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Linked data and online classifications to organise mined patterns in patient data

Nicolas Jay, Mathieu d'Aquin
2013 AMIA Annual Symposium Proceedings  
We employ linked data, especially as exposed through the BioPortal system, to create a navigation structure within the patterns obtained form sequential pattern mining.  ...  Interpreting such patterns is naturally a challenge for an analyst, as it requires going through large amounts of results and access to sufficient background knowledge.  ...  Interpretation of sequential patterns with linked data Linked Data 15 is a set of principles and technologies that rely on the architecture of the Web (URIs and links) to share, model and integrate data  ... 
pmid:24551369 pmcid:PMC3900210 fatcat:xpip3io5grd3xcylgu5feg2j6i

Towards an Ontology of Data Mining Investigations [chapter]

Panče Panov, Larisa N. Soldatova, Sašo Džeroski
2009 Lecture Notes in Computer Science  
In this paper we present an updated version of the OntoDM ontology, that is based on a recent proposal of a general framework for data mining and it is aligned with the ontology of biomedical investigations  ...  Unlike most existing approaches to constructing ontologies of data mining, OntoDM is compliant to best practices in engineering ontologies that describe scientific investigations (e.g., OBI ) and is a  ...  OBO to facilitate integration and automatic reasoning.  ... 
doi:10.1007/978-3-642-04747-3_21 fatcat:udpyd7id4bbpbkinidhnpn5b3a

Text-mining approaches in molecular biology and biomedicine

2005 Drug Discovery Today  
Also , the use of text mining to aid the interpretation of microarray data and the analysis of pathology reports will be discussed.  ...  These technologies have a key role in integrating biomedical information through analysis of scientific literature.  ...  The aim of the knowledgediscovery and data-mining (KDD) challenge cup [70] was to study how text-mining tools can assist biological databases by evaluating how they can support the process of database  ... 
doi:10.1016/s1359-6446(05)03376-3 pmid:15808823 fatcat:w5i3ciuq4zhk7oq4kbbv5wqfma

Conjoint Mining of Data and Content with Applications in Business, Bio-medicine, Transport Logistics and Electrical Power Systems [chapter]

Tharam S. Dillon, Yi-Ping Phoebe Chen, Elizabeth Chang, Mukesh Mohania
2014 IFIP Advances in Information and Communication Technology  
Digital information within an enterprise consists of (1) structured data and (2) unstructured content.  ...  The structured data and the unstructured content generally reside in entirely separate repositories with the former being managed by a DBMS and the latter by a content manager frequently provided by an  ...  Applications to Biomedical Applications Existing biomedical information is distributed across a large number of information resources and is heterogeneous in its content, format and structure.  ... 
doi:10.1007/978-3-662-44654-6_1 fatcat:vpjpcvapsrh53ehxqacfhmnyvy

A Brief Survey of Text Mining: Classification, Clustering and Extraction Techniques [article]

Mehdi Allahyari, Seyedamin Pouriyeh, Mehdi Assefi, Saied Safaei, Elizabeth D. Trippe, Juan B. Gutierrez, Krys Kochut
2017 arXiv   pre-print
Additionally, we briefly explain text mining in biomedical and health care domains.  ...  Therefore, efficient and effective techniques and algorithms are required to discover useful patterns.  ...  Therefore for the data integrity and management considerations, data analysis requires to be integrated with databases [105] .  ... 
arXiv:1707.02919v2 fatcat:uiwsrz6wgrb65dcnp54wmkrase

Conjoint Knowledge Discovery Utilizing Data and Content with Applications in Business, Bio-medicine, Transport Logistics and Electrical Power Systems

Tharam S. Dillon, Yi-Ping Phoebe Chen, Elizabeth Chang, Mukesh Mohania, Vish Ramakonar
2020 Computer systems science and engineering  
In Digital Enterprises Structured Data and Semi/Unstructured Content are normally stored in two different repositories, with the first often being stored in relational Databases and the second in a content  ...  This storage of complementary information in two different silos has led to the information being processed and data mined separately which is undesirable.  ...  Technology and Innovation, Malaysia)  ... 
doi:10.32604/csse.2020.35.321 fatcat:in5kk5xa5nchxdzputdckwvnpq

Text mining and its potential applications in systems biology

Sophia Ananiadou, Douglas B. Kell, Jun-ichi Tsujii
2006 Trends in Biotechnology  
Text mining techniques, which involve the processes of information retrieval, information extraction and data mining, provide a means of solving this.  ...  With biomedical literature increasing at a rate of several thousand papers per week, it is impossible to keep abreast of all developments; therefore, automated means to manage the information overload  ...  Acknowledgements We thank the BBSRC, EPSRC and JISC for financial support.  ... 
doi:10.1016/j.tibtech.2006.10.002 pmid:17045684 fatcat:ppkcfka7yrenjkz3z3ad4dj6ha

Ontology of core data mining entities

Panče Panov, Larisa Soldatova, Sašo Džeroski
2014 Data mining and knowledge discovery  
OntoDM-core defines the most essential data mining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer.  ...  In this article, we present OntoDM-core, an ontology of core data mining entities.  ...  Acknowledgments We would like to acknowledge the support of the European Commission through the project MAESTRA-Learning from Massive, Incompletely annotated, and Structured Data (Grant Number ICT-2013  ... 
doi:10.1007/s10618-014-0363-0 fatcat:ccfbyblvnneojoquj4ig3locaa

Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge

Martin Krallinger, Alexander Morgan, Larry Smith, Florian Leitner, Lorraine Tanabe, John Wilbur, Lynette Hirschman, Alfonso Valencia
2008 Genome Biology  
The 'gold standard' data used for evaluating submissions for the third task was provided by the interaction databases MINT (Molecular Interaction Database) and IntAct.  ...  of text-mining systems applied to biologically relevant problems.  ...  The PPI task and the second BioCreative assessment workshop was sponsored by grant ENFIN NoE (LSHG-CT-2005-518254) and by the Spanish National Bioinformatics Institute a platform of  ... 
doi:10.1186/gb-2008-9-s2-s1 pmid:18834487 pmcid:PMC2559980 fatcat:oebtobhdtbfexgyrmymmy7o6vi

Evolution Paths for Knowledge Discovery and Data Mining Process Models

Anna Rotondo, Fergus Quilligan
2020 SN Computer Science  
Data mining process models then become fundamental means to support analytics project management and minimise the risk of data dredging.  ...  Various research studies show that the main barriers to analytics adoption are organisational and the lack of structured approaches on how to conduct analytics initiatives is a possible cause of analytics  ...  The integration of ontology engineering and KDD is a recent trend in KDD research.  ... 
doi:10.1007/s42979-020-0117-6 fatcat:cz77cevwazed3ojqlecosy3khy

Integrating image data into biomedical text categorization

H. Shatkay, N. Chen, D. Blostein
2006 Bioinformatics  
We show preliminary results, demonstrating that the method has a strong potential to enhance and complement traditional text-based categorization methods.  ...  We examine the possibility of using information derived directly from image data, and of integrating it with text-based classification, for biomedical document categorization.  ...  We gratefully acknowledge the financial support provided by NSERC -Canada's Natural Sciences and Engineering Research Council, CFI -the Canadian Foundation for Innovation, and by the Xerox Foundation.  ... 
doi:10.1093/bioinformatics/btl235 pmid:16873506 fatcat:wcwxlrfb5ngc5ep4nkx7nsac7y

Intelligent Approaches to Mining the Primary Research Literature: Techniques, Systems, and Examples [chapter]

Gully A. P. C. Burns, Donghui Feng, Eduard Hovy
2008 Studies in Computational Intelligence  
Such tools are not easy to build, by and large, and require expertise in a variety of computer science specialties, including database management, data analysis, natural language processing, and text mining  ...  The overwhelming amount of information available to the biomedical researcher makes the use of intelligent computational tools a necessity.  ...  Even so, given the importance of biocuration and the high cost of maintaining biomedical databases, developing methods to improve efficency of constructing knowledge bases will still have a large impact  ... 
doi:10.1007/978-3-540-75767-2_2 fatcat:k64qvz27p5hn3fqohql4ps2qwu

A survey of intelligent assistants for data analysis

Floarea Serban, Joaquin Vanschoren, Jörg-Uwe Kietz, Abraham Bernstein
2013 ACM Computing Surveys  
To do this, however, data needs to be analyzed in typically non-trivial refinement processes, which require technical expertise about methods and algorithms, experience with how a precise analysis should  ...  Research and industry increasingly make use of large amounts of data to guide decision-making.  ...  For instance, if a data mining operator is known to perform badly on skewed data distributions, it makes sense to store this property in the ontology as an operator property and measure the data skewness  ... 
doi:10.1145/2480741.2480748 fatcat:eqp6aoh23rbibdnjnc5k6qu3p4

: Three Approaches to GO-Tagging Biomedical Abstracts

Neil Davis, Henk Harkema, Robert J. Gaizauskas, Yikun Guo, Moustafa Ghanem, Tom Barnwell, Yike Guo, Jon Ratcliffe
2006 International Symposium for Semantic Mining in Biomedicine  
In this paper we explore three approaches to assigning Gene Ontology semantic classifications to abstracts from the PubMed database: lexical lookup, information retrieval and machine learning.  ...  To evaluate the approaches we use two "gold" standards derived from the yeast genome database (SGD).  ...  data mining (DM) (Hearst, 1999) .  ... 
dblp:conf/smbm/DavisHGGGBGR06 fatcat:bzemutbnefb5jdx3saye4dflaq

Mining the Biomedical Literature in the Genomic Era: An Overview

Hagit Shatkay, Ronen Feldman
2003 Journal of Computational Biology  
This paper provides a road map to the various literature-mining methods, both in general and within bioinformatics.  ...  The past decade has seen a tremendous growth in the amount of experimental and computational biomedical data, specifically in the areas of genomics and proteomics.  ...  HS was supported by an NIH IRTA fellowship while developing GenTheme, and was a member of the Informatics Research group at Celera/ABI when writing this article.  ... 
doi:10.1089/106652703322756104 pmid:14980013 fatcat:vbwcpl66ujhqdgq4wdjtllbg5e
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