FlavorDB: a database of flavor molecules

Garg, Neelansh; Sethupathy, Apuroop; Tuwani, Rudraksh; Nk, Rakhi; Dokania, Shubham; Iyer, Arvind; Gupta, Ayushi; Agrawal, Shubhra; Singh, Navjot; Shukla, Shubham; Kathuria, Kriti; Badhwar, Rahul; Kanji, Rakesh; Jain, Anupam; Kaur, Avneet; Nagpal, Rashmi; Bagler, Ganesh

doi:10.1093/nar/gkx957

Cited by 126 publications

(95 citation statements)

References 22 publications

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“…We text mined spice-disease associations from abstracts available in MEDLINE, the largest database of biomedical literature containing more than 28 million references to research articles in biomedicine. First, a comprehensive dictionary of 188 species of culinary spices and herbs was manually compiled from various sources such as FooDB ( http://foodb.ca ), Wikipedia ( https://en.wikipedia.org/wiki/List_of_culinary_herbs_and_spices ), PFAF (Plants For A Future, http://www.pfaf.org/user/Default.aspx ), FPI (Food Plants International, http://foodplantsinternational.com ) and FlavorDB [ 18 ] ( http://cosylab.iiitd.edu.in/flavordb ). This dictionary was then used to retrieve relevant abstracts from MEDLINE database.…”

Section: Resultsmentioning

confidence: 99%

Data-driven analysis of biomedical literature suggests broad-spectrum benefits of culinary herbs and spices

et al. 2018

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Spices and herbs are key dietary ingredients used across cultures worldwide. Beyond their use as flavoring and coloring agents, the popularity of these aromatic plant products in culinary preparations has been attributed to their antimicrobial properties. Last few decades have witnessed an exponential growth of biomedical literature investigating the impact of spices and herbs on health, presenting an opportunity to mine for patterns from empirical evidence. Systematic investigation of empirical evidence to enumerate the health consequences of culinary herbs and spices can provide valuable insights into their therapeutic utility. We implemented a text mining protocol to assess the health impact of spices by assimilating, both, their positive and negative effects. We conclude that spices show broad-spectrum benevolence across a range of disease categories in contrast to negative effects that are comparatively narrow-spectrum. We also implement a strategy for disease-specific culinary recommendations of spices based on their therapeutic tradeoff against adverse effects. Further by integrating spice-phytochemical-disease associations, we identify bioactive spice phytochemicals potentially involved in their therapeutic effects. Our study provides a systems perspective on health effects of culinary spices and herbs with applications for dietary recommendations as well as identification of phytochemicals potentially involved in underlying molecular mechanisms.

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Section: Resultsmentioning

confidence: 99%

Data-driven analysis of biomedical literature suggests broad-spectrum benefits of culinary herbs and spices

et al. 2018

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“…The repertoire of culinary spices and herbs were collected from various sources including Foodb (Garg et al, 2017). All 188 spices were normalized to NCBI Taxonomy IDs using their scientific names.…”

Section: Methodsmentioning

confidence: 99%

SpiceRx: an integrated resource for the health impacts of culinary spices and herbs

Tuwani

Garg

et al. 2018

Preprint

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Spices and herbs are key dietary ingredients used in cuisines across the world. They have been reported to be of medicinal value for a wide variety of diseases through a large body of biomedical investigations. Bioactive phytochemicals in these plant products form the basis of their therapeutic potential as well as adverse effects. A systematic compilation of empirical data involving these aspects of culinary spices and herbs could help unravel molecular mechanisms underlying their effects on health.SpiceRx provides a platform for exploring the health impact of spices and herbs used in food preparations through a structured database of tripartite relationships with their phytochemicals and disease associations. Starting with an extensive dictionary of culinary spices and herbs, their disease associations were text mined from MEDLINE, the largest database of biomedical abstracts, assisted with manual curation. This information was further combined with spice-phytochemical and phytochemical-disease associations. SpiceRx is an integrated repertoire of evidence-based knowledge pertaining to the health impacts of culinary spices and herbs, and facilitates their disease-specific culinary recommendations as well as exploration of molecular mechanisms underlying their health effects. Availability and Implementation:SpiceRx is available at http://cosylab.iiitd.edu.in/spicerx and supports all modern browsers. SpiceRx is implemented with Python web development framework Django and relational database PostgreSQL; the front-end was built using HTML, CSS,

