FooDrugs database: A database with molecular and text information about food - drug interactions

FooDrugs database is a development done by the Computational Biology Group at IMDEA Food Institute (Madrid, Spain), in the context of the Food Nutrition Security Cloud (FNS-Cloud) project. Food Nutrition Security Cloud (FNS-Cloud) has received funding from the European Union's Horizon 2020 Research and Innovation programme (H2020-EU.3.2.2.3. – A sustainable and competitive agri-food industry) under Grant Agreement No. 863059 – www.fns-cloud.eu (See more details about FNS-Cloud below)

FooDrugs stores information extracted from transcriptomics and text documents for foo-drug interactiosn and it is part of a demonstrator to be done in the FNS-Cloud project. The database was built using MySQL, an open source relational database management system. FooDrugs_V2 host information for a total of 161 transcriptomics GEO series with 585 conditions for food or bioactive compounds (see below changes in versions V3 and V4). Each condition is defined as a food/biocomponent per time point, per concentration, per cell line, primary culture or biopsy per study. FooDrugs includes information about a bipartite network with 510 nodes and their similarity scores (tau score; https://clue.io/connectopedia/connectivity_scores) related with possible drug interactions with drugs assayed in conectivity map (https://www.broadinstitute.org/connectivity-map-cmap). The information is stored in eight tables: 

• Table “study” : This table contains basic information about study identifiers from GEO, pubmed or platform, study type,  title and abstract 

• Table “sample”: This table contains basic information about the different experiments in a study, like the identifier of the sample, treatment, origin type, time point or concentration.

• Table “misc_study”: This table contains additional information about different attributes of the study.

• Table “misc_sample”: This table contains additional information about different attributes of the sample.

• Table “cmap”: This table contains information about 70895 nodes, compromising drugs, foods or bioactives, overexpressed and knockdown genes (see section 3.4). The information includes cell line, compound and perturbation type.

• Table “cmap_foodrugs”: This table contains information about the tau score (see section 3.4) that relates food with drugs or genes and the node identifier in the FooDrugs network.

• Table “topTable”: This table contains information about 150 over and underexpressed genes from each GEO study condition, used to calculate the tau score (see section 3.4). The information stored is the logarithmic fold change, average expression, t-statistic, p-value, adjusted p-value and if the gene is up or downregulated.

• Table “nodes”: This table stores the information about the identification of the sample and the node in the bipartite network connecting the tables “sample”, “cmap_foodrugs” and “topTable”.

In addition, FooDrugs_V2 database stores a total of 6422 food/drug interactions from 2849 text documents, obtained from three different sources: 2312 documents from PubMed, 285 from DrugBank, and 252 from drugs.com. These documents describe potential interactions between 1464 food/bioactive compounds and 3009 drugs (see below changes in versions V3 and V4). The information is stored in two tables:

• Table “texts”: This table contains all the documents with its identifiers where interactions have been identified with strategy described in section 4. 

• Table “TM_interactions”: This table contains information about interaction identifiers, the food and drug entities, and the start and the end positions of the context for the interaction in the document.

FNS-Cloud will overcome fragmentation problems by integrating existing FNS data, which is essential for high-end, pan-European FNS research, addressing FNS, diet, health, and consumer behaviours as well as on sustainable agriculture and the bio-economy. Current fragmented FNS resources not only result in knowledge gaps that inhibit public health and agricultural policy, and the food industry from developing effective solutions, making production sustainable and consumption healthier, but also do not enable exploitation of FNS knowledge for the benefit of European citizens.
FNS-Cloud will, through three Demonstrators; Agri-Food, Nutrition & Lifestyle and NCDs & the Microbiome to facilitate:
(1) Analyses of regional and country-specific differences in diet including nutrition, (epi)genetics, microbiota, consumer behaviours, culture and lifestyle and their effects on health (obesity, NCDs, ethnic and traditional foods), which are essential for public health and agri-food and health policies;
(2) Improved understanding agricultural differences within Europe and what these means in terms of creating a sustainable, resilient food systems for healthy diets; and
(3) Clear definitions of boundaries and how these affect the compositions of foods and consumer choices and, ultimately, personal and public health in the future.
Long-term sustainability of the FNS-Cloud will be based on Services that have the capacity to link with new resources and enable cross-talk amongst them; access to FNS-Cloud data will be open access, underpinned by FAIR principles (findable, accessible, interoperable and re-useable). FNS-Cloud will work closely with the proposed Food, Nutrition and Health Research Infrastructure (FNHRI) as well as METROFOOD-RI and other existing ESFRI RIs (e.g. ELIXIR, ECRIN) in which several FNS-Cloud Beneficiaries are involved directly. (https://cordis.europa.eu/project/id/863059)

***** changes between version FooDrugs_v2 and FooDrugs_V3 (31st January 2023) are:

• Increased the amount of text documents by 85.675 from PubMed and ClinicalTrials.gov, and the amount of Text Mining interactions by 168.826.

• Increased the amount of transcriptomic studies by 32 GEO series.

• Removed all rows in table cmap_foodrugs representing interactions with values of  tau=0

• Removed 43 GEO series that after manually checking didn't correspond to food compounds.

• Added a new column to the table texts: citation  to hold the citation of the text. 

• Added these columns to the table study: contributor to contain the authors of the study, publication_date to store the date of publication of the study in GEO and pubmed_id to reference the publication associated with the study if any.

• Added a new column to topTable to hold the top 150 up-regulated and 150 down-regulated genes

***** changes between version FooDrugs_v3 and FooDrugs_V4 (28th July 2023) are:

• Increased the amount of text documents by 439.338 from PubMed, ClinicalTrials.gov and DDI corpus (Herrero-Zazo et al.), and the amount of Text Mining interactions by 1108429.