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A systematic survey of temporal requirements of bio-health ontologies

Jared Leo, Nicolas Matentzoglu, Uli Sattler, Bijan Parsia, Pascal Hitzler
2019 Semantic Web Journal  
Such analysis will give rise to a set of temporal requirements of those bio-health ontologies.  ...  It may be the case that some of the proposed extensions may, in fact, be suitable for modelling the temporal requirements of bio-health ontologies, but since the temporal requirements of bio-health ontologies  ...  Comment (a) Give a more precise definition of the temporal attributes you consider.  ... 
doi:10.3233/sw-190357 fatcat:77ialkpv4rbsrhkd4yqlffdia4

Applying an Exposome-Wide (ExWAS) Approach to Cancer Research

Paul D. Juarez, Patricia Matthews-Juarez
2018 Frontiers in Oncology  
Exposome-wide association study (ExWAS) provides a new approach for conceptualizing the roles and relationships of multiple chemical and nonchemical exposures in the etiology and progression of cancer  ...  ExWAS challenges us to consider the influence of both internal and external environment, chemical and non-chemical stressors, risk and protective factors, and spatial and temporal dimensions of exposures  ...  SNOMED CT was developed as a systematic ontology of terms that can be used in health informatics anywhere in the world to ensure systematic recording of clinical data to support patient care.  ... 
doi:10.3389/fonc.2018.00313 pmid:30211112 pmcid:PMC6119827 fatcat:cvnnc4f4ajf5teutqcyuze64ha

Knowledge-data integration for temporal reasoning in a clinical trial system

Martin J. O'Connor, Ravi D. Shankar, David B. Parrish, Amar K. Das
2009 International Journal of Medical Informatics  
Knowledge-based systems Semantic Web Ontology SWRL OWL a b s t r a c t Managing time-stamped data is essential to clinical research activities and often requires the use of considerable domain knowledge  ...  In this paper, we present a set of methodologies for undertaking ontology-based specification of temporal information, and discuss their application to the verification of protocol-specific temporal constraints  ...  Acknowledgements This research was supported in part by the Immune Tolerance Network, funded by Grant NO1-AI-15416 from the National Institutes of Health (USA), and by a Pharmaceutical Research and Manufacturers  ... 
doi:10.1016/j.ijmedinf.2008.07.013 pmid:18789876 fatcat:u73izixak5ft7m26h6qsbxlh7m

MIRO: guidelines for minimum information for the reporting of an ontology

Nicolas Matentzoglu, James Malone, Chris Mungall, Robert Stevens
2018 Journal of Biomedical Semantics  
We found that only 41.38% of the information items were covered by the majority of the papers (and deemed important by the survey respondents) and a large number of important items are not covered at all  ...  Results: We propose the Minimum Information for Reporting an Ontology (MIRO) guidelines as a means to facilitate a higher degree of completeness and consistency between ontology documentation, including  ...  We recommend the MIRO guidelines to both ontology users, authors and reviewers in the ontology community to improve the presentation of their work.  ... 
doi:10.1186/s13326-017-0172-7 pmid:29347969 pmcid:PMC5774126 fatcat:aszk2gjxlzbdxcvi6aig2sj2iu

Emerging multidisciplinary research across database management systems

Anisoara Nica, Fabian M. Suchanek, Aparna S. Varde
2011 SIGMOD record  
The database community is exploring more and more multidisciplinary avenues: Data semantics overlaps with ontology management; reasoning tasks venture into the domain of artificial intelligence; and data  ...  This paper surveys the emerging multidisciplinary research by doctoral students in database systems and related areas.  ...  All of this helped set the stage for writing this article.  ... 
doi:10.1145/1942776.1942786 fatcat:d4mwnixqtrb5libbq5k5urxrcy

Knowledge Representation and Ontologies [chapter]

Kin Wah Fung, Olivier Bodenreider
2012 Health Informatics Series  
The existence of multiple representations for the same entity makes it difficult for ontology users to select 5 the right ontology for a given purpose and requires the development of mappings between ontologies  ...  BFO forms the backbone of several ontologies form the Open Biomedical Ontologies (OBO) family and Bio-Top has also been reused by several ontologies.  ...  Acknowledgments This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
doi:10.1007/978-1-84882-448-5_14 fatcat:r7e2fbulcrcddpxh7jo6lu77wa

Uncovering text mining: A survey of current work on web-based epidemic intelligence

Nigel Collier
2012 Global Public Health  
Real world pandemics such as SARS 2002 as well as popular fiction like the movie Contagion graphically depict the health threat of a global pandemic and the key role of epidemic intelligence (EI).  ...  While EI relies heavily on established indicator sources a new class of methods based on event alerting from unstructured digital Internet media is rapidly becoming acknowledged within the public health  ...  It requires a combination of clues from the health ministry name and the local name to fix the actual specific location.  ... 
doi:10.1080/17441692.2012.699975 pmid:22783909 pmcid:PMC3438486 fatcat:wcfi2qf4j5cgzgk4p7gbt6dnqe

Towards GFO 2.0: Architecture, Modules and Applications [chapter]

Patryk Burek, Frank Loebe, Heinrich Herre
2020 Frontiers in Artificial Intelligence and Applications  
Finally, a rigorous and systematic development process is indicated.  ...  For this purpose we summarize key features of GFO so far, outline a novel modular architecture and survey first modules for GFO 2.0, linking to applications.  ...  Aspects of this module were applied in the analysis of the notion of core ontology and the development of GFO-Bio [35] , a core ontology for biology, as well as in an ontological theory of the notion  ... 
doi:10.3233/faia200658 fatcat:ags4zsgwm5fbhezps5uvspulie

