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The Veterans Affairs Precision Oncology Data Repository, a Clinical, Genomic, and Imaging Research Database

Danne C. Elbers, Nathanael R. Fillmore, Feng-Chi Sung, Spyridon S. Ganas, Andrew Prokhorenkov, Christopher Meyer, Robert B. Hall, Samuel J. Ajjarapu, Daniel C. Chen, Frank Meng, Robert L. Grossman, Mary T. Brophy (+1 others)
<span title="2020-08-17">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5cekcl3stvfxxfsctgk6zwoqwe" style="color: black;">Patterns</a> </i> &nbsp;
A subset of the repository is available at the Genomic Data Commons (GDC) and The Cancer Imaging Archive (TCIA), and the full repository is available through the Veterans Precision Oncology Data Commons  ...  The Veterans Affairs Precision Oncology Data Repository (VA-PODR) is a large, nationwide repository of de-identified data on patients diagnosed with cancer at the Department of Veterans Affairs (VA).  ...  VA-PODR consolidates de-identified VA clinical, genomic, and imaging data needed for research in precision oncology in a large, nationwide repository.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.patter.2020.100083">doi:10.1016/j.patter.2020.100083</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33205130">pmid:33205130</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7660389/">pmcid:PMC7660389</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tkei4fighbcnlmys3kvhhjwpsu">fatcat:tkei4fighbcnlmys3kvhhjwpsu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210526230116/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7660389&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/05/f4/05f4b0da97d5c83542cb8081c475a671d6096af8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.patter.2020.100083"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7660389" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Data Sharing, Clinical Trials, and Biomarkers in Precision Oncology: Challenges, Opportunities, and Programs at the Department of Veterans Affairs

LD Fiore, MT Brophy, RE Ferguson, C Shannon, SJ Turek, K Pierce-Murray, S Ajjarapu, GD Huang, CSE Lee, PW Lavori
<span title="2017-03-20">2017</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/x4gh7d4fdjaj5ow3knnza5u3hq" style="color: black;">Clinical Pharmacology and Therapeutics</a> </i> &nbsp;
Cancer genomic research reveals that a similar cancer clinical phenotype (e.g., non-small cell lung cancer) can arise from various mutations in tumor DNA. Thus, organ of origin is not a defini-1  ...  The repository houses clinical health record and genomic data (FASTQ file format) and complements the Cancer Imaging Archive, 7 another NCI-sponsored repository that contains radiographic and pathology  ...  The National Cancer Institute (NCI) has created the Genomic Data Commons, a unified data repository 6 that enables data sharing across these and other cancer genomic studies, in support of precision medicine  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cpt.660">doi:10.1002/cpt.660</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28182272">pmid:28182272</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5414893/">pmcid:PMC5414893</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j2qxptrkbbgvlkyrnu75yj3jdm">fatcat:j2qxptrkbbgvlkyrnu75yj3jdm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208221151/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5414893&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/37/40/37407b31cb20f24093f1b7f91136d8cd296d670f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cpt.660"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5414893" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

How Will Big Data Improve Clinical and Basic Research in Radiation Therapy?

Barry S. Rosenstein, Jacek Capala, Jason A. Efstathiou, Jeff Hammerbacher, Sarah L. Kerns, Feng-Ming (Spring) Kong, Harry Ostrer, Fred W. Prior, Bhadrasain Vikram, John Wong, Ying Xiao
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r3z6tg2rqbbd3fflq2iu4rgpky" style="color: black;">International Journal of Radiation Oncology, Biology, Physics</a> </i> &nbsp;
Historically, basic scientists and clinical researchers have transduced reality into data so that they might explain or predict the world.  ...  In addition, wellcurated research and trial data are being pooled in public data repositories to support large-scale analyses.  ...  HHSN261200800001E and 1U01CA187013. Dr. Andre Dekker and Dr. Jatinder Palta are thanked for the information concerning EUROCAT and VA system, respectively.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ijrobp.2015.11.009">doi:10.1016/j.ijrobp.2015.11.009</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26797542">pmid:26797542</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4864183/">pmcid:PMC4864183</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2cqg7gkca5hpxn4ekmfcup664q">fatcat:2cqg7gkca5hpxn4ekmfcup664q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722001002/https://manuscript.elsevier.com/S036030161526703X/pdf/S036030161526703X.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6b/46/6b4676c7fa6fc74bd48f1a5386caf04130672976.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ijrobp.2015.11.009"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864183" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

