The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health

Abstract Objective Overconsumption of processed foods has led to an increase in chronic diet-related diseases such obesity and type 2 diabetes. Although diets high in fresh fruits and vegetables are linked with healthier outcomes, the specific mechanisms for these relationships are poorly understood...

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Autores principales:	Aaron Trautman, Richard Linchangco, Rachel Walstead, Jeremy J. Jay, Cory Brouwer
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Knowledgebase Precision nutrition Graph database Neo4j Text mining Knowledge discovery Medicine R Biology (General) QH301-705.5 Science (General) Q1-390
Acceso en línea:	https://doaj.org/article/109a9c221ca34845924181ac25a20573
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spelling	oai:doaj.org-article:109a9c221ca34845924181ac25a205732021-11-28T12:25:12ZThe Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health10.1186/s13104-021-05835-x1756-0500https://doaj.org/article/109a9c221ca34845924181ac25a205732021-11-01T00:00:00Zhttps://doi.org/10.1186/s13104-021-05835-xhttps://doaj.org/toc/1756-0500Abstract Objective Overconsumption of processed foods has led to an increase in chronic diet-related diseases such obesity and type 2 diabetes. Although diets high in fresh fruits and vegetables are linked with healthier outcomes, the specific mechanisms for these relationships are poorly understood. Experiments examining plant phytochemical production and breeding programs, or separately on the health effects of nutritional supplements have yielded results that are sparse, siloed, and difficult to integrate between the domains of human health and agriculture. To connect plant products to health outcomes through their molecular mechanism an integrated computational resource is necessary. Results We created the Aliment to Bodily Condition Knowledgebase (ABCkb) to connect plants to human health by creating a stepwise path from plant $$\rightarrow$$ → plant product $$\rightarrow$$ → human gene $$\rightarrow$$ → pathways $$\rightarrow$$ → indication. ABCkb integrates 11 curated sources as well as relationships mined from Medline abstracts by loading into a graph database which is deployed via a Docker container. This new resource, provided in a queryable container with a user-friendly interface connects plant products with human health outcomes for generating nutritive hypotheses. All scripts used are available on github ( https://github.com/atrautm1/ABCkb ) along with basic directions for building the knowledgebase and a browsable interface is available ( https://abckb.charlotte.edu ).Aaron TrautmanRichard LinchangcoRachel WalsteadJeremy J. JayCory BrouwerBMCarticleKnowledgebasePrecision nutritionGraph databaseNeo4jText miningKnowledge discoveryMedicineRBiology (General)QH301-705.5Science (General)Q1-390ENBMC Research Notes, Vol 14, Iss 1, Pp 1-7 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Knowledgebase Precision nutrition Graph database Neo4j Text mining Knowledge discovery Medicine R Biology (General) QH301-705.5 Science (General) Q1-390
spellingShingle	Knowledgebase Precision nutrition Graph database Neo4j Text mining Knowledge discovery Medicine R Biology (General) QH301-705.5 Science (General) Q1-390 Aaron Trautman Richard Linchangco Rachel Walstead Jeremy J. Jay Cory Brouwer The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health
description	Abstract Objective Overconsumption of processed foods has led to an increase in chronic diet-related diseases such obesity and type 2 diabetes. Although diets high in fresh fruits and vegetables are linked with healthier outcomes, the specific mechanisms for these relationships are poorly understood. Experiments examining plant phytochemical production and breeding programs, or separately on the health effects of nutritional supplements have yielded results that are sparse, siloed, and difficult to integrate between the domains of human health and agriculture. To connect plant products to health outcomes through their molecular mechanism an integrated computational resource is necessary. Results We created the Aliment to Bodily Condition Knowledgebase (ABCkb) to connect plants to human health by creating a stepwise path from plant $$\rightarrow$$ → plant product $$\rightarrow$$ → human gene $$\rightarrow$$ → pathways $$\rightarrow$$ → indication. ABCkb integrates 11 curated sources as well as relationships mined from Medline abstracts by loading into a graph database which is deployed via a Docker container. This new resource, provided in a queryable container with a user-friendly interface connects plant products with human health outcomes for generating nutritive hypotheses. All scripts used are available on github ( https://github.com/atrautm1/ABCkb ) along with basic directions for building the knowledgebase and a browsable interface is available ( https://abckb.charlotte.edu ).
format	article
author	Aaron Trautman Richard Linchangco Rachel Walstead Jeremy J. Jay Cory Brouwer
author_facet	Aaron Trautman Richard Linchangco Rachel Walstead Jeremy J. Jay Cory Brouwer
author_sort	Aaron Trautman
title	The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health
title_short	The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health
title_full	The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health
title_fullStr	The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health
title_full_unstemmed	The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health
title_sort	aliment to bodily condition knowledgebase (abckb): a database connecting plants and human health
publisher	BMC
publishDate	2021
url	https://doaj.org/article/109a9c221ca34845924181ac25a20573
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The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health

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