Thirty years of artificial intelligence in medicine (AIME) conferences: A review of research themes

Niels Peek, Carlo Combi, Roque Marin, Riccardo Bellazzi
2015 Artificial Intelligence in Medicine  
Methods: We analyzed a total of 122 session titles to create a taxonomy of research themes and topics. We classified all 734 AIME conference papers published between 1985 and 2013 with this taxonomy.  ...  The Artificial Intelligence in Medicine journal has published theme issues with extended versions of selected AIME papers since 1998.  ...  A comprehensive survey of the entire field is beyond the scope of this paper.  ... 
doi:10.1016/j.artmed.2015.07.003 pmid:26265491 fatcat:bnzr2hwtifbd7dckguz5mgjhmq

Mobile Health Technologies for Diabetes Mellitus: Current State and Future Challenges

Shaker El-Sappagh, Farman Ali, Samir El-Masri, Kyehyun Kim, Amjad Ali, Kyung-Sup Kwak
2019 IEEE Access  
We conducted a comprehensive survey of MH research on diabetes management articles published between 2011 and September 27, 2017.  ...  Discussing the current state of MH technologies is required in order to address their limitations.  ...  The OpenIoT ontology is a recent one based on the W3C SSN. 28 However, these ontologies are generic, which require extensions.  ... 
doi:10.1109/access.2018.2881001 fatcat:ha4lscdyxfbi7jed5w2blan5yu

Community challenges in biomedical text mining over 10 years: success, failure and the future

Chung-Chi Huang, Zhiyong Lu
2015 Briefings in Bioinformatics  
Following the success of the Critical Assessment of protein Structure Prediction (CASP) in bioinformatics research, a number of challenge evaluations have been organized by the text-mining research community  ...  Finally, we summarize the impact and contributions by taking into account different BioNLP challenges as a whole, followed by a discussion of their limitations and difficulties.  ...  Funding This work was supported by the National Institutes of Health intramural research program, National Library of Medicine.  ... 
doi:10.1093/bib/bbv024 pmid:25935162 pmcid:PMC4719069 fatcat:z7wlyvovnnbrrkufmqaxycqdyi

Mobile Health in Remote Patient Monitoring for Chronic Diseases: Principles, Trends, and Challenges

Nora El-Rashidy, Shaker El-Sappagh, S. M. Riazul Islam, Hazem M. El-Bakry, Samir Abdelrazek
2021 Diagnostics  
A total of 56 articles are reviewed based on the combination of a set of selected search terms including RPM, data mining, clinical decision support system, electronic health record, cloud computing, internet  ...  We followed the (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) PRISMA, which is a standard methodology for systematic reviews and meta-analyses.  ...  A systematic review about medical data interoperability reported that FHIR is one of the messaging standards that most satisfied the requirement of healthcare interoperability and provided several client-side  ... 
doi:10.3390/diagnostics11040607 pmid:33805471 pmcid:PMC8067150 fatcat:a42vma6mlfan3cqs5z7e2bs47a

Data Management and Interactive Visualizations for the Evolving Marine Biodiversity Observation Network

Abigail Benson, US Geological Survey, Tylar Murray, Gabrielle Canonico, Enrique Montes, Frank Muller-Karger, Maria Kavanaugh, Joaquin Trinanes, Lynn deWitt
2021 Oceanography  
Assessing the current state of and predicting change in the ocean's biological and ecosystem resources requires observations and research to safeguard these valuable public assets.  ...  By following this flow, data collected and managed by MBON have contributed to our understanding of the Global Ocean Observing System Essential Ocean Variables and demonstrated the value of web-based,  ...  Answering these questions requires establishing global programs for the systematic collection of biological and ecosystem observations concurrently with environmental variables, following a minimum set  ... 
doi:10.5670/oceanog.2021.220 fatcat:v6antqxo5jhnjf26gs2f62fsd4

Domain-specific Knowledge Graphs: A survey [article]

Bilal Abu-Salih
2021 arXiv   pre-print
This survey is the first to offer a comprehensive definition of a domain-specific KG.  ...  An examination of current approaches reveals a range of limitations and deficiencies.  ...  Table A . A 5: Overview of KG approaches in Finance domain• Lack of temporal dimension, • limited data sources, • discussion on KG construction is inadequate Ref.  ... 
arXiv:2011.00235v3 fatcat:oc2loewqdjfgvlapy4kmult5li

Research protocol: EB-GIS4HEALTH UK - foundation evidence base and ontology-based framework of modular, reusable models for UK/NHS health and healthcare GIS applications

Maged N Kamel Boulos
2005 International Journal of Health Geographics  
of affairs within the NHS; help the NHS understand and harness the importance of spatial information in the health sector in order to better respond to national health plans, priorities, and requirements  ...  NHS organisations adopting such frameworks will achieve a common understanding of spatial data and processes, which will enable them to efficiently and effectively share, compare, and integrate their data  ...  A systematic and critical review and consolidation are needed of the evidence for GIS for specific preventable, mitigable and treatable health conditions.  ... 
doi:10.1186/1476-072x-4-2 pmid:15649328 pmcid:PMC546191 fatcat:vjzm2ih6gbhydpcuihhh42ndbe
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