From Discovery to Practice and Survivorship: Building a National Real-World Data Learning Healthcare Framework for Military and Veteran Cancer Patients

Jerry S.H. Lee, Kathleen M. Darcy, Hai Hu, Yovanni Casablanca, Clifton L. Dalgard, John B. Freymann, Sean E. Hanlon, Grant D. Huang, Leonid Kvecher, George L. Maxwell, Frank Meng, Joel T. Moncur (+6 others)
<span title="2019-03-05">2019</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/x4gh7d4fdjaj5ow3knnza5u3hq" style="color: black;">Clinical Pharmacology and Therapeutics</a> </i> &nbsp;
of Veterans Affairs.  ...  figure and paper.  ...  Lower-level raw molecular and imaging data of very large size, on the other hand, will be directly uploaded to public data repositories, including The Cancer Imaging Archive (TCIA), 11 Genomic Data Commons  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cpt.1425">doi:10.1002/cpt.1425</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30838639">pmid:30838639</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6617989/">pmcid:PMC6617989</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4ni377qig5h2lkdl6ibns2w5na">fatcat:4ni377qig5h2lkdl6ibns2w5na</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200505172903/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6617989&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8a/1d/8a1d65b3d18651a96e01787fa70b116e42070c01.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/cpt.1425"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6617989" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Comprehensive Infrastructure for Big Data in Cancer Research: Accelerating Cancer Research and Precision Medicine

Izumi V. Hinkson, Tanja M. Davidsen, Juli D. Klemm, Ishwar Chandramouliswaran, Anthony R. Kerlavage, Warren A. Kibbe
<span title="2017-09-21">2017</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4dl6zyzmsrhczjurbzfc3hrzn4" style="color: black;">Frontiers in Cell and Developmental Biology</a> </i> &nbsp;
These NCI-led efforts are continuously being refined to better support open data practices and precision oncology, and to serve as building blocks of the NCI Cancer Research Data Commons.  ...  The GDC ensures data and metadata quality, ingests and harmonizes genomic data, and securely redistributes the data.  ...  ACKNOWLEDGMENTS We thank NCI Center for Biomedical Informatics and Information Technology (CBIIT), Center for Cancer Genomics, Office of Clinical Cancer Proteomics Research, GDC, and the CGC Pilot teams  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fcell.2017.00083">doi:10.3389/fcell.2017.00083</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28983483">pmid:28983483</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5613113/">pmcid:PMC5613113</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jzwud34zvbgcbk5myj2kaffjnq">fatcat:jzwud34zvbgcbk5myj2kaffjnq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190305082639/http://pdfs.semanticscholar.org/c6c7/23f28174f78816e862445a364ecacbd25a85.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c6/c7/c6c723f28174f78816e862445a364ecacbd25a85.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fcell.2017.00083"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613113" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Defining next generation medicine for the patient through translational care: big data scientist training enhancement program (BD-STEP)

Connie S E Lee, Louis D Fiore
<span title="2017-12-22">2017</span> <i title="IOP Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jcj72hysgjc5zosk6ll75jqvfq" style="color: black;">Convergent Science Physical Oncology</a> </i> &nbsp;
positively impact patient care, led to a collaboration between the Department of Veterans Affairs (VA) and the National Cancer Institute (NCI).  ...  the gap between the administrative, clinical, and research worlds to achieving a common goal-to train the next generation of data scientists to understand data in the context of health care delivery.  ...  Their projects range from utilizing basic EHR phenotype data (including imaging data) to accessing the Million Veterans Program genomics data using a series of different analytical tools including predictive  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1088/2057-1739/aa9264">doi:10.1088/2057-1739/aa9264</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ux5ytygfhfhuvle4snxy3sp22q">fatcat:ux5ytygfhfhuvle4snxy3sp22q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180726213055/http://iopscience.iop.org/article/10.1088/2057-1739/aa9264/pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/56/5a/565a445e2ca626d78cbf6c9a04ba51d7feaf2847.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1088/2057-1739/aa9264"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> iop.org </button> </a>

