the challenges of matching biomedical ontologies
2018
Journal of Biomedical Semantics
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We show that accounting for all lexical annotations (e.g., labels and synonyms) in biomedical ontologies leads to a substantial improvement in F-measure over using only the primary name, and that accounting ...
to perform lexical expansion. ...
Availability of data and material The datasets used in this study are publicly available at the OAEI 2016 website [38] . AML is open source and is publicly available through GitHub [39] . 1 ...
doi:10.1186/s13326-017-0170-9
pmid:29335022
pmcid:PMC5769431
fatcat:mjrauqajbvbb7bttodtejtp74y
The Cognitive Paradigm Ontology: Design and Application
2011
Neuroinformatics
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The key components of CogPO include the representation of experimental conditions focused on the stimuli presented, the instructions given, and the responses requested. ...
The goal of CogPO is to develop, evaluate, and distribute a domain ontology of cognitive paradigms for application and use in the functional neuroimaging community. ...
Laird and Turner (co-PIs). We would like to acknowledge Fahim Imam from the Neuroscience Information Framework (www.neuinfo.org) for his work in integrating CogPO version 1 into NeuroLex, as well. ...
doi:10.1007/s12021-011-9126-x
pmid:21643732
pmcid:PMC3682219
fatcat:pnbtq2bt4rahzpzounbgkgu7a4
Ontologies and Bayesian Networks in Medical Diagnosis
2011
2011 44th Hawaii International Conference on System Sciences
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The amount of information that must be taken into account in medical diagnosis is huge and subject to evolution. Ontologies are a means for formalizing the concepts of the domain of interest. ...
Bayesian networks (BNs) offer a coherent and intuitive representation of uncertain domain knowledge. This paper presents an approach to the use of ontologies and BNs in medical diagnosis. ...
Acknowledgements The system has been developed in collaboration with the "Ospedale di Careggi" the largest clinical installation in the town of Florence (Italy). ...
doi:10.1109/hicss.2011.333
dblp:conf/hicss/BucciSV11
fatcat:rcvgzs3gx5c2roj4c7t4ourpea
Communications, Multimedia, Ontology, Photonics and Internet Engineering 2012
2012
International Journal of Electronics and Telecommunications
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This paper is the second part of a concise review digest focused on optoelectronics, communications, multimedia and ontology of information technologies. ...
The organizers present here a research survey of the WILGA Symposium work. Also a digest of chosen Wilga references is presented [1]-[39]. ...
In clinical stationary conditions several methods to measure respirations may be used, which are completely unsuitable for ambulatory conditions. ...
doi:10.2478/v10177-012-0061-z
fatcat:s6nm5vnwoneotjyny4ld5dp7ve
Vaidurya: A multiple-ontology, concept-based, context-sensitive clinical-guideline search engine
2009
Journal of Biomedical Informatics
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We describe the Vaidurya ontological and algorithmic framework; we also briefly summarize the results of a detailed evaluation in the clinical-guideline domain, demonstrating that both concept-based and ...
context-sensitive ontology-independent search are highly feasible and significantly improve on free text search retrieval performance. ...
Tu and Dr. Peleg,, for useful discussions regarding the need for supporting the use of multiple guideline ontologies. Drs. Shiffman and Karras assisted us in using their GEM ontology. Drs. ...
doi:10.1016/j.jbi.2008.07.003
pmid:18721900
fatcat:mpskzpizxnemtag3vepn4h3cx4
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