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GenomicKB: a knowledge graph for the human genome

Genomic Knowledgebase (GenomicKB) is a graph database for researchers to explore and investigate human genome, epigenome, transcriptome, and 4D nucleome with simple and efficient queries. The database uses a knowledge graph to consolidate genomic datasets and annotations from over 30 consortia and p...

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Autores principales: Feng, Fan, Tang, Feitong, Gao, Yijia, Zhu, Dongyu, Li, Tianjun, Yang, Shuyuan, Yao, Yuan, Huang, Yuanhao, Liu, Jie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825430/
https://www.ncbi.nlm.nih.gov/pubmed/36318240
http://dx.doi.org/10.1093/nar/gkac957
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author Feng, Fan
Tang, Feitong
Gao, Yijia
Zhu, Dongyu
Li, Tianjun
Yang, Shuyuan
Yao, Yuan
Huang, Yuanhao
Liu, Jie
author_facet Feng, Fan
Tang, Feitong
Gao, Yijia
Zhu, Dongyu
Li, Tianjun
Yang, Shuyuan
Yao, Yuan
Huang, Yuanhao
Liu, Jie
author_sort Feng, Fan
collection PubMed
description Genomic Knowledgebase (GenomicKB) is a graph database for researchers to explore and investigate human genome, epigenome, transcriptome, and 4D nucleome with simple and efficient queries. The database uses a knowledge graph to consolidate genomic datasets and annotations from over 30 consortia and portals, including 347 million genomic entities, 1.36 billion relations, and 3.9 billion entity and relation properties. GenomicKB is equipped with a web-based query system (https://gkb.dcmb.med.umich.edu/) which allows users to query the knowledge graph with customized graph patterns and specific constraints on entities and relations. Compared with traditional tabular-structured data stored in separate data portals, GenomicKB emphasizes the relations among genomic entities, intuitively connects isolated data matrices, and supports efficient queries for scientific discoveries. GenomicKB transforms complicated analysis among multiple genomic entities and relations into coding-free queries, and facilitates data-driven genomic discoveries in the future.
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spelling pubmed-98254302023-01-10 GenomicKB: a knowledge graph for the human genome Feng, Fan Tang, Feitong Gao, Yijia Zhu, Dongyu Li, Tianjun Yang, Shuyuan Yao, Yuan Huang, Yuanhao Liu, Jie Nucleic Acids Res Database Issue Genomic Knowledgebase (GenomicKB) is a graph database for researchers to explore and investigate human genome, epigenome, transcriptome, and 4D nucleome with simple and efficient queries. The database uses a knowledge graph to consolidate genomic datasets and annotations from over 30 consortia and portals, including 347 million genomic entities, 1.36 billion relations, and 3.9 billion entity and relation properties. GenomicKB is equipped with a web-based query system (https://gkb.dcmb.med.umich.edu/) which allows users to query the knowledge graph with customized graph patterns and specific constraints on entities and relations. Compared with traditional tabular-structured data stored in separate data portals, GenomicKB emphasizes the relations among genomic entities, intuitively connects isolated data matrices, and supports efficient queries for scientific discoveries. GenomicKB transforms complicated analysis among multiple genomic entities and relations into coding-free queries, and facilitates data-driven genomic discoveries in the future. Oxford University Press 2022-11-01 /pmc/articles/PMC9825430/ /pubmed/36318240 http://dx.doi.org/10.1093/nar/gkac957 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Database Issue
Feng, Fan
Tang, Feitong
Gao, Yijia
Zhu, Dongyu
Li, Tianjun
Yang, Shuyuan
Yao, Yuan
Huang, Yuanhao
Liu, Jie
GenomicKB: a knowledge graph for the human genome
title GenomicKB: a knowledge graph for the human genome
title_full GenomicKB: a knowledge graph for the human genome
title_fullStr GenomicKB: a knowledge graph for the human genome
title_full_unstemmed GenomicKB: a knowledge graph for the human genome
title_short GenomicKB: a knowledge graph for the human genome
title_sort genomickb: a knowledge graph for the human genome
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825430/
https://www.ncbi.nlm.nih.gov/pubmed/36318240
http://dx.doi.org/10.1093/nar/gkac957
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