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Genomic CDS: an Example of a Complex Ontology for Pharmacogenetics and Clinical Decision Support

Matthias Samwald
2013 International Workshop on OWL Reasoner Evaluation  
The Genomic Clinical Decision Support (Genomic CDS) ontology aims to utilize advanced Web Ontology Language 2 (OWL 2) reasoning for this task.  ...  The important, clear-cut medical use case, the complex axioms in the ontology and the heavy use of qualified cardinality restrictions make the ontology an interesting test object for new OWL 2 reasoners  ...  Conclusions and outlook The Genomic CDS ontology is an example of an OWL 2 ontology for clinical genetics and decision support.  ... 
dblp:conf/ore/Samwald13 fatcat:6jm2rkyzpjh7pd2n3ccirtcx5e

An Update on Genomic CDS, a Complex Ontology for Pharmacogenomics and Clinical Decision Support

José Antonio Miñarro-Giménez, Matthias Samwald
2014 International Workshop on OWL Reasoner Evaluation  
We present an update of the Genomic CDS ontology which covers a significantly larger number of clinical decision support rules and where inconsistencies presented in previous versions of the ontology have  ...  The Genomic Clinical Decision Support (Genomic CDS) ontology utilizes Web Ontology Language 2 (OWL 2) reasoning for this task.  ...  Conclusions and outlook The Genomic CDS ontology is an example of an OWL 2 ontology for clinical genetics and decision support.  ... 
dblp:conf/ore/Minarro-Gimenez14 fatcat:e5x6cvtuyjeptdzgoeoj2nnzn4

Genomic Information for Clinicians in the Electronic Health Record: Lessons Learned From the Clinical Genome Resource Project and the Electronic Medical Records and Genomics Network

Marc S. Williams, Casey Overby Taylor, Nephi A. Walton, Scott R. Goehringer, Samuel Aronson, Robert R. Freimuth, Luke V. Rasmussen, Eric S. Hall, Cynthia A. Prows, Wendy K. Chung, Alexander Fedotov, Jordan Nestor (+5 others)
2019 Frontiers in Genetics  
Utilizing the electronic health record to present information to support the use of genomic medicine in clinical care to improve outcomes represents a tremendous opportunity.  ...  To fully realize the value, it is critical to place credible information in the hands of clinicians in time to support clinical decision making.  ...  Examples of SMART on FHIR apps with integrated information displays for clinical genomics are available FIGURE 2 | Example of narrative or L1 (left) and wire frame or L2 (right) clinical decision support  ... 
doi:10.3389/fgene.2019.01059 pmid:31737042 pmcid:PMC6830110 fatcat:gclp4ndqlbddncpmxv5yelzauq

Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies

Matthias Samwald, Jose Antonio Miñarro Giménez, Richard D Boyce, Robert R Freimuth, Klaus-Peter Adlassnig, Michel Dumontier
2015 BMC Medical Informatics and Decision Making  
The Genomic Clinical Decision Support (Genomic CDS) ontology represents 336 SNPs with 707 variants; 665 haplotypes related to 43 genes; 22 rules related to drug-response phenotypes; and 308 clinical decision  ...  Only a modest number of clinical decision support rules were triggered for a collection of 943 public genetic profiles. We found significant performance differences across available OWL reasoners.  ...  Acknowledgements We thank Yuan Ren and all other persons from the TrOWL team for their support.  ... 
doi:10.1186/s12911-015-0130-1 pmid:25880555 pmcid:PMC4340468 fatcat:m27ol6hprjdhfc2373zjiabcme

Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio

Teri A. Manolio
2016 Atherosclerosis  
In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine.  ...  As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas  ...  InfoButton pointing physicians to clinical decision support (CDS) resources; the pharmacogenetics variant and phenotype data repository (SPHINX); and MyResults. org, an online educational resource on  ... 
doi:10.1016/j.atherosclerosis.2016.08.034 pmid:27612677 pmcid:PMC5064852 fatcat:ilm6n5x4onbxrkjqqgroidtwa4

