scholarly journals Design, Implementation and Maintenance of a Model Organism Database forArabidopsis thaliana

2004 ◽  
Vol 5 (4) ◽  
pp. 362-369 ◽  
Author(s):  
Danforth Weems ◽  
Neil Miller ◽  
Margarita Garcia-Hernandez ◽  
Eva Huala ◽  
Seung Y. Rhee
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Metabolic Pathways ◽  
Model Organism ◽  
Information Resource ◽  
Model Organism Database ◽  
Software Developers ◽  
Web Based ◽  
Model Plant ◽  
Community Information

TheArabidopsisInformation Resource (TAIR) is a web-based community database for the model plantArabidopsis thaliana. It provides an integrated view of genes, sequences, proteins, germplasms, clones, metabolic pathways, gene expression, ecotypes, polymorphisms, publications, maps and community information. TAIR is developed and maintained by collaboration between software developers and biologists. Biologists provide specification and use cases for the system, acquire, analyse and curate data, interact with users and test the software. Software developers design, implement and test the database and software. In this review, we briefly describe how TAIR was built and is being maintained.

scholarly journals The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching

2016 ◽  
Vol 45 (D1) ◽  
pp. D758-D768 ◽  
Author(s):  
Douglas G. Howe ◽  
Yvonne M. Bradford ◽  
Anne Eagle ◽  
David Fashena ◽  
Ken Frazer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Disease ◽  
Model Organism ◽  
Disease Models ◽  
Model Organism Database ◽  
Zebrafish Model

scholarly journals The EcoCyc Database in 2021

2021 ◽  
Vol 12 ◽  
Author(s):  
Ingrid M. Keseler ◽  
Socorro Gama-Castro ◽  
Amanda Mackie ◽  
Richard Billington ◽  
César Bonavides-Martínez ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Regulation Of Gene Expression ◽  
Model Organism ◽  
Web Interface ◽  
Model Organism Database ◽  
Manual Curation ◽  
Genome Viewer ◽  
User Access ◽  
Visualization Tools ◽  
K 12

The EcoCyc model-organism database collects and summarizes experimental data for Escherichia coli K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways, and by the programmatic addition of results from select high-throughput analyses. Updates to the Pathway Tools software that supports EcoCyc and to the web interface that enables user access have continuously improved its usability and expanded its functionality. This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression. New and revised data analysis and visualization tools include an interactive metabolic network explorer, a circular genome viewer, and various improvements to the speed and usability of existing tools.

scholarly journals ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates

2019 ◽  
Author(s):  
Justine Dardaillon ◽  
Delphine Dauga ◽  
Paul Simion ◽  
Emmanuel Faure ◽  
Takeshi A Onuma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Model Organism ◽  
Gene Expression Profiles ◽  
Sister Group ◽  
Model Organism Database ◽  
Oikopleura Dioica ◽  
Genetic Features ◽  
Taxonomic Range ◽  
Or Gene

Abstract ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.

scholarly journals Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database

2019 ◽  
Author(s):  
Joshua D Fortriede ◽  
Troy J Pells ◽  
Stanley Chu ◽  
Praneet Chaturvedi ◽  
DongZhuo Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Model Organism ◽  
Gene Expression Omnibus ◽  
The Body ◽  
Data Mapping ◽  
Model Organism Database ◽  
Ncbi Gene Expression Omnibus ◽  
Network Analyses ◽  
Deep Integration ◽  
Next Generation Sequencing Ngs

Abstract Xenbase (www.xenbase.org) is a knowledge base for researchers and biomedical scientists that employ the amphibian Xenopus as a model organism in biomedical research to gain a deeper understanding of developmental and disease processes. Through expert curation and automated data provisioning from various sources Xenbase strives to integrate the body of knowledge on Xenopus genomics and biology together with the visualization of biologically significant interactions. Most current studies utilize next generation sequencing (NGS) but until now the results of different experiments were difficult to compare and not integrated with other Xenbase content. Xenbase has developed a suite of tools, interfaces and data processing pipelines that transforms NCBI Gene Expression Omnibus (GEO) NGS content into deeply integrated gene expression and chromatin data, mapping all aligned reads to the most recent genome builds. This content can be queried and visualized via multiple tools and also provides the basis for future automated ‘gene expression as a phenotype’ and gene regulatory network analyses.

scholarly journals Photoperiod-dependent transcriptional modifications in key metabolic pathways in Coffea arabica

2020 ◽  
Author(s):  
Doâa Djerrab ◽  
Benoît Bertrand ◽  
Jean-Christophe Breitler ◽  
Sophie Léran ◽  
Eveline Dechamp ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Metabolic Pathways ◽  
Coffea Arabica ◽  
Clock Genes ◽  
Tropical Species ◽  
Perennial Species ◽  
Natural Photoperiod ◽  
Coffea Arabica L ◽  
Short Days

