bibliography.bib

@article{scott_personalizing_2011,
	title = {Personalizing medicine with clinical pharmacogenetics},
	volume = {13},
	issn = {10983600},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1098360021036121},
	doi = {10.1097/GIM.0b013e318238b38c},
	abstract = {Clinical genetic testing has grown substantially over the past 30 years as the causative mutations for Mendelian diseases have been identified, particularly aided in part by the recent advances in molecular-based technologies. Importantly, the adoption of new tests and testing strategies (e.g., diagnostic confirmation, prenatal testing, and population-based carrier screening) has often been met with caution and careful consideration before clinical implementation, which facilitates the appropriate use of new genetic tests. Although the field of pharmacogenetics was established in the 1950s, clinical testing for constitutional pharmacogenetic variants implicated in interindividual drug response variability has only recently become available to help clinicians guide pharmacotherapy, in part due to {US} Food and Drug Administration-mediated product insert revisions that include pharmacogenetic information for selected drugs. However, despite pharmacogenetic associations with adverse outcomes, physician uptake of clinical pharmacogenetic testing has been slow. Compared with testing for Mendelian diseases, pharmacogenetic testing for certain indications can have a lower positive predictive value, which is one reason for underutilization. A number of other barriers remain with implementing clinical pharmacogenetics, including clinical utility, professional education, and regulatory and reimbursement issues, among others. This review presents some of the current opportunities and challenges with implementing clinical pharmacogenetic testing. Genet Med 2011:13(12):987–995.},
	pages = {987--995},
	number = {12},
	journaltitle = {Genetics in Medicine},
	author = {Scott, Stuart A},
	urldate = {2022-07-10},
	date = {2011-12},
	langid = {english},
	file = {Scott - 2011 - Personalizing medicine with clinical pharmacogenet.pdf:/Users/jannisbaum/Zotero/storage/CA5X62GY/Scott - 2011 - Personalizing medicine with clinical pharmacogenet.pdf:application/pdf},
}

@article{wishart_drugbank_2018,
	title = {{DrugBank} 5.0: a major update to the {DrugBank} database for 2018},
	volume = {46},
	issn = {0305-1048, 1362-4962},
	url = {http://academic.oup.com/nar/article/46/D1/D1074/4602867},
	doi = {10.1093/nar/gkx1037},
	shorttitle = {{DrugBank} 5.0},
	pages = {D1074--D1082},
	issue = {D1},
	journaltitle = {Nucleic Acids Research},
	author = {Wishart, David S and Feunang, Yannick D and Guo, An C and Lo, Elvis J and Marcu, Ana and Grant, Jason R and Sajed, Tanvir and Johnson, Daniel and Li, Carin and Sayeeda, Zinat and Assempour, Nazanin and Iynkkaran, Ithayavani and Liu, Yifeng and Maciejewski, Adam and Gale, Nicola and Wilson, Alex and Chin, Lucy and Cummings, Ryan and Le, Diana and Pon, Allison and Knox, Craig and Wilson, Michael},
	urldate = {2022-07-10},
	date = {2018-01-04},
	langid = {english},
	file = {Wishart et al. - 2018 - DrugBank 5.0 a major update to the DrugBank datab.pdf:/Users/jannisbaum/Zotero/storage/PCYG6TVG/Wishart et al. - 2018 - DrugBank 5.0 a major update to the DrugBank datab.pdf:application/pdf},
}

@article{liu_rxnorm_2005,
	title = {{RxNorm}: prescription for electronic drug information exchange},
	volume = {7},
	issn = {1520-9202},
	url = {http://ieeexplore.ieee.org/document/1516084/},
	doi = {10.1109/MITP.2005.122},
	shorttitle = {{RxNorm}},
	pages = {17--23},
	number = {5},
	journaltitle = {{IT} Prof.},
	author = {Liu, S. and {Wei Ma} and Moore, R. and Ganesan, V. and Nelson, S.},
	urldate = {2022-07-10},
	date = {2005-09},
	langid = {english},
	file = {Liu et al. - 2005 - RxNorm prescription for electronic drug informati.pdf:/Users/jannisbaum/Zotero/storage/ALMWIZW2/Liu et al. - 2005 - RxNorm prescription for electronic drug informati.pdf:application/pdf},
}

