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A Web-based platform to find out relations between OMIC data and clinical features

Teruyoshi Hishiki
2006 AMIA Annual Symposium Proceedings  
We developed a platform that visualizes all the dimensions of so-called 'OMIC' data from genomic, transcriptomic, and proteomic domains, and helps users identify interesting data dimensions that might  ...  For this, we organized the textual descriptions of Clinical Synopsis fields in OMIM (Online Mendelian Inheritance in Man) into a quantitative format, and developed a Web-based interactive and graphical  ...  concentration of transcripts in 50 types of normal human tissues using a competitive PCR-based method. We clustered the gene expression patterns in the same way as clinical features.  ... 
pmid:17238569 pmcid:PMC1839352 fatcat:l5tm2lnv5beapalwsppsj2snlq

crcTRP: A Translational Research Platform for Colorectal Cancer

Ning Deng, Ling Zheng, Fang Liu, Li Wang, Huilong Duan
2013 Computational and Mathematical Methods in Medicine  
A preliminary exploration of conducting translational research on crcTRP was implemented and worked out a set of clinic-genomic relations, linking clinical data with genomic data.  ...  The information, including clinical data, epidemiology data, individual omics data, and public omics data, was collected through a multisource biomedical information collection solution and then integrated  ...  Results and Discussions A translational research platform for colorectal cancer, named crcTRP, was developed and lots of clinic-genomic relations were found out based on information provided by the platform  ... 
doi:10.1155/2013/930362 pmid:23431356 pmcid:PMC3575041 fatcat:2uj7tg6plrarlm2qkbslsz54ju

Translational research platforms integrating clinical and omics data: a review of publicly available solutions

V. Canuel, B. Rance, P. Avillach, P. Degoulet, A. Burgun
2014 Briefings in Bioinformatics  
A large heterogeneity was observed in regard to the capability to manage phenotype information in addition to omics data, their security and interoperability features.  ...  We reviewed the biomedical literature for translational platforms allowing the management and exploration of clinical and omics data, and identified seven platforms: BRISK, caTRIP, cBio Cancer Portal,  ...  Acknowledgements The authors thank the contributors of the BRISK, iDASH, cBioPortal and tranSMART platforms who answered our request for information.  ... 
doi:10.1093/bib/bbu006 pmid:24608524 pmcid:PMC4364065 fatcat:vrf326vuybc37bnl7fp7zbqpg4

Bringing radiomics into a multi-omics framework for a comprehensive genotype–phenotype characterization of oncological diseases

Mario Zanfardino, Monica Franzese, Katia Pane, Carlo Cavaliere, Serena Monti, Giuseppina Esposito, Marco Salvatore, Marco Aiello
2019 Journal of Translational Medicine  
Despite several data structures based on multi-layer architecture proposed to combine multi-omic biological information, none of these has been designed and assessed to include radiomic data as well.  ...  To meet this need, we propose to use the MultiAssayExperiment (MAE), an R package that provides data structures and methods for manipulating and integrating multi-assay experiments, as a suitable tool  ...  Therefore, from a data structure point of view, the challenge is to ensure structured relations between patient data and experiments/assays features.  ... 
doi:10.1186/s12967-019-2073-2 pmid:31590671 pmcid:PMC6778975 fatcat:nwlos7y25jgjfh65t7suykhgze

G-DOC Plus – an integrative bioinformatics platform for precision medicine

Krithika Bhuvaneshwar, Anas Belouali, Varun Singh, Robert M. Johnson, Lei Song, Adil Alaoui, Michael A. Harris, Robert Clarke, Louis M. Weiner, Yuriy Gusev, Subha Madhavan
2016 BMC Bioinformatics  
The system allows researchers to explore clinical-omic data one sample at a time, as a cohort of samples; or at the level of population, providing the user with a comprehensive view of the data.  ...  G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays  ...  in data loading and curation; and Laura Sheahan for technical editing.  ... 
doi:10.1186/s12859-016-1010-0 pmid:27130330 pmcid:PMC4851789 fatcat:evsfljlx25eq7kc25iezsionuu

A data management infrastructure for the integration of imaging and omics data in life sciences

