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Elements About Exploratory, Knowledge-Based, Hybrid, and Explainable Knowledge Discovery [chapter]

Miguel Couceiro, Amedeo Napoli
2019 Lecture Notes in Computer Science  
Knowledge Discovery in Databases (KDD) and especially pattern mining can be interpreted along several dimensions, namely data, knowledge, problem-solving and interactivity.  ...  The data space and the pattern space can be explored in several ways, depending on specific evaluation functions and heuristics, possibly related to domain knowledge.  ...  Accordingly, in [28] , we aimed at discovering in metabolomic data a small set of relevant predictive features using a hybrid and exploratory knowledge discovery approach.  ... 
doi:10.1007/978-3-030-21462-3_1 fatcat:diskhipnbjc73banfdegh6rxqa

The Search for Clinically Useful Biomarkers of Complex Disease: A Data Analysis Perspective

Elizabeth C. Considine
2019 Metabolites  
This review is presented as a research perspective on how data analysis methods in metabolomics biomarker discovery may contribute to the failure of biomarker studies and suggests how such failures might  ...  The study design and data pretreatment steps are reviewed briefly in this context, and the actual data analysis step is examined more closely.  ...  Local, global or hybrid methods are likely to be unsuitable due to the presence of an unknown substructure in the data and also due to low sample numbers typical of most metabolomics studies, which would  ... 
doi:10.3390/metabo9070126 pmid:31269649 pmcid:PMC6680669 fatcat:o26ptkjltncude4rprxro2mt3e

Advances in metabolome information retrieval: turning chemistry into biology. Part II: biological information recovery

Abdellah Tebani, Carlos Afonso, Soumeya Bekri
2017 Journal of Inherited Metabolic Disease  
It can be divided into two main fields: knowledge discovery (or data-mining) and simulation-based analysis.  ...  Both approaches exploit the interrelationships contained in the metabolomic data.  ... 
doi:10.1007/s10545-017-0080-0 pmid:28842777 pmcid:PMC5959951 fatcat:xgc3q2ogrjgznb3eqgxscpyghe

Clinical Metabolomics: The New Metabolic Window for Inborn Errors of Metabolism Investigations in the Post-Genomic Era

Abdellah Tebani, Lenaig Abily-Donval, Carlos Afonso, Stéphane Marret, Soumeya Bekri
2016 International Journal of Molecular Sciences  
The rise of "omic" approaches, enabled by the tremendous technological shift in both multiscale biological information capture and data management, offers an amazing opportunity to provide new effective  ...  Systems biology is a new scientific field that tries to achieve this systemic understanding of biology and to fill in the gap between information and context from a biological standpoint.  ...  This gave birth to computational biology which could be divided into two distinct branches: knowledge discovery or data-mining, and simulation-based analysis.  ... 
doi:10.3390/ijms17071167 pmid:27447622 pmcid:PMC4964538 fatcat:bgxb5gotyffujacdtq44rvx7iu

Integrated Omics: Tools, Advances, and Future Approaches

Biswapriya B Misra, Carl D Langefeld, Michael Olivier, Laura A Cox
2018 Journal of Molecular Endocrinology  
With the rapid adoption of high-throughput omic approaches to analyze biological samples such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can generate tera- to peta-byte sized  ...  data files on a daily basis.  ...  Quantification of the metabolome Metabolomics data can link genetic and proteomic variation to functional variation and provide novel insights into metabolic, regulatory and signaling activities in a given  ... 
doi:10.1530/jme-18-0055 pmid:30006342 fatcat:62c6xglxcbhhnkxgqo5gt7garq

Advances in Nutrigenomics research: Novel and future analytical approaches to investigate the biological activity of natural compounds and food functions

V. García-Cañas, C. Simó, C. León, A. Cifuentes
2010 Journal of Pharmaceutical and Biomedical Analysis  
Thus, to carry out these studies Transcriptomics, Proteomics and Metabolomics approaches are employed together with an adequate integration of the information that they provide.  ...  Following this trend, Nutrigenomics has emerged as a novel and multidisciplinary research field in nutritional science that aims to elucidate how diet can influence human health.  ...  Data analysis in Metabolomics.  ... 
doi:10.1016/j.jpba.2009.04.019 pmid:19467817 fatcat:jf6atsrki5dmxinec53tbvug6u

