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A Web-based platform to find out relations between OMIC data and clinical features
2006
AMIA Annual Symposium Proceedings
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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
2013
Computational and Mathematical Methods in Medicine
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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
2014
Briefings in Bioinformatics
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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
2019
Journal of Translational Medicine
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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
2016
BMC Bioinformatics
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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
2022
BMC Bioinformatics
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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
2021
BMC Bioinformatics
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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]
2019
bioRxiv
pre-print
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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
2016
Briefings in Bioinformatics
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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
2020
Methods of Information in Medicine
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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
2020
Frontiers in Oncology
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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
2021
International Journal of Molecular Sciences
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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]
2019
bioRxiv
pre-print
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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)
2020
Frontiers in Genetics
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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
2021
Cancer Genomics & Proteomics
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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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