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The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications

Jennifer R Smith, Carissa A Park, Rajni Nigam, Stanley JF Laulederkind, G Hayman, Shur-Jen Wang, Timothy F Lowry, Victoria Petri, Jeff Pons, Marek Tutaj, Weisong Liu, Elizabeth A Worthey (+2 others)
2013 Journal of Biomedical Semantics  
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

Donna Fritzsche, Michael Grüninger, Ken Baclawski, Mike Bennett, Gary Berg-Cross, Todd Schneider, Ram Sriram, Mark Underwood, Andrea Westerinen
2017 Applied Ontology  
(what functionality do they offer consuming applications/ecosystem participants), ⋅ characterization of semantic interoperability ecosystems as a whole, ⋅ measures of appropriate SI, andconditions  ...  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

Montserrat Batet
2011 AI Communications  
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]

Luke T Slater, William Bradlow, Simon Ball, Robert Hoehndorf, Georgios V Gkoutos
2020 biorxiv/medrxiv   pre-print
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

Luke T. Slater, William Bradlow, Simon Ball, Robert Hoehndorf, Georgios V Gkoutos
2021 Journal of Biomedical Semantics  
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]

Ying Shen, Joël Colloc, Armelle Jacquet-Andrieu, Ziyi Guo, Yong Liu
2018 arXiv   pre-print
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

Davide Chicco, Fernando Palluzzi, Marco Masseroli
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
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

Robert M. Bilder, Fred W. Sabb, D. Stott Parker, Donald Kalar, Wesley W. Chu, Jared Fox, Nelson B. Freimer, Russell A. Poldrack
2009 Cognitive Neuropsychiatry  
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

Toshiharu NAKAI, Epifanio BAGARINAO, Yoshio TANAKA, Kayako MATSUO, Daniel RACOCEANU
2008 Magnetic Resonance in Medical Sciences  
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

Hongfang Liu, Xin Li, Victoria Yoon, Robert Clarke
2008 AMIA Annual Symposium Proceedings  
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

Daniel Faria, Catia Pesquita, Isabela Mott, Catarina Martins, Francisco M. Couto, Isabel F. Cruz
2018 Journal of Biomedical Semantics  
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

Jessica A. Turner, Angela R. Laird
2011 Neuroinformatics  
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

G Bucci, V Sandrucci, E Vicario
2011 2011 44th Hawaii International Conference on System Sciences  
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

Ryszard S. Romaniuk
2012 International Journal of Electronics and Telecommunications  
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

Robert Moskovitch, Yuval Shahar
2009 Journal of Biomedical Informatics  
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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