Merging Electronic Health Record Data and Genomics for Cardiovascular Research

Jennifer L. Hall, John J. Ryan, Bruce E. Bray, Candice Brown, David Lanfear, L. Kristin Newby, Mary V. Relling, Neil J. Risch, Dan M. Roden, Stanley Y. Shaw, James E. Tcheng, Jessica Tenenbaum (+2 others)
2016 Circulation: Cardiovascular Genetics  
The purpose of this statement is to discuss the current challenges in and the potential for merging electronic health record data and genomics for cardiovascular research.  ...  The addition of biobanks and genomic data to the information contained in the electronic health record has been demonstrated.  ...  Given the complexity of both clinical and genomic data, computerized clinical decision support has been proposed to assist clinicians in making decisions based on genomic data. 69 Results from analyses  ... 
doi:10.1161/hcg.0000000000000029 pmid:26976545 pmcid:PMC5646218 fatcat:a5j6up5wijestgkpr2uc6ztzay

An Ontology-Based, Mobile-Optimized System for Pharmacogenomic Decision Support at the Point-of-Care

Jose Antonio Miñarro-Giménez, Kathrin Blagec, Richard D. Boyce, Klaus-Peter Adlassnig, Matthias Samwald, Chris Mavergames
2014 PLoS ONE  
and to provide clinical decision support functionalities.  ...  Conclusions: The MSC system provides a novel approach for enabling the implementation of personalized medicine in clinical routine.  ...  Acknowledgments We thank Yuan Ren and other members of the TrOWL team for their support. Author Contributions  ... 
doi:10.1371/journal.pone.0093769 pmid:24787444 pmcid:PMC4008421 fatcat:7e6sjetw2zchdhx6765z2txckm

The Electronic Medical Records and Genomics (eMERGE) Network: past, present and future

Omri Gottesman, Helena Kuivaniemi, Gerard Tromp, W. Andrew Faucett, Rongling Li, Teri A. Manolio, Saskia C. Sanderson, Joseph Kannry, Randi Zinberg, Melissa A. Basford, Murray Brilliant, David J. Carey (+19 others)
2013 Genetics in Medicine  
the development of methods and best practices for using the electronic medical record as a tool for genomic research.  ...  Now in its sixth year and second funding cycle, and comprising nine research groups and a coordinating center, the network has played a major role in validating the concept that clinical data derived from  ...  ACKNOWLEDGMENTS The eMERGE Network is funded by the NHGRI, with additional funding from the National Institute of General Medical Sciences through the following grants: U01HG004438 to Johns Hopkins  ... 
doi:10.1038/gim.2013.72 pmid:23743551 pmcid:PMC3795928 fatcat:onqmiqi3trcxjga45pncvquts4

A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record

Peter Tarczy-Hornoch, Laura Amendola, Samuel J. Aronson, Levi Garraway, Stacy Gray, Robert W. Grundmeier, Lucia A Hindorff, Gail Jarvik, Dean Karavite, Matthew Lebo, Sharon E. Plon, Eliezer Van Allen (+3 others)
2013 Genetics in Medicine  
results into the EMR/electronic health record (EHR) and EHR-enabled clinical decision support (CDS).  ...  literature about using Original research article CDS engines for pharmacogenomics decision support using different types of genomic data.  ... 
doi:10.1038/gim.2013.120 pmid:24071794 pmcid:PMC3951437 fatcat:s7j4rh3epjgsffm2xygh4d3bqu

Pharmacogenomics in the clinic

Mary V. Relling, William E. Evans
2015 Nature  
Additional somatically acquired genomic variants direct the choice of "targeted" anticancer drugs for individual patients.  ...  evidenced-based strategy for improving the use of medications, thereby providing an important cornerstone for precision medicine.  ...  Appropriate clinical decision support (CDS) should be built and deployed to provide prescribers with recommendations, and pharmacogenetic considerations must be harmonized with other policies for the affected  ... 
doi:10.1038/nature15817 pmid:26469045 pmcid:PMC4711261 fatcat:cmi4hd56mfbx7in4nkquiz2bqq

Cohort Profile: The Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment Protocol (RIGHT Protocol)

