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Construction of coffee transcriptome networks based on gene annotation semantics

Luis F. Castillo, Narmer Galeano, Gustavo A. Isaza, Alvaro Gaitan
2012 Journal of Integrative Bioinformatics  
Relationships between sequence annotations and semantic concepts were graphically represented through a total of 6845 oriented vectors, which were reduced to 745 non-redundant associations.  ...  Meanwhile, term descriptors for molecular biology and biochemistry were obtained along the Wordnet dictionary in order to construct a Resource Description Framework (RDF) using Ruby scripts and Methontology  ...  Acknowledgements This work was supported by the Universidad de Caldas, the National Coffee Research Center (Cenicafé) and the Colombian Ministry of Agriculture.  ... 
doi:10.1515/jib-2012-205 fatcat:joyn6ozlyffs3nxwy2kq6angeu

Construction of coffee transcriptome networks based on gene annotation semantics

Luis F Castillo, Narmer Galeano, Gustavo A Isaza, Alvaro Gaitán
2012 Journal of Integrative Bioinformatics  
Relationships between sequence annotations and semantic concepts were graphically represented through a total of 6845 oriented vectors, which were reduced to 745 non-redundant associations.  ...  Meanwhile, term descriptors for molecular biology and biochemistry were obtained along the Wordnet dictionary in order to construct a Resource Description Framework (RDF) using Ruby scripts and Methontology  ...  Acknowledgements This work was supported by the Universidad de Caldas, the National Coffee Research Center (Cenicafé) and the Colombian Ministry of Agriculture.  ... 
doi:10.2390/biecoll-jib-2012-205 pmid:22829576 fatcat:2snceaevfjehhcvruasfh4x5t4

Expert system methodologies and applications—a decade review from 1995 to 2004

Shu-Hsien Liao
2005 Expert systems with applications  
This paper surveys expert systems (ES) development using a literature review and classification of articles from 1995 to 2004 with a keyword index and article abstract in order to explore how ES methodologies  ...  applications development is a problem-oriented domain. (2) It is suggested that different social science methodologies, such as psychology, cognitive science, and human behavior could implement ES as another  ...  Instead of passing data to procedures, programs send a message for an object to perform a procedure that is already embedded in it.  ... 
doi:10.1016/j.eswa.2004.08.003 fatcat:bneyzjdknrcivmzst6bm3ddvxq

OnWARD: Ontology-driven web-based framework for multi-center clinical studies

Van-Anh Tran, Nathan Johnson, Susan Redline, Guo-Qiang Zhang
2011 Journal of Biomedical Informatics  
In this paper, we demonstrate the initial deployment of OnWARD for a Phase II multi-center clinical trial after a development period of merely three months.  ...  Because of the flexible framework, the data management system can be extended to accommodate a large variety of data types, including genetic, genomic and proteomic data.  ...  VT also acknowledges support from the Choose Ohio First Scholarship (UT15439) from the Ohio Board of Regents through the Ohio Consortium for Bioinformatics.  ... 
doi:10.1016/j.jbi.2011.08.019 pmid:21924379 pmcid:PMC3251701 fatcat:zug5vnxsozf5xn25tiqhrgyvry

The development of non-coding RNA ontology

Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin (+11 others)
2016 International Journal of Data Mining and Bioinformatics  
On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field.  ...  We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a Huang et al.  ...  The views contained in this paper are solely the responsibility of the authors and do not represent the official views, either expressed or implied, of the NIH, NSF, the US Government, or the Abraham A  ... 
doi:10.1504/ijdmb.2016.077072 pmid:27990175 pmcid:PMC5156483 fatcat:i62jsm2cdze23pdoevo3gtxnjq

Annotation of Rhetorical Moves in Biochemistry Articles

Mohammed Alliheedi, Robert E. Mercer, Robin Cohen
2019 Proceedings of the 6th Workshop on Argument Mining  
adopt an approach of identifying rhetorical moves that are procedure-oriented.  ...  These components are designed to support a computational model that extends a promising proposal of appropriate rhetorical moves for this domain, but one which is merely descriptive.  ...  Acknowledgments This research was funded by Al Baha University and the University of Waterloo. We thank our annotators for their dedication to the annotation effort.  ... 
doi:10.18653/v1/w19-4514 dblp:conf/argmining/AlliheediMC19 fatcat:wpep7uqo6bc7jde2mwzqgh2o64

Research on E-Science - Serverless Semantic E-Science Framework (SSE-SF)

2019 International journal of recent technology and engineering  
Serverless implementation for a semantic e-science framework (SSe-SF) is all about pushing code to a compute service and networking with third party services and APIs to get the work done.  ...  Serverless semantic e-science framework (SSe-SF) includes Knowledge Search and Navigation, Identity Management, URI/ Content Negotiation, RDF & RDF Schema annotated information resources, Shared Ontologies  ...  Semantic web services in the form of microservices which is a descendant of service-oriented architecture has given rise to free access to many research organization's ontologies.  ... 
doi:10.35940/ijrte.b1230.0782s319 fatcat:qva2y755jrgypm25vepgfhhm3y

Conceptual metaphor types in oncology: Cognitive and communicative functions

Ignasi Navarro i Ferrando
2017 Ibérica  
According to Conceptual Metaphor Theory (CMT), four conceptual types are described: imagistic, orientational, ontological and structural.  ...  In this paper, an analysis of conceptual metaphor types and their relation with cognitive and communicative functions is carried out on a sample of oncology research papers.  ...  The only orientational metaphor found in our data fulfils a categorizing function, given that the term "follow-up" designates a process, with no further implications in the conceptualization of the whole  ... 
doaj:9c1a87c365984418acb0b9ee2be1d555 fatcat:v344ge4ohnewpocbgcj76gjxx4