Influential Usage of Big Data and Artificial Intelligence in Healthcare

Yan Cheng Yang, Saad Ul Islam, Asra Noor, Sadia Khan, Waseem Afsar, Shah Nazir
<span title="2021-09-06">2021</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xytabl7eh5a5lle2ofnetovd7u" style="color: black;">Computational and Mathematical Methods in Medicine</a> </i> &nbsp;
In clinical work and imaging, cancer care is getting improved by knowing the tumor biology and helping in the implementation of precision medicine.  ...  For example, cardiovascular imaging has now accurate imaging combined with big data from the eHealth record and pathology to better characterize the disease and personalized therapy.  ...  VA-PODR (Veterinary Affairs Accurate Oncology Data Collection) is a worldwide large repository of well-known data concerned with diagnosed patients of cancer in VA's (Veterans Affairs) department.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2021/5812499">doi:10.1155/2021/5812499</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34527076">pmid:34527076</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8437645/">pmcid:PMC8437645</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lmpwildgefggrisquu6ebwu2iu">fatcat:lmpwildgefggrisquu6ebwu2iu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210923184032/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC8437645&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ed/1c/ed1c0f66f1e0429ba3611c061d26737e54b11717.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2021/5812499"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8437645" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Uniformed Services University's Surgical Critical Care Initiative (SC2i): Bringing Precision Medicine to the Critically Ill

Arnaud Belard, Timothy Buchman, Christopher J Dente, Benjamin K Potter, Allan Kirk, Eric Elster
<span title="2018-03-01">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p2g77rcmcjaozgihldxgdylqs4" style="color: black;">Military medicine</a> </i> &nbsp;
We present the SC2i experience as a generalizable template for the national integration of federal and non-federal research databanks to foster critical and surgical care precision medicine.  ...  Precision medicine endeavors to leverage all available medical data in pursuit of individualized diagnostic and therapeutic plans to improve patient outcomes in a cost-effective manner.  ...  The NIH has taken a prominent role in answering the Executive Branch's call-to-arms (e.g., National Cancer Moonshot Initiative) and other agencies (Department of Defense and Department of Veterans Affairs  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/milmed/usx164">doi:10.1093/milmed/usx164</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29635571">pmid:29635571</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6usq7nocqrcrln5tyh7dnmiwk4">fatcat:6usq7nocqrcrln5tyh7dnmiwk4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180726210527/https://watermark.silverchair.com/usx164.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAbQwggGwBgkqhkiG9w0BBwagggGhMIIBnQIBADCCAZYGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMw_KTuuxepKk_1mXiAgEQgIIBZ9LcbYaROy9RpxliG6X8itmSRfR6yu858eJZ0AZEdl2EqZwcogGtO0wIJs5VOI80DzlCicbJhaOFHcD17FYqd30utgH_mNPQ-hNeeUxY8I-99EF7t7EqTUDAtV2Q1C-1hGxKip4Yl2r5D-vXV1cfVfYDZ1s5y2zcAatbsI85HC6VMgWCdYuQYCzqRTvza-e63WLFRRW93GeamrWbtnMWroVZKqIJ-kbNsXb6YdbXEPkKw-zTNl3p7RdhUOqMNpnMq3nZkQOVUirxIFtSHkYHs8fQucUrcdwvznAKRovCXzaQMCMJpIsiL-hhdzlkVxCVUZD3SndlJaNkgjy0rq971aBhNTq8jLHsD9jKMEfyDZmw1A69_W9HU4Qepz-8LcPFpl40ozCfDDTaUUGEp0TKN-_0r4gOi_bbd27fLeDxfq6Vo_qQo5-WorFirDDYia8sl2H5ixgBp-pIk-0DW-NlevIsYvkthITk" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d0/ce/d0cedcca0a3a9359cbc82c81f74fa8d77401a891.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/milmed/usx164"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Future cancer research priorities in the USA: a Lancet Oncology Commission

