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Challenges in Realism-Based Ontology Design: a Case Study on Creating an Ontology for Motivational Learning Theories. 基于现实主义的本体设计面临的挑战：关于创建动机学习理论本体的案例研究。
CEUR workshop proceedings Pub Date : 2021-01-01
Irshad Ally, Werner Ceusters
{"title":"Challenges in Realism-Based Ontology Design: a Case Study on Creating an Ontology for Motivational Learning Theories.","authors":"Irshad Ally, Werner Ceusters","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Objective: </strong>to identify on the basis of a use case major problem types novices in realism-based ontology design face when attempting to construct an ontology intended to explain differences and commonalities between competing scientific theories.</p><p><strong>Methodology: </strong>an ontology student was tasked (1) to extract manually from a paper about five distinct motivational learning theories the scientific terms used to explain the theories, (2) to map these terms where possible to type-terms from existing realism-based ontologies or create new ones otherwise, (3) to indicate for new type-terms their immediate subsumer, and (4) to document at every step issues that were encountered.</p><p><strong>Results: </strong>where term extraction and type-term assignment were handled satisfactorily, correct classification in function of the BFO was a major challenge. Root causes identified included ambiguous and underspecified term use in the theories, the ontological status of psychological constructs, lack of high quality ontologies for the behavioral sciences and insufficient 'deep' understanding of some BFO entities, in part because of insufficient documentation thereof suitable for learners. The issues the student encountered were often insufficiently described for the instructor to identify the problem without analyzing the source paper itself.</p><p><strong>Conclusion: </strong>whereas behavioral scientists need to do efforts to make their theories comparable, realism-based ontologies can help them therein only when ontology developers and educators put more effort in making them more accessible without violating the principles.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11164408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141302264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView. CTO：基于社区的临床试验本体及其在 PubChemRDF 和 SCAIView 中的应用。
CEUR workshop proceedings Pub Date : 2020-09-01
Asiyah Yu Lin, Stephan Gebel, Qingliang Leon Li, Sumit Madan, Johannes Darms, Evan Bolton, Barry Smith, Martin Hofmann-Apitius, Yongqun Oliver He, Alpha Tom Kodamullil
{"title":"CTO: a Community-Based Clinical Trial Ontology and its Applications in PubChemRDF and SCAIView.","authors":"Asiyah Yu Lin, Stephan Gebel, Qingliang Leon Li, Sumit Madan, Johannes Darms, Evan Bolton, Barry Smith, Martin Hofmann-Apitius, Yongqun Oliver He, Alpha Tom Kodamullil","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple clinical trials investigating Gleevec's related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9389640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40415209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The OhioT1DM Dataset for Blood Glucose Level Prediction: Update 2020. 用于血糖水平预测的OhioT1DM数据集:更新2020。
CEUR workshop proceedings Pub Date : 2020-09-01
Cindy Marling, Razvan Bunescu
{"title":"The OhioT1DM Dataset for Blood Glucose Level Prediction: Update 2020.","authors":"Cindy Marling,&nbsp;Razvan Bunescu","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This paper documents the OhioT1DM Dataset, which was developed to promote and facilitate research in blood glucose level prediction. It contains eight weeks' worth of continuous glucose monitoring, insulin, physiological sensor, and self-reported life-event data for each of 12 people with type 1 diabetes. An associated graphical software tool allows researchers to visualize the integrated data. The paper details the contents and format of the dataset and tells interested researchers how to obtain it. The OhioT1DM Dataset was first released in 2018 for the first Blood Glucose Level Prediction (BGLP) Challenge. At that time, the dataset was half its current size, containing data for only six people with type 1 diabetes. Data for an additional six people is being released in 2020 for the second BGLP Challenge. This paper subsumes and supersedes the paper which documented the original dataset.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7881904/pdf/nihms-1668254.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25370909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Foundations for a Realism-Based Ontology of Protein Aggregates. 基于现实主义的蛋白质聚集体本体的基础。
CEUR workshop proceedings Pub Date : 2020-09-01 Epub Date: 2021-02-02
Lauren Wishnie, Alexander P Cox, Alexander D Diehl, Werner Ceusters
