otargen: GraphQL-based R package for tidy data accessing and processing from Open Targets Genetics
Abstract Motivation Open Target Genetics is a comprehensive resource portal that offers variant-centric statistical evidence, enabling the prioritization of causal variants and the identification of potential drug targets. The portal uses GraphQL technology for efficient data query and provides endp...
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| Vydáno v: | Bioinformatics (Oxford, England) Ročník 39; číslo 8 |
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| Hlavní autoři: | , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
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England
Oxford University Press
01.08.2023
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| ISSN: | 1367-4811, 1367-4803, 1367-4811 |
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| Abstract | Abstract
Motivation
Open Target Genetics is a comprehensive resource portal that offers variant-centric statistical evidence, enabling the prioritization of causal variants and the identification of potential drug targets. The portal uses GraphQL technology for efficient data query and provides endpoints for programmatic access for R and Python users. However, leveraging GraphQL for data retrieval can be challenging, time-consuming, and repetitive, requiring familiarity with the GraphQL query language and processing outputs in nested JSON (JavaScript Object Notation) format into tidy data tables. Therefore, developing open-source tools are required to simplify data retrieval processes to integrate valuable genetic information into data-driven target discovery pipelines seamlessly.
Results
otargen is an open-source R package designed to make data retrieval and analysis from the Open Target Genetics portal as simple as possible for R users. The package offers a suite of functions covering all query types, allowing streamlined data access in a tidy table format. By executing only a single line of code, the otargen users avoid the repetitive scripting of complex GraphQL queries, including the post-processing steps. In addition, otargen contains convenient plotting functions to visualize and gain insights from complex data tables returned by several key functions.
Availability and implementation
otargen is available at https://amirfeizi.github.io/otargen/. |
|---|---|
| AbstractList | Abstract
Motivation
Open Target Genetics is a comprehensive resource portal that offers variant-centric statistical evidence, enabling the prioritization of causal variants and the identification of potential drug targets. The portal uses GraphQL technology for efficient data query and provides endpoints for programmatic access for R and Python users. However, leveraging GraphQL for data retrieval can be challenging, time-consuming, and repetitive, requiring familiarity with the GraphQL query language and processing outputs in nested JSON (JavaScript Object Notation) format into tidy data tables. Therefore, developing open-source tools are required to simplify data retrieval processes to integrate valuable genetic information into data-driven target discovery pipelines seamlessly.
Results
otargen is an open-source R package designed to make data retrieval and analysis from the Open Target Genetics portal as simple as possible for R users. The package offers a suite of functions covering all query types, allowing streamlined data access in a tidy table format. By executing only a single line of code, the otargen users avoid the repetitive scripting of complex GraphQL queries, including the post-processing steps. In addition, otargen contains convenient plotting functions to visualize and gain insights from complex data tables returned by several key functions.
Availability and implementation
otargen is available at https://amirfeizi.github.io/otargen/. Open Target Genetics is a comprehensive resource portal that offers variant-centric statistical evidence, enabling the prioritization of causal variants and the identification of potential drug targets. The portal uses GraphQL technology for efficient data query and provides endpoints for programmatic access for R and Python users. However, leveraging GraphQL for data retrieval can be challenging, time-consuming, and repetitive, requiring familiarity with the GraphQL query language and processing outputs in nested JSON (JavaScript Object Notation) format into tidy data tables. Therefore, developing open-source tools are required to simplify data retrieval processes to integrate valuable genetic information into data-driven target discovery pipelines seamlessly.MOTIVATIONOpen Target Genetics is a comprehensive resource portal that offers variant-centric statistical evidence, enabling the prioritization of causal variants and the identification of potential drug targets. The portal uses GraphQL technology for efficient data query and provides endpoints for programmatic access for R and Python users. However, leveraging GraphQL for data retrieval can be challenging, time-consuming, and repetitive, requiring familiarity with the GraphQL query language and processing outputs in nested JSON (JavaScript Object Notation) format into tidy data tables. Therefore, developing open-source tools are required to simplify data retrieval processes to integrate