@article{relling_cpic_2011,
	title = {{CPIC}: Clinical Pharmacogenetics Implementation Consortium of the Pharmacogenomics Research Network},
	volume = {89},
	issn = {0009-9236, 1532-6535},
	url = {http://doi.wiley.com/10.1038/clpt.2010.279},
	doi = {10.1038/clpt.2010.279},
	shorttitle = {{CPIC}},
	pages = {464--467},
	number = {3},
	journaltitle = {Clin Pharmacol Ther},
	author = {Relling, M V and Klein, T E},
	urldate = {2022-07-10},
	date = {2011-03},
	langid = {english},
	file = {Relling and Klein - 2011 - CPIC Clinical Pharmacogenetics Implementation Con.pdf:/Users/jannisbaum/Zotero/storage/EB8MJ7NF/Relling and Klein - 2011 - CPIC Clinical Pharmacogenetics Implementation Con.pdf:application/pdf},
}

@online{the_postgresql_global_development_group_postgresql_2022,
	title = {{PostgreSQL} Homepage},
	url = {https://www.postgresql.org/},
	abstract = {The world's most advanced open source database.},
	author = {{The PostgreSQL Global Development Group}},
	urldate = {2022-07-11},
	date = {2022-07-11},
	langid = {english},
	file = {Snapshot:/Users/jannisbaum/Zotero/storage/IQAFIXRL/www.postgresql.org.html:text/html},
}

@article{lee_clinical_2022,
	title = {Clinical Pharmacogenetics Implementation Consortium Guideline for \textit{{CYP}2C19} Genotype and Clopidogrel Therapy: 2022 Update},
	issn = {0009-9236, 1532-6535},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/cpt.2526},
	doi = {10.1002/cpt.2526},
	shorttitle = {Clinical Pharmacogenetics Implementation Consortium Guideline for \textit{{CYP}2C19} Genotype and Clopidogrel Therapy},
	pages = {cpt.2526},
	journaltitle = {Clin Pharma and Therapeutics},
	author = {Lee, Craig R. and Luzum, Jasmine A. and Sangkuhl, Katrin and Gammal, Roseann S. and Sabatine, Marc S. and Stein, Charles Michael and Kisor, David F. and Limdi, Nita A. and Lee, Yee Ming and Scott, Stuart A. and Hulot, Jean‐Sébastien and Roden, Dan M. and Gaedigk, Andrea and Caudle, Kelly E. and Klein, Teri E. and Johnson, Julie A. and Shuldiner, Alan R.},
	urldate = {2022-07-12},
	date = {2022-02-08},
	langid = {english},
	file = {Lee et al. - 2022 - Clinical Pharmacogenetics Implementation Consortiu.pdf:/Users/jannisbaum/Zotero/storage/7PHATQL8/Lee et al. - 2022 - Clinical Pharmacogenetics Implementation Consortiu.pdf:application/pdf},
}

@report{nottingham_http_2010,
	title = {{HTTP} Cache-Control Extensions for Stale Content},
	url = {https://datatracker.ietf.org/doc/rfc5861},
	abstract = {This document defines two independent {HTTP} Cache-Control extensions that allow control over the use of stale responses by caches. This document is not an Internet Standards Track specification; it is published for informational purposes.},
	number = {{RFC} 5861},
	institution = {Internet Engineering Task Force},
	type = {Request for Comments},
	author = {Nottingham, Mark},
	urldate = {2022-07-13},
	date = {2010-05},
	doi = {10.17487/RFC5861},
	note = {Num Pages: 6},
	file = {Full Text PDF:/Users/jannisbaum/Zotero/storage/KW99GG4V/Nottingham - 2010 - HTTP Cache-Control Extensions for Stale Content.pdf:application/pdf},
}

@article{legrand_pgxcorpus_2020,
	title = {{PGxCorpus}, a manually annotated corpus for pharmacogenomics},
	volume = {7},
	issn = {2052-4463},
	url = {http://www.nature.com/articles/s41597-019-0342-9},
	doi = {10.1038/s41597-019-0342-9},
	abstract = {Abstract
            Pharmacogenomics ({PGx}) studies how individual gene variations impact drug response phenotypes, which makes {PGx}-related knowledge a key component towards precision medicine. A significant part of the state-of-the-art knowledge in {PGx} is accumulated in scientific publications, where it is hardly reusable by humans or software. Natural language processing techniques have been developed to guide experts who curate this amount of knowledge. But existing works are limited by the absence of a high quality annotated corpus focusing on {PGx} domain. In particular, this absence restricts the use of supervised machine learning. This article introduces {PGxCorpus}, a manually annotated corpus, designed to fill this gap and to enable the automatic extraction of {PGx} relationships from text. It comprises 945 sentences from 911 {PubMed} abstracts, annotated with {PGx} entities of interest (mainly gene variations, genes, drugs and phenotypes), and relationships between those. In this article, we present the corpus itself, its construction and a baseline experiment that illustrates how it may be leveraged to synthesize and summarize {PGx} knowledge.},
	pages = {3},
	number = {1},
	journaltitle = {Sci Data},
	author = {Legrand, Joël and Gogdemir, Romain and Bousquet, Cédric and Dalleau, Kevin and Devignes, Marie-Dominique and Digan, William and Lee, Chia-Ju and Ndiaye, Ndeye-Coumba and Petitpain, Nadine and Ringot, Patrice and Smaïl-Tabbone, Malika and Toussaint, Yannick and Coulet, Adrien},
	urldate = {2022-07-16},
	date = {2020-12},
	langid = {english},
	file = {Legrand et al. - 2020 - PGxCorpus, a manually annotated corpus for pharmac.pdf:/Users/jannisbaum/Zotero/storage/QEVBTPHB/Legrand et al. - 2020 - PGxCorpus, a manually annotated corpus for pharmac.pdf:application/pdf},
}