{"title":"Foundations for a Realism-Based Ontology of Protein Aggregates.","authors":"Lauren Wishnie,&nbsp;Alexander P Cox,&nbsp;Alexander D Diehl,&nbsp;Werner Ceusters","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The objective of this paper is to propose formal definitions for the terms 'protein aggregate' and 'protein-containing complex' such that the descriptions and usages of these terms in biomedical literature are unified and that those portions of reality are correctly represented. To this end, we surveyed the literature to assess the need for a distinction between these entities, then compared the features of usages and definitions found in the literature to the definitions for those terms found in Bioportal ontologies. Based on the results of this comparison, we propose updated definitions for the terms 'protein aggregate' and 'protein-containing complex'. Thus far, we propose the following distinguishing factors: first, that one important difference lies in whether an entity is disposed to change type in response to certain structural alterations, such as dissociation of a continuant part, and second that an important difference lies in the ability of the entity to realize its function after such an event occurs. These distinctions are reflected in the proposed definitions.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8547170/pdf/nihms-1648743.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39563967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An Ontology-Powered Dialogue Engine For Patient Communication of Vaccines. 用于疫苗患者交流的本体驱动对话引擎。
CEUR workshop proceedings Pub Date : 2019-10-01
Muhammad Amith, Rebecca Lin, Licong Cui, Dennis Wang, Anna Zhu, Grace Xiong, Hua Xu, Kirk Roberts, Cui Tao
{"title":"An Ontology-Powered Dialogue Engine For Patient Communication of Vaccines.","authors":"Muhammad Amith,&nbsp;Rebecca Lin,&nbsp;Licong Cui,&nbsp;Dennis Wang,&nbsp;Anna Zhu,&nbsp;Grace Xiong,&nbsp;Hua Xu,&nbsp;Kirk Roberts,&nbsp;Cui Tao","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In this study, we introduce an ontology-driven software engine to provide dialogue interaction functionality for a conversational agent for HPV vaccine counseling. Currently, the HPV vaccination rates are low that risks unprotected individuals at being infected with HPV, a virus that leads to life-threatening cancers. In addition, we developed a question answering subsystem to support the dialogue engine. In this paper, we discuss our design and development of an ontology-driven dialogue engine that uses the Patient Health Information Dialogue Ontology, an ontology that we previously developed, and a question answering subsystem based on various previous methods to supplement the dialogue engine's interaction with the user. Our next step is to test the functional ability of the ontology-driven software components and deploy the engine in a live environment to be integrated with a speech interface.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7376741/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38194009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparing the representation of medicinal products in RxNorm and SNOMED CT - Consequences on interoperability. 比较RxNorm和SNOMED CT中药品的表示——对互操作性的影响。
CEUR workshop proceedings Pub Date : 2019-08-01
Jean Noel Nikiema, Olivier Bodenreider
{"title":"Comparing the representation of medicinal products in RxNorm and SNOMED CT - Consequences on interoperability.","authors":"Jean Noel Nikiema,&nbsp;Olivier Bodenreider","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Objectives: </strong>To compare the representation of medicinal products in RxNorm and SNOMED CT and assess the consequences on interoperability.</p><p><strong>Methods: </strong>To compare the two models, we manually establish equivalences between the types and definitional features of medicinal products entities in RxNorm and SNOMED CT. We highlight their similarities and differences.</p><p><strong>Results: </strong>Both models share major definitional features including ingredient (or substance), strength and dose form. SNOMED CT is more rigorous and better aligned with international standards. In contrast, RxNorm contains implicit knowledge, simplifications and ambiguities, but its model is simpler.</p><p><strong>Conclusions: </strong>Since their models are largely compatible, medicinal products from RxNorm and SNOMED CT are expected to be interoperable. However, specific aspects of the alignment between the two models require particular attention.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9584356/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40567815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Explaining Deep Classification of Time-Series Data with Learned Prototypes. 用学习原型解释时间序列数据的深度分类。
CEUR workshop proceedings Pub Date : 2019-08-01
Alan H Gee, Diego Garcia-Olano, Joydeep Ghosh, David Paydarfar