Abstract Photoperiod length induces in temperate plants major changes in growth rates, morphology and metabolism with, for example, modifications in the partitioning of photosynthates to avoid starvation at the end of long nights. However, this has never been studied for a tropical perennial species adapted to grow in a natural photoperiod close to 12 h/12 h all year long. We grew Coffea arabica L., an understorey perennial evergreen tropical species in its natural 12 h/12 h and in a short 8 h/16 h photoperiod, and we investigated its responses at the physiological, metabolic and transcriptomic levels. The expression pattern of rhythmic genes, including core clock genes, was affected by changes in photoperiod. Overall, we identified 2859 rhythmic genes, of which 89% were also rhythmic in Arabidopsis thaliana L. Under short-days, plant growth was reduced, and leaves were thinner with lower chlorophyll content. In addition, secondary metabolism was also affected with chlorogenic acid and epicatechin levels decreasing, and in agreement, the genes involved in lignin synthesis were overexpressed and those involved in the flavanol pathway were underexpressed. Our results show that the 8 h/16 h photoperiod induces drastic changes in morphology, metabolites and gene expression, and the responses for gene expression are similar to those observed in the temperate annual A. thaliana species. Short photoperiod induces drastic changes in gene expression, metabolites and leaf structure, some of these responses being similar to those observed in A. thaliana.

PedigreeNet: a web-based pedigree viewer for biological databases

2019 ◽  
Vol 35 (20) ◽  
pp. 4184-4186
Author(s):  
Bremen L Braun ◽  
David A Schott ◽  
John L Portwood ◽  
Carson M Andorf ◽  
Taner Z Sen
Keyword(s):  
Model Organism ◽  
Pedigree Analysis ◽  
Supplementary Information ◽  
Biological Databases ◽  
Model Organism Database ◽  
Web Based ◽  
Online Tool ◽  
Wide Range ◽  
Maize Genetics ◽  
Genetics And Genomics

Abstract Motivation Plant breeding aims to improve current germplasm that can tolerate a wide range of biotic and abiotic stresses. To accomplish this goal, breeders rely on developing a deeper understanding of genetic makeup and relationships between plant varieties to make informed plant selections. Although rapid advances in genotyping technology generated a large amount of data for breeders, tools that facilitate pedigree analysis and visualization are scant, leaving breeders to use classical, but inherently limited, hierarchical pedigree diagrams for a handful of plant varieties. To answer this need, we developed a simple web-based tool that can be easily implemented at biological databases, called PedigreeNet, to create and visualize customizable pedigree relationships in a network context, displaying pre- and user-uploaded data. Results As a proof-of-concept, we implemented PedigreeNet at the maize model organism database, MaizeGDB. The PedigreeNet viewer at MaizeGDB has a dynamically-generated pedigree network of 4706 maize lines and 5487 relationships that are currently available as both a stand-alone web-based tool and integrated directly on the MaizeGDB Stock Pages. The tool allows the user to apply a number of filters, select or upload their own breeding relationships, center a pedigree network on a plant variety, identify the common ancestor between two varieties, and display the shortest path(s) between two varieties on the pedigree network. The PedigreeNet code layer is written as a JavaScript wrapper around Cytoscape Web. PedigreeNet fills a great need for breeders to have access to an online tool to represent and visually customize pedigree relationships. Availability and implementation PedigreeNet is accessible at https://www.maizegdb.org/breeders_toolbox. The open source code is publically and freely available at GitHub: https://github.com/Maize-Genetics-and-Genomics-Database/PedigreeNet. Supplementary information Supplementary data are available at Bioinformatics online.

Western Faculty Profile: Dr. Susanne Kohalmi

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Anthony Wong
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Graduate Students ◽  
Molecular Genetics ◽  
Protein Interactions ◽  
Regulation Of Gene Expression ◽  
Model Organism ◽  
Associate Professor ◽  
Academic Affairs ◽  
Plant Model

Dr. Susanne Kohalmi is an Associate Professor in the Department of Biology at the Western University in London, Ontario. Her research is in molecular genetics, with focus on the regulation of gene expression and protein interactions. Currently her research is investigating the arogenate dehydratase enzyme family (ADTs) in the plant model organism Arabidopsis thaliana. In addition to research, she teaches undergraduate courses in genetics as well as supervising both undergraduate and graduate students. Anthony Wong, member of the Academic Affairs Committee at WURJHNS, interviewed Dr. Kohalmi to learn more about her research, her path to Western, and her advice to students.

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