Database Commons
Database Commons

a catalog of worldwide biological databases

Database Profile

KBase

General information

URL: http://kbase.us
Full name:
Description: The Department of Energy Systems Biology Knowledgebase (KBase) is a software and data platform designed to meet the grand challenge of systems biology: predicting and designing biological function. KBase integrates data and tools in a unified graphical interface so users do not need to access them from numerous sources or learn multiple systems in order to create and run sophisticated systems biology workflows. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics.
Year founded: 2015
Last update:
Version:
Accessibility:
Accessible
Country/Region: United States

Classification & Tag

Data type:
DNA
Data object:
Database category:
Major species:
Keywords:

Contact information

University/Institution: Cold Spring Harbor Laboratory
Address: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
City:
Province/State:
Country/Region: United States
Contact name (PI/Team): Christos Noutsos
Contact email (PI/Helpdesk): cnoutsos@cshl.edu

Publications

25933103
Metabolomic Profiling of the Nectars of Aquilegia pubescens and A. Canadensis. [PMID: 25933103]
Noutsos C, Perera AM, Nikolau BJ, Seaver SM, Ware DH.

To date, variation in nectar chemistry of flowering plants has not been studied in detail. Such variation exerts considerable influence on pollinator-plant interactions, as well as on flower traits that play important roles in the selection of a plant for visitation by specific pollinators. Over the past 60 years the Aquilegia genus has been used as a key model for speciation studies. In this study, we defined the metabolomic profiles of flower samples of two Aquilegia species, A. Canadensis and A. pubescens. We identified a total of 75 metabolites that were classified into six main categories: organic acids, fatty acids, amino acids, esters, sugars, and unknowns. The mean abundances of 25 of these metabolites were significantly different between the two species, providing insights into interspecies variation in floral chemistry. Using the PlantSEED biochemistry database, we found that the majority of these metabolites are involved in biosynthetic pathways. Finally, we explored the annotated genome of A. coerulea, using the PlantSEED pipeline and reconstructed the metabolic network of Aquilegia. This network, which contains the metabolic pathways involved in generating the observed chemical variation, is now publicly available from the DOE Systems Biology Knowledge Base (KBase; http://kbase.us).

PLoS One. 2015:10(5) | 16 Citations (from Europe PMC, 2025-12-20)

Ranking

All databases:
4507/6895 (34.648%)
Raw bio-data:
351/582 (39.863%)
4507
Total Rank
16
Citations
1.6
z-index

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Record metadata

Created on: 2018-01-29
Curated by:
Rabail Raza [2018-12-27]
Alia Rafique [2018-04-10]