2019 International Journal of Epidemiology  
The RIGHT cohort is a resource for pharmacogenomic research. 11 As part of the infrastructure, a RIGHT Data Access Committee has been created to review data requests for use of RIGHT data.  ...  External access to the data is facilitated by the Mayo Clinic Biobank 31 https://www. overview  ...  EHR integration and clinical decision support Since 2013, Mayo Clinic has developed and implemented a comprehensive multidisciplinary model 26 to integrate pharmacogenomic test results and clinical decision  ... 
doi:10.1093/ije/dyz123 pmid:31378813 pmcid:PMC7124480 fatcat:vikqtxie2rft3gcttugucilvhq

Human genome meeting 2016

A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson, R. Polimanti, J. Gelernter, X. Lin (+828 others)
2016 Human Genomics  
Methods Plasma samples from a clinically well-defined cohort of 100 male individuals, ages 2-16+ years, with ASD and 32 age-matched typically developing (TD) controls were subjected to global metabolomic  ...  The specific etiology of the majority of cases of autism spectrum disorder (ASD) is unknown, although numerous genetic/genomic variants and alterations of diverse cellular functions have been reported.  ...  Acknowledgements Funding for research and development is acknowledged for Project: "Research Oriented Data Management and Analysis" at the Ucar Lab by The Jackson Laboratory, USA.  ... 
doi:10.1186/s40246-016-0063-5 pmid:27294413 pmcid:PMC4896275 fatcat:ycjj53ixrbauvnusibuz76y7bm

CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record

Brian H Shirts, Joseph S Salama, Samuel J Aronson, Wendy K Chung, Stacy W Gray, Lucia A Hindorff, Gail P Jarvik, Sharon E Plon, Elena M Stoffel, Peter Z Tarczy-Hornoch, Eliezer M Van Allen, Karen E Weck (+11 others)
2015 JAMIA Journal of the American Medical Informatics Association  
There is a critical need to develop systems to effectively display genetic information in EHRs and augment clinical decision support (CDS).  ...  The highest priority recommendation was to address the need to implement CDS mechanisms and content for decision support for medically actionable genetic information.  ...  ACKNOWLEDGEMENTS The authors would like to acknowledge the following individuals for assistance with surveys and other interactions with collaborating sites: Beth Cobb at Cincinnati Children's Hospital  ... 
doi:10.1093/jamia/ocv065 pmid:26142422 pmcid:PMC5009914 fatcat:i3r7gfkz25f5vipplai2pod5ma

Evolution of HLA-B Pharmacogenomics and the Importance of PGx Data Integration in Health Care System: A 10 Years Retrospective Study in Thailand

Napatrupron Koomdee, Chiraphat Kloypan, Pimonpan Jinda, Jiratha Rachanakul, Thawinee Jantararoungtong, Rattanaporn Sukprasong, Santirhat Prommas, Nutthan Nuntharadthanaphong, Apichaya Puangpetch, Maliheh Ershadian, Shobana John, Mohitosh Biswas (+1 others)
2022 Frontiers in Pharmacology  
Incorporating PGx data, along with other clinical and non-clinical data, into clinical decision support systems (CDS) and national formularies, on the other hand, would assist prescribers in prioritizing  ...  There is a lot of evidence associating several risk alleles to life-threatening adverse drug reactions, and a few of them have been approved as valid biomarkers for predicting life-threatening hypersensitivity  ...  Hence, every ethnic/geographical community requires a PGx clinical decision support tool.  ... 
doi:10.3389/fphar.2022.866903 pmid:35450046 pmcid:PMC9016335 fatcat:ivvyq2ngbbdixogao5v2xafj7q

Creating Shareable Clinical Decision Support Rules for a Pharmacogenomics Clinical Guideline Using Structured Knowledge Representation

Margaret K Linan, Davide Sottara, Robert R Freimuth
2015 AMIA Annual Symposium Proceedings  
Pharmacogenomics (PGx) guidelines contain drug-gene relationships, therapeutic and clinical recommendations from which clinical decision support (CDS) rules can be extracted, rendered and then delivered  ...  through clinical decision support systems (CDSS) to provide clinicians with just-in-time information at the point of care.  ...  Acknowledgments The authors would like to thank Pooja Raghani for reviewing the modeling protocol.  ... 
pmid:26958298 pmcid:PMC4765632 fatcat:6ofsrkxll5fjvpibq3t3zkmvpe
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