Evaluation of diversity among common beans (Phaseolus vulgaris L.) from two centers of domestication using 'omics' technologies

Meghan M Mensack, Vanessa K Fitzgerald, Elizabeth P Ryan, Matthew R Lewis, Henry J Thompson, Mark A Brick
2010 BMC Genomics  
Results: Three 'omics' approaches: transcriptomics, proteomics, and metabolomics were used to qualitatively evaluate the diversity of common bean from two Centers of Domestication (COD).  ...  All three approaches were able to classify common bean according to their COD using unsupervised analyses; these findings are consistent with the hypothesis that differences exist in gene transcription  ...  assistance in proteomic analyses, and Erica Daniell for harvesting the beans from ARDEC fields and RNA extraction for transcriptomics analysis.  ... 
doi:10.1186/1471-2164-11-686 pmid:21126341 pmcid:PMC3014982 fatcat:hm77jv6iineezce2nhlrvgsyza

Foodomics [chapter]

Virginia Garcia-Cañas, Carolina Simó, Miguel Herrero, Elena Ibañez, Alejandro Cifuentes
2012 OMICs Technologies  
Over the last years, the use of biological knowledge accumulated in public databases by means of bioinformatics, allows to systematically analyse large data lists in an attempt to assemble a summary of  ...  A particular case on the application of "omics" approaches to guarantee food safety is the biomarker discovery in body fluids and tissues regarding prion diseases (Huzarewich et al. 2010) .  ...  ACKNOWLEDGMENT This work was supported by Projects AGL2008-05108-C03-01 and CONSOLIDER INGENIO 2010 CSD2007-00063 FUN-C-FOOD (Ministerio de Educación y Ciencia).  ... 
doi:10.1201/b11534-5 fatcat:6qqxv7hqkrc6blyu63t2b5354e

Toxicogenomics Investigation Under the eTOX Project

Olivier Taboureau, Anne Hersey
2012 Journal of Pharmacogenomics & Pharmacoproteomics  
Acknowledgement The authors would like to acknowledge the Innovative Medicines Initiative Joint Undertaking (eTOX) for supporting the work.  ...  To our knowledge, comparison of the data studied in TG-GATEs and DrugMatrix has not been yet performed and an in-depth comparison will be one of the aims in the eTOX project to evaluate the reproducibility  ...  models will be investigated with the same set of available data and combined when possible into a hybrid model.  ... 
doi:10.4172/2153-0645.s7-001 fatcat:p3zasutmibc7xckgrzb2dcy5kq

Untargeted Metabolomics Shows Alterations in Homocysteine, Lipids, and Fatty Acids Predicting Memory Decline in Healthy Middle-Aged Individuals [article]

Ihab Hajjar, Qingpo Cai, Tianwei Yu, Dean P. Jones
2020 bioRxiv   pre-print
This is the first Metabolome-Wide Association Study of the human plasma for the longitudinal change in memory in healthy adults.  ...  RESULTS: From 10,201 measured metabolic features, 558 differed between those experiencing change vs no change in memory (False Discovery Rate, FDR< 0.2).  ...  Improving peak detection in high-resolution LC/MS metabolomics data using preexisting knowledge and machine learning approach. Bioinformatics. 2014;30(20):2941-2948.  ... 
doi:10.1101/2020.02.23.949537 fatcat:krn4axjzv5bupop452q75dlw34

Pathomx: an interactive workflow-based tool for the analysis of metabolomic data

Martin A Fitzpatrick, Catherine M McGrath, Stephen P Young
2014 BMC Bioinformatics  
However, the development of robust methods for the analysis of metabolomic data is a work-in-progress.  ...  Here we present Pathomx, a workflow-based tool for the processing, analysis and visualisation of metabolomic and associated data in an intuitive and extensible environment.  ...  Acknowledgements This work was supported by a Wellcome Trust studentship to MAF (grant 14844) and an Academic Clinical Fellowship from the National Institute for Health Research to CMMcG.  ... 
doi:10.1186/s12859-014-0396-9 pmid:25490956 pmcid:PMC4271363 fatcat:66rlqvvxbzbvvnagjfcuaeb4fu

Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium

Signe Altmäe, Francisco J. Esteban, Anneli Stavreus-Evers, Carlos Simón, Linda Giudice, Bruce A. Lessey, Jose A. Horcajadas, Nick S. Macklon, Thomas D'Hooghe, Cristina Campoy, Bart C. Fauser, Lois A. Salamonsen (+1 others)
2013 Human Reproduction Update  
alone or in a panel was 'unequivocally clinically useful' due to low numbers of subjects in discovery and replication studies, cycle-and stage dependence and low sensitivity and specificity (May et al  ...  (variability in composition and abundance of the proteins, i.e. proteomics) or metabolome (variability in composition and abundance of metabolites, i.e. metabolomics or metabonomics) in a biological sample  ... 
doi:10.1093/humupd/dmt048 pmid:24082038 pmcid:PMC3845681 fatcat:y2l6zh3qnzhtdp5ish4exdxhoq

A global approach to analysis and interpretation of metabolic data for plant natural product discovery

Manhoi Hur, Alexis Ann Campbell, Marcia Almeida-de-Macedo, Ling Li, Nick Ransom, Adarsh Jose, Matt Crispin, Basil J. Nikolau, Eve Syrkin Wurtele
2013 Natural product reports (Print)  
We detail a public database repository for metabolomics, tools and approaches for statistical analysis of metabolomics data, and methods for integrating these datasets with transcriptomic data to create  ...  We detail a public database repository for metabolomics, tools and approaches for statistical analysis of metabolomics data, and methods for integrating these dataset with transcriptomic data to create  ...  Approaches and innovation in metabolomics data storage and visualization Metabolomics data storage Combining metabolomics data from targeted and non-targeted analytical platforms is often a good approach  ... 
doi:10.1039/c3np20111b pmid:23447050 pmcid:PMC3629923 fatcat:wukjadvc5rhbvoboj7xlqnqlua

Application of NMR-based metabolomics for environmental assessment in the Great Lakes using zebra mussel (Dreissena polymorpha)

Miki Watanabe, Kathryn A. Meyer, Tyler M. Jackson, Tracey B. Schock, W. Edward Johnson, Daniel W. Bearden
2015 Metabolomics  
This study has demonstrated the feasibility of the NMR-based metabolomics approach to assess whole-body metabolomics of zebra mussels to study the physiological impact of toxicant exposure at field sites  ...  A total of 26 altered metabolites (including two unidentified peaks) were successfully identified in a comparison of zebra mussels from the LMMB1 site and LMMB5 reference site.  ...  Commercial equipment or materials are identified in this paper to specify adequately the experimental procedure.  ... 
doi:10.1007/s11306-015-0789-4 pmid:26366138 pmcid:PMC4559106 fatcat:ovj5i4vb75cmhnixa7ofdgwdyu

A simultaneous exploratory and quantitative amino acid and biogenic amine metabolic profiling platform for rapid disease phenotyping via UPLC-QToF-MS

Nicola Gray, Nathan G. Lawler, Rongchang Yang, Aude-Claire Morillon, Melvin C.L. Gay, Sze-How Bong, Elaine Holmes, Jeremy K. Nicholson, Luke Whiley
2020 Talanta: The International Journal of Pure and Applied Analytical Chemistry  
Both the QQQ and QToF approaches were equivalent in being able to correctly classify SARS-CoV-2 positivity.  ...  Using the HRAM-MS data, retrospective phenotypic data mining could be performed, demonstrating the versatility of HRAM-MS instrumentation in a clinical and molecular epidemiological environment.  ...  The authors would like to thank Dale Edgar and Ruey Leng Loo for their contribution to the ethics and sample collection and Professor Toby Richards for his intellectual contributions to the project.  ... 
doi:10.1016/j.talanta.2020.121872 pmid:33298292 fatcat:dfpd5vkt75c2neurs6c3qdgrla
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