Elizabeth M Jaffee, Chi Van Dang, David B Agus, Brian M Alexander, Kenneth C Anderson, Alan Ashworth, Anna D Barker, Roshan Bastani, Sangeeta Bhatia, Jeffrey A Bluestone, Otis Brawley, Atul J Butte (+42 others)
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/w47me2ybknd6ro6kiyc5ho2uei" style="color: black;">The Lancet Oncology</a> </i> &nbsp;
and precision medicine.  ...  Enactment of the Cancer Moonshot within the 21st Century Cures Act in the USA arrived at a propitious moment in the advancement of knowledge, providing nearly US$2 billion of funding for cancer research  ...  ; and (3) develop a national database similar to The Cancer Genome Atlas database with links to clinical annotations that can be accessed by any investigator.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1470-2045(17)30698-8">doi:10.1016/s1470-2045(17)30698-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29208398">pmid:29208398</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6178838/">pmcid:PMC6178838</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iuvqtecywja5flhlmvbcvcvrhe">fatcat:iuvqtecywja5flhlmvbcvcvrhe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206064306/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6178838&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/21/d4/21d42f1153010ce862a5653360ff710f16337f38.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1470-2045(17)30698-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178838" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Report of the Second Asian Prostate Cancer (A-CaP) Study Meeting

Choung-Soo Kim, Ji Youl Lee, Byung Ha Chung, Wun-Jae Kim, Ng Chi Fai, Lukman Hakim, Rainy Umbas, Teng Aik Ong, Jasmine Lim, Jason L. Letran, Edmund Chiong, Tong-lin Wu (+17 others)
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/oo2zvxwqxrfnvgf23mn2yi5z6i" style="color: black;">Prostate International</a> </i> &nbsp;
databases and registration studies around the world.  ...  review board requirements, and the need for dedicated data managers.  ...  To create a clinical decision supporting system, it is important to create a smart clinical database (phenotype), engage in bio-banking and create genomic databases.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.prnil.2017.03.006">doi:10.1016/j.prnil.2017.03.006</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28828352">pmid:28828352</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5551923/">pmcid:PMC5551923</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5v5cak4iivd25kzplg42pujfui">fatcat:5v5cak4iivd25kzplg42pujfui</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718030803/https://minerva-access.unimelb.edu.au/bitstream/handle/11343/259403/PMC5551923.pdf;jsessionid=64B74B4A21BA2983381854E503E15749?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/25/18/2518148eb955c8bc8ff709b5777ee8e8bff2efed.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.prnil.2017.03.006"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5551923" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR

Gopal Pawar, Judith C. Madden, David Ebbrell, James W. Firman, Mark T. D. Cronin
<span title="2019-06-11">2019</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qigargnicncadmdn56ei23yjnu" style="color: black;">Frontiers in Pharmacology</a> </i> &nbsp;
This review also specifically addresses the need for solutions for mapping and integration of databases into a common platform for better translatability of preclinical data to clinical data.  ...  However, a systematic review and grouping of databases, based on purpose and information content, consolidated in a single source, has been lacking.  ...  Cancer GenomicHub is a repository that enables data sharing across cancer genomic studies in support of precision medicine.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fphar.2019.00561">doi:10.3389/fphar.2019.00561</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31244651">pmid:31244651</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6580867/">pmcid:PMC6580867</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t3junhqvxfeslcu37pihztlxiq">fatcat:t3junhqvxfeslcu37pihztlxiq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200307114837/http://researchonline.ljmu.ac.uk/id/eprint/11064/20/In%20Silico%20Toxicology%20Data%20Resources%20to%20Support%20Read-Across%20and%20%28Q%29SAR.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/63/4f/634f63cc882184e64ee95880378e48032c8be51e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fphar.2019.00561"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580867" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration

Robert H Dolin, Shaileshbhai R Gothi, Aziz Boxwala, Bret S E Heale, Ammar Husami, James Jones, Himanshu Khangar, Shubham Londhe, Frank Naeymi-Rad, Soujanya Rao, Barbara Rapchak, James Shalaby (+4 others)
<span title="2021-03-02">2021</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
The second, 'Precision Genomics Integration Platform', intersects a patient's FHIR-formatted clinical and genomic data with knowledge bases in order to provide on-demand delivery of contextually relevant  ...  Additional testing will be a critical step towards the clinical validation of this utility, enabling it to be integrated in a variety of real world data flow scenarios.  ...  Acknowledgements This work would not be possible without the collegial engagement with the HL7 community, particularly the HL7 Clinical Genomics committee, where the free sharing of ideas, the commaradary  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-021-04039-1">doi:10.1186/s12859-021-04039-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33653260">pmid:33653260</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/n7gx52u3ubaw5ad4dyv7igjg4q">fatcat:n7gx52u3ubaw5ad4dyv7igjg4q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210501125710/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04039-1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c6/5e/c65efcbe0a914ec831e8f1365fe4a3b1c788ed4d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-021-04039-1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Translational Bioinformatics: Past, Present, and Future