The Rat Genome Database 2009: variation, ontologies and pathways

M. R. Dwinell, E. A. Worthey, M. Shimoyama, B. Bakir-Gungor, J. DePons, S. Laulederkind, T. Lowry, R. Nigram, V. Petri, J. Smith, A. Stoddard, S. N. Twigger (+1 others)
2009 Nucleic Acids Research  
access to the data in a variety of formats including linear genome viewers, pathway diagrams and biological ontologies.  ...  To support pathophysiological analysis of data, RGD Disease Portals provide an entryway to integrated gene, QTL and strain data specific to a particular disease.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkn842 pmid:18996890 pmcid:PMC2686558 fatcat:nz5sci74qfegtnyvq2zzsfbiu4

An overview of graph databases and their applications in the biomedical domain

Santiago Timón-Reina, Mariano Rincón, Rafael Martínez-Tomás
2021 Database: The Journal of Biological Databases and Curation  
In this work, we survey the literature to explore the evolution, performance and how the most recent graph database solutions are applied in the biomedical domain, compiling a great variety of use cases  ...  Over the past couple of decades, the explosion of densely interconnected data has stimulated the research, development and adoption of graph database technologies.  ...  Applications in biological and medicinal chemistry The fields of Biology and Biochemistry have been a pioneer in the development of new data standards and knowledge representation paradigms, such as ontologies  ... 
doi:10.1093/database/baab026 pmid:34003247 pmcid:PMC8130509 fatcat:xku5npedwzgs3ayzsuvz6iattq

Metaphorical Concepts and Their Cognitive Functions in Medical Discourse: Research Papers vs. Press Articles

Ignasi Navarro i Ferrando
2021 ESP Today  
Four types of conceptual metaphorical projections are identified according to Conceptual Metaphor Theory (i.e. structural, image, ontological, and orientational).  ...  For that purpose, a sample of texts in both genres is analysed.  ...  This analysis provided a set of conceptual metaphorical mappings including structural, image, ontological, and orientational types.  ... 
doi:10.18485/esptoday.2021.9.1.8 fatcat:enpbglcytneb3a3zv4bmuiskki

Using Vampire to Reason with OWL [chapter]

Dmitry Tsarkov, Alexandre Riazanov, Sean Bechhofer, Ian Horrocks
2004 Lecture Notes in Computer Science  
OWL DL corresponds to a Description Logic (DL) that is a fragment of classical first-order predicate logic (FOL).  ...  In this paper we report on some experiments designed to explore the feasibility of using existing general-purpose FOL provers to reason with OWL DL.  ...  4 A biochemistry ontology developed in the Tambis project [4] . 5 A wine and food ontology which forms part of the OWL test suite [25] . 6 A GCI is an axiom of the form C D, where C may be an arbitrarily  ... 
doi:10.1007/978-3-540-30475-3_33 fatcat:chmwcice3jfuzkhwdpr4n7dqyu

An ontology for the formalization and visualization of scientific knowledge [article]

Vincenzo Daponte, Gilles Falquet
2021 arXiv   pre-print
The construction of an ontology of scientific knowledge objects, presented here, is part of the development of an approach oriented towards the visualization of scientific knowledge.  ...  on this topic and presents them in a simple and easily understandable organization.  ...  Acknowledgement This work has been enriched by the valuable advice and experience of Giuseppe Cosenza and Jean-Pierre Hurni, whom the authors would like to thank.  ... 
arXiv:2107.04347v2 fatcat:bas5uasp7fh3xpswihxtvljysu

Altered Long Noncoding RNA and Messenger RNA Expression in Experimental Intracerebral Hemorrhage - a Preliminary Study

Cui Hanjin, Liu Tao, Li Pengfei, Yang Ali, Zhou Huajun, Luo Jiekun, Wang Yang, Tang Tao
2018 Cellular Physiology and Biochemistry  
Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to determine bio-functions and signaling pathways, with which differentially expressed genes are  ...  Results: A total of 625 differentially expressed ln-cRNAs and 826 expressed mRNAs were identified.  ...  P value calculated from significance testing value of the GO ID. Term: the name of gene ontology term. Ontology: the ontology of GO ID belongs to.  ... 
doi:10.1159/000487464 pmid:29448258 fatcat:tkp42p7kvvbllnd7jklkgwnpvm

Towards Semantic e-Science for Traditional Chinese Medicine

Huajun Chen, Yuxin Mao, Xiaoqing Zheng, Meng Cui, Yi Feng, Shuiguang Deng, Aining Yin, Chunying Zhou, Jinming Tang, Xiaohong Jiang, Zhaohui Wu
2007 BMC Bioinformatics  
We use domain ontologies to integrate TCM database resources and services in a semantic cyberspace and deliver a semantically superior experience including browsing, searching, querying and knowledge discovering  ...  We have developed a collection of semantic-based toolkits to facilitate TCM scientists and researchers in information sharing and collaborative research.  ...  Follow this general procedure and we are able to develop a large-scale domain ontology for e-Science system.  ... 
doi:10.1186/1471-2105-8-s3-s6 pmid:17493289 pmcid:PMC1892103 fatcat:zalpg6pzcbhc7dti7wq7dvzea4
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