Filters








321 Hits in 5.9 sec

Big linked cancer data: Integrating linked TCGA and PubMed

Muhammad Saleem, Maulik R. Kamdar, Aftab Iqbal, Shanmukha Sampath, Helena F. Deus, Axel-Cyrille Ngonga Ngomo
2014 Journal of Web Semantics  
We present the concept of Big Linked Data by showing how the constant stream of new bio-medical publications can be integrated with the Linked Cancer Genome Atlas dataset (TCGA) within a virtual integration  ...  Finally, the lack of an integrated vocabulary makes querying this data more difficult.In this paper, we advocate the use of Linked Data to integrate, query and visualize bio-medical data.  ...  An over-estimation of sources can be very expensive while dealing with Big Linked Data sources such as the integrated Linked TCGA and PubMed datasets.  ... 
doi:10.1016/j.websem.2014.07.004 fatcat:4wk2simqhbgjpnon4f2f5przsu

Big Linked Cancer Data: Integrating Linked TCGA and PubMed

Muhammad Saleem, Maulik R. Kamdar, Aftab Iqbal, Shanmukha Sampath, Helena Deus, Axel-Cyrille Ngonga Ngomo
2014 Social Science Research Network  
We present the concept of Big Linked Data by showing how the constant stream of new bio-medical publications can be integrated with the Linked Cancer Genome Atlas dataset (TCGA) within a virtual integration  ...  Finally, the lack of an integrated vocabulary makes querying this data more difficult.In this paper, we advocate the use of Linked Data to integrate, query and visualize bio-medical data.  ...  An over-estimation of sources can be very expensive while dealing with Big Linked Data sources such as the integrated Linked TCGA and PubMed datasets.  ... 
doi:10.2139/ssrn.3199108 fatcat:syntoecj6vhoxot5t2uuqecp6q

Enabling Web-scale data integration in biomedicine through Linked Open Data

Maulik R. Kamdar, Javier D. Fernández, Axel Polleres, Tania Tudorache, Mark A. Musen
2019 npj Digital Medicine  
Semantic Web technologies and Linked Data principles may aid toward Web-scale semantic processing and data integration in biomedicine.  ...  In this paper, we provide our perspective on some opportunities proffered by the use of LSLOD to integrate biomedical data and knowledge in three domains: (1) pharmacology, (2) cancer research, and (3)  ...  J.F. and A.P. contribute to several initiatives to enable decentralized Web-scale semantic processing and data integration.  ... 
doi:10.1038/s41746-019-0162-5 pmid:31531395 pmcid:PMC6736878 fatcat:othhm3v53bc6hkcdzm4ugqc2yy

Knowledge and Theme Discovery across Very Large Biological Data Sets Using Distributed Queries: A Prototype Combining Unstructured and Structured Data

Uma S. Mudunuri, Mohamad Khouja, Stephen Repetski, Girish Venkataraman, Anney Che, Brian T. Luke, F. Pascal Girard, Robert M. Stephens, Jan Aerts
2013 PLoS ONE  
Our results suggest that the available technologies within the Big Data domain can reduce the time and effort needed to utilize and apply distributed queries over large datasets in practical clinical applications  ...  In order to achieve useful results, researchers require methods that consolidate, store and query combinations of structured and unstructured data sets efficiently and effectively.  ...  Acknowledgments The authors wish to thank Tom Plunkett for his technical contributions and edits to this manuscript, Ted Coyle for his ongoing Mahout/Hive counsel, Tyler Muth for his R expertise and detailed  ... 
doi:10.1371/journal.pone.0080503 pmid:24312478 pmcid:PMC3846626 fatcat:2or3whazpjc2lpg6wgz7qhp3ie

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)

Tsung-Jung Wu, Amirhossein Shamsaddini, Yang Pan, Krista Smith, Daniel J. Crichton, Vahan Simonyan, Raja Mazumder
2014 Database: The Journal of Biological Databases and Curation  
Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients.  ...  This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate  ...  Yu for help with database and interface development, S. Kelly for EDRN data integration and Dr V.  ... 
doi:10.1093/database/bau022 pmid:24667251 pmcid:PMC3965850 fatcat:cob43ptnp5hgnfmouec26ozvp4

"Big Data" for breast cancer: where to look and what you will find

Susan E Clare, Pamela L Shaw
2016 npj Breast Cancer  
Sanger, TCGA; (5) a list of journals focused on data science that include cancer-related "Big Data"; and (6) miscellaneous resources.  ...  In this review, we provide an overview of data resources focusing on high-throughput data and on cancer-related data resources.  ...  Special note: BMC publishes GigaScience, an open access, open data journal that links manuscripts to data, software tools, and workflows from all areas of "big data" science.  ... 
doi:10.1038/npjbcancer.2016.31 pmid:28164152 pmcid:PMC5289822 fatcat:eiwpevaamfh5fdmqvzda7eez3m

Methods and Trends in Information Retrieval in Big Data Genomic Research

2019 VOLUME-8 ISSUE-10, AUGUST 2019, REGULAR ISSUE  
This paper presented the recent research trends, survey, reviews, experiments, and concepts in information retrieval applied to text, images and object features in big data genomic research.  ...  This paper described information retrieval (IR) and the common methods of finding, extracting, and mining information in genomic research through text mining, and natural language processing (NLP).  ...  It was estimated by IDC and Statista in 2025 there will 163 zettabytes volume of data [11, 12] or generated knowledge can be essential uses for big data.  ... 
doi:10.35940/ijitee.i1109.0789s219 fatcat:j2uramagd5a75jusrcor75w7ue