Jessica D. Tenenbaum
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mjqabxhzeveopm6sdbvzz2rmvy" style="color: black;">Genomics, Proteomics &amp; Bioinformatics</a> </i> &nbsp;
Though a relatively young discipline, translational bioinformatics (TBI) has become a key component of biomedical research in the era of precision medicine.  ...  Development of high-throughput technologies and electronic health records has caused a paradigm shift in both healthcare and biomedical research.  ...  Acknowledgments This work was supported in part by the Clinical and Translational Science Award (Grant No. UL1TR001117) to Duke University from the National Institutes of Health (NIH), United States.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.gpb.2016.01.003">doi:10.1016/j.gpb.2016.01.003</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26876718">pmid:26876718</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4792852/">pmcid:PMC4792852</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/he67bcd2xzh5hnj7t3qp65koi4">fatcat:he67bcd2xzh5hnj7t3qp65koi4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170926024130/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/355/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMTY3MjAyMjkxNjAwMDQwMQ%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ce/f2/cef2b29a95643090957c3e7e784e3b2b7ec8783c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.gpb.2016.01.003"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792852" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ethical, legal, social, and policy issues in the use of genomic technology by the U.S. Military

Maxwell J. Mehlman, Tracy Yeheng Li
<span title="2014-09-01">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ip2ipp63czgshmuqiuswm66uay" style="color: black;">Journal of Law and the Biosciences</a> </i> &nbsp;
In December 2010, JASON, a group of scientific advisors to the military, issued a report entitled "The $100 Genome: Implications for the Department of Defense" that outlined an ambitious plan to employ  ...  Introduction The U.S. military is beginning to employ genetic and genomic science to achieve military objectives, and is planning to expand these efforts in the future.  ...  14 Finally, in 2011, the US Department of Veterans Affairs (VA) established the Million Veteran Program, a geno-phenobank that collects DNA and health information from veterans and combines it with their  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/jlb/lsu021">doi:10.1093/jlb/lsu021</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25937933">pmid:25937933</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4410969/">pmcid:PMC4410969</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tk4dwtxqsbayjfzi5435jmhe7a">fatcat:tk4dwtxqsbayjfzi5435jmhe7a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720033928/https://scholarlycommons.law.case.edu/cgi/viewcontent.cgi?article=1011&amp;context=jil" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1d/c4/1dc45770f44de5e06d1d101338241f2ed18b8afa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/jlb/lsu021"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410969" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A longitudinal big data approach for precision health

Sophia Miryam Schüssler-Fiorenza Rose, Kévin Contrepois, Kegan J. Moneghetti, Wenyu Zhou, Tejaswini Mishra, Samson Mataraso, Orit Dagan-Rosenfeld, Ariel B. Ganz, Jessilyn Dunn, Daniel Hornburg, Shannon Rego, Dalia Perelman (+18 others)
<span title="2019-05-08">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/aowhseoqprea3b5rljynk52q4m" style="color: black;">Nature Medicine</a> </i> &nbsp;
We explored the ability of deep longitudinal profiling to make health-related discoveries, identify clinically relevant molecular pathways and affect behavior in a prospective longitudinal cohort (n =  ...  The cohort underwent integrative personalized omics profiling from samples collected quarterly for up to 8 years (median, 2.8 years) using clinical measures and emerging technologies including genome,  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH, the Department of Veteran Affairs, or the SNSF.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41591-019-0414-6">doi:10.1038/s41591-019-0414-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31068711">pmid:31068711</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6713274/">pmcid:PMC6713274</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ejbfv35cp5cipjajelbzkh6mvi">fatcat:ejbfv35cp5cipjajelbzkh6mvi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200505220956/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6713274&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a1/88/a1886a57cf2b92a9692551a50263be85faeba52a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41591-019-0414-6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6713274" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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