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“…D3 helped us to obtain a dynamic view of the data using HTML, SVG, and CSS. D3's emphasis on web standards provides the maximum capabilities of modern browsers without being tied to a proprietary framework, combining powerful visualization components and a data-driven approach for DOM manipulation (Garg et al, 2017). The complete draft genome profile has been plotted using Gbrowse at www.nicg.in and is reported as "The Under-utilized Crop Genomic Facility" by NIC, ICGEB.…”

Section: Distributionsmentioning

confidence: 99%

Rice Bean (Vigna umbellata) draft genome sequence: unravelling the late flowering and unpalatability related genomic resources for efficient domestication of this underutilized crop

Kaul

Eswaran

Thangaraj

et al. 2019

Preprint

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Rice bean is a less well known and underutilized legume crop that has proved to be highly favourable due to its rich nutritional value in comparison with other members of the Vigna family. As an initiative to compose rice bean (Vigna umbellata) genomic resource, the size of 414 mega-base pairs with an estimate of 31276 highly confidential genes from 15521 scaffolds and functional coverage of 96.08% was sequenced from 30X coverage data from Illumina and PacBio platform. Rice bean genome assembly was found to be exquisitely close to V. angularis (experimental control/outgroup), V. radiata and V. unguiculata, however, V. angularis being the closest. Heuristically, the assembled genome was further aligned with 31 leguminous plants (13 complete genomes and 18 partial genomes), by collinearity block mapping. Further, we predicted similar discriminant results by complete CDS alignment. In contrast, 17 medically influential genomes from NIGMS-NIH, when compared with rice bean assembly for LCB clusters led to identification of more than 18000 genes from the entire selected medicinal genomes. Empirical construction of all genome comparisons revealed symplesiomorphic character in turn uncovering the lineage of genetic and functional features of rice beans. Signifiacantly, we found deserving late-flowering genes, palatablyindexed uncommon genes that regulate various metabolite pathways, related to abiotic and biotic stress pathways and those that are specific to photoperiod and disease resistance and so on. Further, we developed a repository for underutilised crop genome facility using D3.js at www.nicg.in. Therefore, the findings from this report addresses the genomic value of rice bean to be escalated via breeding by allied and applied approaches.Research), IBPR (International Board for Plant Genetic Resources) and ICUC (International Centre for Underutilized Crops) organisations, form a network called FOSRIN (Food Security through Ricebean Research in India and Nepal), wherein Rice bean has been labeled as one of the future crops foreseen for domestication by farmers in marginal lands (Venkatesha 2012).Despite the nutritional excellence of rice bean, the prevailing lack of awareness of its complete nutritional benefits means that rice bean can be categorized as an underutilized crop. Rice bean can become established and grow in various soil types. It is pest resistant and presents tremendous potential as a nutritious fodder and high-quality grain. The major drawbacks of this pulse crop of the kharif season include late flowering, indeterminate nature and tastelessness. Furthermore, there are meagre possibilities for the improvement of rice bean due to its predominant landraces, nominal modern plant breeding and limited seed supply. Consequently, the high diversity retained within its limited geographical distribution and the existence of few marketing channels mean that there is a great scope for the genetic improvement of rice bean. Despite the importance of rice bean as a multipurpose legume utilized for culinary purpos...

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FlavorDB: a database of flavor molecules

Cited by 126 publications

References 22 publications

Data-driven analysis of biomedical literature suggests broad-spectrum benefits of culinary herbs and spices

Data-driven analysis of biomedical literature suggests broad-spectrum benefits of culinary herbs and spices

SpiceRx: an integrated resource for the health impacts of culinary spices and herbs

Rice Bean (Vigna umbellata) draft genome sequence: unravelling the late flowering and unpalatability related genomic resources for efficient domestication of this underutilized crop

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