Exploring and visualizing multidimensional data in translational research platforms

William Dunn, Anita Burgun, Marie-Odile Krebs, Bastien Rance
2016 Briefings in Bioinformatics  
genomics patient stratification explorer, Igloo-Plot, The Georgetown Database of Cancer Plus, tranSMART, an unnamed data-cube-based model supporting heterogeneous data, Papilio, Caleydo Domino, Qlucore  ...  The unprecedented advances in technology and scientific research over the past few years have provided the scientific community with new and more complex forms of data.  ...  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

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data

Charles Cole, Konstantinos Krampis, Konstantinos Karagiannis, Jonas S Almeida, William J Faison, Mona Motwani, Quan Wan, Anton Golikov, Yang Pan, Vahan Simonyan, Raja Mazumder
2014 BMC Bioinformatics  
As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program -The Cancer Genome Atlas (TCGA).  ...  (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome.  ...  Acknowledgements We want to thank P Satti and JH Yu for help with database and interface development. We thank the TCGA tumor-specific groups for providing the data.  ... 
doi:10.1186/1471-2105-15-28 pmid:24467687 pmcid:PMC3916084 fatcat:b2o3s5grcrf6hi6xkm2j64un6m

Pan-cancer analysis of TCGA data reveals notable signaling pathways

Richard Neapolitan, Curt M. Horvath, Xia Jiang
2015 BMC Cancer  
The Cancer Genome Atlas (TCGA) makes available gene expression level data on cases and controls in ten different types of cancer including breast cancer, colon adenocarcinoma, glioblastoma, kidney renal  ...  We analyzed each of the ten cancer types mentioned above separately, and we perform a pan-cancer analysis by grouping the data for all the cancer types.  ...  This work was supported by National Library of Medicine grants number R00LM010822 and R01LM011663.  ... 
doi:10.1186/s12885-015-1484-6 pmid:26169172 pmcid:PMC4501083 fatcat:3w7fww4dprefrkrqmo54hf35na

In Search of Big Medical Data Integration Solutions -A Comprehensive Survey

Houssein Dhayne, Rafiqul Haque, Rima Kilany, Yehia Taher
2019 IEEE Access  
Furthermore, this paper discusses future research directions in the integration of Big healthcare data.  ...  These diverse and unprecedented characteristics have engendered the notion of "Big Data."  ...  The bridging process is performed by matching the synonyms for every disease and gene found in Linked TCGA with PubMed article's abstract.  ... 
doi:10.1109/access.2019.2927491 fatcat:6ooixehrznfdnbwghzfeds3mky

Semantic Web technologies for the big data in life sciences

Hongyan Wu, Atsuko Yamaguchi
2014 BioScience Trends  
The life sciences field is entering an era of big data with the breakthroughs of science and technology. More and more big data-related projects and activities are being performed in the world.  ...  The paper presents a survey of big data in life sciences, big data related projects and Semantic Web technologies.  ...  Acknowledgements This work has been supported by the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST).  ... 
doi:10.5582/bst.2014.01048 fatcat:x2rlpyjel5cybarma34ji6sq3y

Genomics big data hybrid depositories architecture to unlock precision medicine: a conceptual framework

Ummul H. Mohamad, Mohamad T. Ijab, Rabiah A. Kadir
2018 International Journal of Engineering & Technology  
The genomics big data hybrid depositories architecture design is composed of few components; storage layer and service layer interconnected system such as visualization, data protection modeling, event  ...  processing engine and decision support, to carry out their purpose of merging the genomics data with the healthcare data.  ...  data, annotations and specimen data) to allow collaboration among its users [84] This platform also allow access to public datasets such as The Cancer Genome Atlas (TCGA) and other National Cancer Institute  ... 
doi:10.14419/ijet.v7i4.16893 fatcat:4lgua7ixtbcxhhcwvenadbc2va

Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data

Chao Zhang, Jochem Bijlard, Christine Staiger, Serena Scollen, David van Enckevort, Youri Hoogstrate, Alexander Senf, Saskia Hiltemann, Susanna Repo, Wibo Pipping, Mariska Bierkens, Stefan Payralbe (+14 others)
2017 F1000Research  
.: The national institutes of health's big data to knowledge (BD2K) initiative: capitalizing on biomedical big data. J Am Med Inform Assoc. 2014; 21(6): 957-958.  ...  PubMed Abstract | Free Full Text 11. Cerami E, Gao J, Dogrusoz U, et al.: The cbio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.  ...  EGA) with a workflow environment (Galaxy) and a data integration platform hosting interpreted data (transMART).  ... 
doi:10.12688/f1000research.12168.1 pmid:29123641 pmcid:PMC5657030 fatcat:pmccjyaoffbmfd4rdcreqnx7je

An empirical meta-analysis of the life sciences linked open data on the web

Maulik R. Kamdar, Mark A. Musen
2021 Scientific Data  
To tackle these challenges, the community has experimented with Semantic Web and linked data technologies to create the Life Sciences Linked Open Data (LSLOD) cloud.  ...  not useful for data integration from a biomedical perspective.  ...  for seamless integration of big data.  ... 
doi:10.1038/s41597-021-00797-y pmid:33479214 fatcat:iealrgcwwbhjlicg7m43mj4mee
« Previous Showing results 1 — 15 out of 321 results