@online{pharmgkb_university_dpwg_nodate,
	title = {{DPWG}: Dutch Pharmacogenetics Working Group},
	url = {https://www.pharmgkb.org/page/dpwg},
	shorttitle = {{DPWG}},
	author = {{PharmGKB} University},
	urldate = {2022-07-16},
	langid = {english},
	file = {Snapshot:/Users/jannisbaum/Zotero/storage/T76MC4BM/dpwg.html:text/html},
}

@online{kamil_mysliwiec_nestjs_nodate,
	title = {{NestJS} Documentation},
	url = {https://docs.nestjs.com},
	abstract = {Nest is a framework for building efficient, scalable Node.js server-side applications. It uses progressive {JavaScript}, is built with {TypeScript} and combines elements of {OOP} (Object Oriented Progamming), {FP} (Functional Programming), and {FRP} (Functional Reactive Programming).},
	author = {{Kamil Mysliwiec}},
	urldate = {2022-07-20},
	langid = {english},
	file = {Snapshot:/Users/jannisbaum/Zotero/storage/M44RFHIE/docs.nestjs.com.html:text/html},
}

@online{typeorm_typeorm_nodate,
	title = {{TypeORM} Documentation},
	url = {https://typeorm.io/},
	author = {{TypeORM}},
	urldate = {2022-07-20},
	file = {TypeORM - Amazing ORM for TypeScript and JavaScript (ES7, ES6, ES5). Supports MySQL, PostgreSQL, MariaDB, SQLite, MS SQL Server, Oracle, WebSQL databases. Works in NodeJS, Browser, Ionic, Cordova and Electron platforms.:/Users/jannisbaum/Zotero/storage/4JSQMLJ4/typeorm.io.html:text/html},
}

@online{vercel_inc_nextjs_nodate,
	title = {Next.js Homepage},
	url = {https://nextjs.org},
	abstract = {Production grade React applications that scale. The world’s leading companies use Next.js by Vercel to build static and dynamic websites and web applications.},
	author = {{Vercel, Inc}},
	urldate = {2022-07-21},
	langid = {english},
	file = {Snapshot:/Users/jannisbaum/Zotero/storage/MWVYEKBZ/nextjs.org.html:text/html},
}

@online{meta_platforms_inc_react_nodate,
	title = {React Homepage},
	url = {https://reactjs.org/},
	abstract = {A {JavaScript} library for building user interfaces},
	author = {{Meta Platforms, Inc}},
	urldate = {2022-07-21},
	langid = {english},
	file = {Snapshot:/Users/jannisbaum/Zotero/storage/THVSJGGV/reactjs.org.html:text/html},
}

@online{mongodb_inc_mongodb_nodate,
	title = {{MongoDB} Homepage},
	url = {https://www.mongodb.com},
	shorttitle = {{MongoDB}},
	abstract = {Get your ideas to market faster with a developer data platform built on the leading modern database. {MongoDB} makes working with data easy.},
	author = {{MongoDB, Inc}},
	urldate = {2022-07-21},
	langid = {english},
	file = {Snapshot:/Users/jannisbaum/Zotero/storage/MT3VI4UG/www.mongodb.com.html:text/html},
}

@online{automattic_inc_mongoose_nodate,
	title = {Mongoose Homepage},
	url = {https://mongoosejs.com/},
	author = {Automattic, Inc},
	urldate = {2022-07-21},
	file = {Mongoose ODM v6.4.6:/Users/jannisbaum/Zotero/storage/QARGAKSY/mongoosejs.com.html:text/html},
}

@online{epic_systems_corporation_epic_nodate,
	title = {Epic Homepage},
	url = {https://www.epic.com/about},
	author = {{Epic Systems Corporation}},
	urldate = {2022-07-21},
	file = {About Us | Epic:/Users/jannisbaum/Zotero/storage/FTC8ME2U/about.html:text/html},
}