Luis Kuhn Cuellar, Andreas Friedrich, Gisela Gabernet, Luis de la Garza, Sven Fillinger, Adrian Seyboldt, Tobias Koch, Sven zur Oven-Krockhaus, Friederike Wanke, Sandra Richter, Wolfgang M. Thaiss, Marius Horger (+4 others)
2022 BMC Bioinformatics  
Our architecture introduces an image management system into a FAIR-supporting, web-based platform for omics data management.  ...  Conclusions We describe a data management architecture for integrated, FAIR-supporting management of omics and biomedical imaging data, and exemplify its applicability for basic biology research and clinical  ...  The web-based qPortal qPortal is a web-based platform for FAIR-driven data management of biomedical data.  ... 
doi:10.1186/s12859-022-04584-3 pmid:35130839 pmcid:PMC8822871 fatcat:dpvaqzuzfnbodfqjnojf6r4m3m

IOAT: an interactive tool for statistical analysis of omics data and clinical data

Lanlan Wu, Fei Liu, Hongmin Cai
2021 BMC Bioinformatics  
By using this tool, users can safely and conveniently try a combination of various methods on their private multi-omics data to find a model suitable for their data, conduct risk assessment and determine  ...  Our mainly targets csv format data, and combines clinical data with high-dimensional multi-omics data.  ...  Availability of data and materials Software and data are available at https:// github. com/ WlSun shine/ IOAT-softw are. Declarations Ethics approval and consent to participate Not applicable.  ... 
doi:10.1186/s12859-021-04253-x pmid:34130622 fatcat:fyjhydr4tbgile2qoevpntkzfy

Efficient data management infrastructure for the integration of imaging and omics data in life science research [article]

Luis Kuhn Cuellar, Andreas Friedrich, Gisela Gabernet, Luis de la Garza, Sven Fillinger, Adrian Seyboldt, Sven zur Oven-Krockhaus, Friederike Wanke, Sandra Richter, Wolfgang M. Thaiss, Marius Horger, Nisar Malek (+3 others)
2019 bioRxiv   pre-print
The proposed architecture introduces an interoperable image management system, the OMERO server, into the backend of qPortal, a FAIR-compliant web-based platform for omics data management.  ...  Here, we propose an approach based on principles of Service Oriented Architecture design, to allow the integrated management and analysis of multi-omics and biomedical imaging data.  ...  The Web-based qPortal qPortal is a web-based platform for FAIR data management of biomedical data.  ... 
doi:10.1101/2019.12.28.889295 fatcat:mpmsznhgw5g7bcrvhdovakv5f4

Exploring and visualizing multidimensional data in translational research platforms

William Dunn, Anita Burgun, Marie-Odile Krebs, Bastien Rance
2016 Briefings in Bioinformatics  
Proper visualization of data at a high level facilitates researcher's abilities to find trends, identify outliers and perform quality checks.  ...  Specifically, we reviewed the biomedical literature for translational platforms allowing the visualization and exploration of clinical and omics data, and identified 11 platforms: cBioPortal, interactive  ...  Acknowledgements We would like to acknowledge the clinical research team headed by Dr Marie-Odile Krebs for providing us with a complex clinical and biological data set that inspired our research for visualization  ... 
doi:10.1093/bib/bbw080 pmid:27585944 fatcat:qcsidegyjbfiloupuk2ghm5kme

Exchange of Clinical and Omics Data According to FAIR Principles: A Review of Open Source Solutions

Philipp Pugliese, Christian Knell, Jan Christoph
2020 Methods of Information in Medicine  
Due to the specialization of the research platforms and the fact that FAIR are only principles and not standards, the platforms have to be examined in individual cases to see whether and how they can be  ...  Background Due to the ongoing increase and importance of the sustainable reusability of data, the findable, accessible, interoperable, reusable or FAIR principles were developed which are also relevant  ...  The authors thank the contributors of the Base, Ensembl, Galaxy, GenePattern, ISA-Tools, LabKey Server, openBIS, SABIO-RK and SEEK platforms who answered our request for information.  ... 
doi:10.1055/s-0040-1712968 pmid:32620018 fatcat:o2acklthsbbzlclmfs7xyrpsg4