valuable genetic information into data-driven target discovery pipelines seamlessly.otargen is an open-source R package designed to make data retrieval and analysis from the Open Target Genetics portal as simple as possible for R users. The package offers a suite of functions covering all query types, allowing streamlined data access in a tidy table format. By executing only a single line of code, the otargen users avoid the repetitive scripting of complex GraphQL queries, including the post-processing steps. In addition, otargen contains convenient plotting functions to visualize and gain insights from complex data tables returned by several key functions.RESULTSotargen is an open-source R package designed to make data retrieval and analysis from the Open Target Genetics portal as simple as possible for R users. The package offers a suite of functions covering all query types, allowing streamlined data access in a tidy table format. By executing only a single line of code, the otargen users avoid the repetitive scripting of complex GraphQL queries, including the post-processing steps. In addition, otargen contains convenient plotting functions to visualize and gain insights from complex data tables returned by several key functions.otargen is available at https://amirfeizi.github.io/otargen/.AVAILABILITY AND IMPLEMENTATIONotargen is available at https://amirfeizi.github.io/otargen/. Open Target Genetics is a comprehensive resource portal that offers variant-centric statistical evidence, enabling the prioritization of causal variants and the identification of potential drug targets. The portal uses GraphQL technology for efficient data query and provides endpoints for programmatic access for R and Python users. However, leveraging GraphQL for data retrieval can be challenging, time-consuming, and repetitive, requiring familiarity with the GraphQL query language and processing outputs in nested JSON (JavaScript Object Notation) format into tidy data tables. Therefore, developing open-source tools are required to simplify data retrieval processes to integrate valuable genetic information into data-driven target discovery pipelines seamlessly. otargen is an open-source R package designed to make data retrieval and analysis from the Open Target Genetics portal as simple as possible for R users. The package offers a suite of functions covering all query types, allowing streamlined data access in a tidy table format. By executing only a single line of code, the otargen users avoid the repetitive scripting of complex GraphQL queries, including the post-processing steps. In addition, otargen contains convenient plotting functions to visualize and gain insights from complex data tables returned by several key functions. otargen is available at https://amirfeizi.github.io/otargen/. |
| Author | Ray, Kamalika Feizi, Amir |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/37467069$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1093/nar/gkaa840 10.1038/ng.3314 10.1016/j.gde.2013.10.003 10.1038/s41586-022-05473-8 10.1093/nar/gkac1046 10.1038/s41588-021-00945-5 10.1016/j.jacbts.2019.02.005 |
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| References_xml | – volume: 49 start-page: D1311 year: 2021 ident: 2023080203202826800_btad441-B2 article-title: Open targets genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics publication-title: Nucleic Acids Res doi: 10.1093/nar/gkaa840 – volume: 47 start-page: 856 year: 2015 ident: 2023080203202826800_btad441-B5 article-title: The support of human genetic evidence for approved drug indications publication-title: Nat Genet doi: 10.1038/ng.3314 – volume: 23 start-page: 611 year: 2013 ident: 2023080203202826800_btad441-B1 article-title: Genotype to phenotype via network analysis publication-title: Curr Opin Genet Dev doi: 10.1016/j.gde.2013.10.003 – volume: 613 start-page: 508 year: 2023 ident: 2023080203202826800_btad441-B3 article-title: FinnGen provides genetic insights from a well-phenotyped isolated population publication-title: Nature doi: 10.1038/s41586-022-05473-8 – volume: 51 start-page: D1353 year: 2022 ident: 2023080203202826800_btad441-B6 article-title: The next-generation open targets platform: reimagined, redesigned, rebuilt publication-title: Nucleic Acids Res doi: 10.1093/nar/gkac1046 – volume: 53 start-page: 1527 year: 2021 ident: 2023080203202826800_btad441-B4 article-title: An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci publication-title: Nat Genet doi: 10.1038/s41588-021-00945-5 – volume: 4 start-page: 428 year: 2019 ident: 2023080203202826800_btad441-B7 article-title: Phase II trials in drug development and adaptive trial design publication-title: JACC Basic Transl Sci doi: 10.1016/j.jacbts.2019.02.005 |
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Motivation
Open Target Genetics is a comprehensive resource portal that offers variant-centric statistical evidence, enabling the prioritization of... Open Target Genetics is a comprehensive resource portal that offers variant-centric statistical evidence, enabling the prioritization of causal variants and... |
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| Title | otargen: GraphQL-based R package for tidy data accessing and processing from Open Targets Genetics |
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