{"title":"Explaining Deep Classification of Time-Series Data with Learned Prototypes.","authors":"Alan H Gee,&nbsp;Diego Garcia-Olano,&nbsp;Joydeep Ghosh,&nbsp;David Paydarfar","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The emergence of deep learning networks raises a need for explainable AI so that users and domain experts can be confident applying them to high-risk decisions. In this paper, we leverage data from the latent space induced by deep learning models to learn stereotypical representations or \"prototypes\" during training to elucidate the algorithmic decision-making process. We study how leveraging prototypes effect classification decisions of two dimensional time-series data in a few different settings: (1) electrocardiogram (ECG) waveforms to detect clinical bradycardia, a slowing of heart rate, in preterm infants, (2) respiration waveforms to detect apnea of prematurity, and (3) audio waveforms to classify spoken digits. We improve upon existing models by optimizing for increased prototype diversity and robustness, visualize how these prototypes in the latent space are used by the model to distinguish classes, and show that prototypes are capable of learning features on two dimensional time-series data to produce explainable insights during classification tasks. We show that the prototypes are capable of learning real-world features - bradycardia in ECG, apnea in respiration, and articulation in speech - as well as features within sub-classes. Our novel work leverages learned prototypical framework on two dimensional time-series data to produce explainable insights during classification tasks.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8050893/pdf/nihms-1668684.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38884015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The New SNOMED CT International Medicinal Product Model. 新型SNOMED CT国际医药产品模型。
CEUR workshop proceedings Pub Date : 2018-12-01
Olivier Bodenreider, Julie James
{"title":"The New SNOMED CT International Medicinal Product Model.","authors":"Olivier Bodenreider,&nbsp;Julie James","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Objectives: </strong>To present the new SNOMED CT international medicinal product model.</p><p><strong>Methods: </strong>We present the main elements of the model, with focus on types of entities and their interrelations, definitional attributes for clinical drugs, and categories of groupers.</p><p><strong>Results: </strong>We present the status of implementation as of July 2018 and illustrate differences between the original and new models through an example.</p><p><strong>Conclusions: </strong>Benefits of the new medicinal product model include comprehensive representation of clinical drugs, logical definitions with necessary and sufficient conditions for all medicinal product entities, better high-level organization through distinct categories of groupers, and compliance with international standards.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9584358/pdf/nihms-1840460.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40665758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Personalized Health Knowledge Graph. 个性化健康知识图谱。
CEUR workshop proceedings Pub Date : 2018-10-01
Amelie Gyrard, Manas Gaur, Saeedeh Shekarpour, Krishnaprasad Thirunarayan, Amit Sheth
{"title":"Personalized Health Knowledge Graph.","authors":"Amelie Gyrard,&nbsp;Manas Gaur,&nbsp;Saeedeh Shekarpour,&nbsp;Krishnaprasad Thirunarayan,&nbsp;Amit Sheth","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Our current health applications do not adequately take into account contextual and personalized knowledge about patients. In order to design \"Personalized Coach for Healthcare\" applications to manage chronic diseases, there is a need to create a Personalized Healthcare Knowledge Graph (PHKG) that takes into consideration a patient's health condition (personalized knowledge) and enriches that with contextualized knowledge from environmental sensors and Web of Data (e.g., symptoms and treatments for diseases). To develop PHKG, aggregating knowledge from various heterogeneous sources such as the Internet of Things (IoT) devices, clinical notes, and Electronic Medical Records (EMRs) is necessary. In this paper, we explain the challenges of collecting, managing, analyzing, and integrating patients' health data from various sources in order to synthesize and deduce meaningful information embodying the vision of the Data, Information, Knowledge, and Wisdom (DIKW) pyramid. Furthermore, we sketch a solution that combines: 1) IoT data analytics, and 2) explicit knowledge and illustrate it using three chronic disease use cases - asthma, obesity, and Parkinson's.</p>","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8532078/pdf/nihms-1743812.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39551742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Towards automated pain detection in children using facial and electrodermal activity 利用面部和皮肤电活动实现儿童疼痛自动检测
CEUR workshop proceedings Pub Date : 2018-07-13 DOI: 10.1007/978-3-030-12738-1_13
Xiaojing Xu, Busra T. Susam, H. Nezamfar, K. Craig, Damaris Diaz, Jeannie S. Huang, M. Goodwin, M. Akçakaya, V. D. Sa
{"title":"Towards automated pain detection in children using facial and electrodermal activity","authors":"Xiaojing Xu, Busra T. Susam, H. Nezamfar, K. Craig, Damaris Diaz, Jeannie S. Huang, M. Goodwin, M. Akçakaya, V. D. Sa","doi":"10.1007/978-3-030-12738-1_13","DOIUrl":"https://doi.org/10.1007/978-3-030-12738-1_13","url":null,"abstract":"","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42071686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 12
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