Comprehensive Review of Web Servers and Bioinformatics Tools for Cancer Prognosis Analysis

Hong Zheng, Guosen Zhang, Lu Zhang, Qiang Wang, Huimin Li, Yali Han, Longxiang Xie, Zhongyi Yan, Yongqiang Li, Yang An, Huan Dong, Wan Zhu (+1 others)
2020 Frontiers in Oncology  
Aim to help researchers to get a quick learning and understand the function of these tools, the current review delves into the introduction of the usage, characteristics and algorithms of tools, and web  ...  as OS/DSS/PFS) of clinical samples from different cohorts, and developed the easy-to-use online bioinformatics tools and web servers to assist the biomarker screening and validation.  ...  PrognoScan 7 Prognoscan is a platform for predicting the relationship between gene expression and patient survival based on a large number of public cancer microarray datasets with clinical information  ... 
doi:10.3389/fonc.2020.00068 pmid:32117725 pmcid:PMC7013087 fatcat:iw4ycc2iczbrxpo3oodcv4hpbq

A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer Research

Efstathios Iason Vlachavas, Jonas Bohn, Frank Ückert, Sylvia Nürnberg
2021 International Journal of Molecular Sciences  
Using data-driven approaches for the integration and interpretation of multi-omics data could stably identify links between structural and functional information and propose causal molecular networks with  ...  Integration of these data with clinical information provides new opportunities to discover how perturbations in biological processes lead to disease.  ...  Acknowledgments: We thank Shraddha Pai for her help with the netDx v. 1.3.1 analysis and Ricard Argelaguet for his contribution in setting and applying the MOFA+ framework.  ... 
doi:10.3390/ijms22062822 pmid:33802234 pmcid:PMC8000236 fatcat:rvwrq77kanh55lp2y3vrp54dqi

Knowledge-guided analysis of 'omics' data using the KnowEnG cloud platform [article]

Charles Blatti, Amin Emad, Matthew J. Berry, Lisa Gatzke, Milt Epstein, Daniel Lanier, Pramod Rizal, Jing Ge, Xiaoxia Liao, Omar Sobh, Mike Lambert, Corey S. Post (+16 others)
2019 bioRxiv   pre-print
We present KnowEnG, a free-to-use computational system for analysis of genomics data sets, designed to accelerate biomedical discovery.  ...  They are made available through multiple access modes including a web-portal, and include specialized visualization modules.  ...  We acknowledge the generous resource contributions from the National Center for Supercomputing Application, University of Illinois at Urbana-Champaign (UIUC); Mayo Clinic & Illinois Alliance for Technology-Based  ... 
doi:10.1101/642124 fatcat:6z643v75tnap5ebej66cr6rpre

Analysis of Pan-omics Data in Human Interactome Network (APODHIN)

Nupur Biswas, Krishna Kumar, Sarpita Bose, Raisa Bera, Saikat Chakrabarti
2020 Frontiers in Genetics  
APODHIN platform contains a web server component where users can upload single/multi omics data to identify TINs and cross-pathway links.  ...  Analysis of Pan-omics Data in Human Interactome Network (APODHIN) is a platform for integrative analysis of transcriptomics, proteomics, genomics, and metabolomics data for identification of key molecular  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This manuscript has been released as a pre-print at bioRxiv .  ... 
doi:10.3389/fgene.2020.589231 pmid:33363571 pmcid:PMC7753071 fatcat:l5wafha4pfauncgqqoa6s6eahq

The Application of Bayesian Methods in Cancer Prognosis and Prediction

JIADONG CHU, NA SUN, WEI HU, XUANLI CHEN, NENGJUN YI, YUEPING SHEN
2021 Cancer Genomics & Proteomics  
These molecular data provide a solid foundation for precision medicine and prognostic prediction of cancer.  ...  Compared with single-omics, multi-omics integration modelling will contribute to improving predictive performance, gaining insights into the underlying mechanisms of tumour occurrence and development,  ...  Firstly, the dependence relationship within and between platform-specific features was assessed.  ... 
doi:10.21873/cgp.20298 pmid:34949654 pmcid:PMC8717957 fatcat:3dyvvgjstrd4pkjuorbr3zxeym
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