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. 2021 Nov 27;14(1):433.
doi: 10.1186/s13104-021-05835-x.

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

Aaron Trautman  1   2 , Richard Linchangco  1   2 , Rachel Walstead  2 , Jeremy J Jay  1   2 , Cory Brouwer  3   4
Affiliations

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

Aaron Trautman et al. BMC Res Notes. .

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 [Formula: see text] plant product [Formula: see text] human gene [Formula: see text] pathways [Formula: see text] 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 ).

Keywords: Graph database; Knowledge discovery; Knowledgebase; Neo4j; Precision nutrition; Text mining.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
ABCkb pipeline overview. The architectural diagram of our Knowledgebase shows the various tools and resources utilized to generate the database
Fig. 2
Fig. 2
Browsing the ABCkb Interface. There are 4 primary steps to browsing using the provided interface. Once the query endpoint is selected and the user clicks submit, they have the option of downloading all results as a csv, or viewing the Cypher query
Fig. 3
Fig. 3
Visualizing the results of Avena sativa to diabetes and heart failure via Hydroxysteroid 11-Beta Dehydrogenase 1. This meta-path highlights the connectivity between oats, diabetes, and heart failure through the gene HSD11B1 from the ABCkb
See this image and copyright information in PMC

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