scholarly journals Gene2Function: An integrated online resource for gene function discovery

2017 ◽  
Author(s):  
Yanhui Hu ◽  
Aram Comjean ◽  
Stephanie E. Mohr ◽  
Norbert Perrimon ◽  
Julie Agapite ◽  
...  
Keyword(s):  
Gene Function ◽  
Model Organism ◽  
Functional Information ◽  
Biological Functions ◽  
Online Resource ◽  
Conserved Genes ◽  
Function Discovery ◽  
Model Organism Databases

AbstractOne of the most powerful ways to develop hypotheses regarding biological functions of conserved genes in a given species, such as in humans, is to first look at what is known about function in another species. Model organism databases (MODs) and other resources are rich with functional information but difficult to mine. Gene2Function (G2F) addresses a broad need by integrating information about conserved genes in a single online resource.

scholarly journals Gene2Function: An Integrated Online Resource for Gene Function Discovery

2017 ◽  
Vol 7 (8) ◽  
pp. 2855-2858 ◽  
Author(s):  
Yanhui Hu ◽  
Aram Comjean ◽  
Stephanie E. Mohr ◽  
Norbert Perrimon ◽  
Keyword(s):  
Gene Function ◽  
Online Resource ◽  
Function Discovery

scholarly journals Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature

Database ◽  
2021 ◽  
Vol 2021 ◽  
Author(s):  
Valerio Arnaboldi ◽  
Jaehyoung Cho ◽  
Paul W Sternberg
Keyword(s):  
Search Engines ◽  
Complex Structure ◽  
Model Organism ◽  
Gene Interaction ◽  
Relevant Information ◽  
Biomedical Literature ◽  
C Elegans ◽  
Word Clouds ◽  
Scientific Papers ◽  
Model Organism Databases

Abstract Finding relevant information from newly published scientific papers is becoming increasingly difficult due to the pace at which articles are published every year as well as the increasing amount of information per paper. Biocuration and model organism databases provide a map for researchers to navigate through the complex structure of the biomedical literature by distilling knowledge into curated and standardized information. In addition, scientific search engines such as PubMed and text-mining tools such as Textpresso allow researchers to easily search for specific biological aspects from newly published papers, facilitating knowledge transfer. However, digesting the information returned by these systems—often a large number of documents—still requires considerable effort. In this paper, we present Wormicloud, a new tool that summarizes scientific articles in a graphical way through word clouds. This tool is aimed at facilitating the discovery of new experimental results not yet curated by model organism databases and is designed for both researchers and biocurators. Wormicloud is customized for the Caenorhabditis  elegans literature and provides several advantages over existing solutions, including being able to perform full-text searches through Textpresso, which provides more accurate results than other existing literature search engines. Wormicloud is integrated through direct links from gene interaction pages in WormBase. Additionally, it allows analysis on the gene sets obtained from literature searches with other WormBase tools such as SimpleMine and Gene Set Enrichment. Database URL: https://wormicloud.textpressolab.com

scholarly journals Alliance of Genome Resources Portal: unified model organism research platform

2019 ◽  
Vol 48 (D1) ◽  
pp. D650-D658 ◽  
Author(s):  
◽  
Julie Agapite ◽  
Laurent-Philippe Albou ◽  
Suzi Aleksander ◽  
Joanna Argasinska ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Model Organism ◽  
Model Organisms ◽  
Data Types ◽  
Primary Model ◽  
Genomic Studies ◽  
Health And Disease ◽  
Extensive Body ◽  
Access To Data ◽  
Model Organism Databases

Abstract The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource.

scholarly journals An Evolutionarily Conserved Pathway Essential for Orsay Virus Infection of Caenorhabditis elegans

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Hongbing Jiang ◽  
Kevin Chen ◽  
Luis E. Sandoval ◽  
Christian Leung ◽  
David Wang
Keyword(s):  
Caenorhabditis Elegans ◽  
Virus Infection ◽  
Tyrosine Kinase ◽  
Model Organism ◽  
Wiskott Aldrich Syndrome ◽  
C Elegans ◽  
Evolutionarily Conserved ◽  
Conserved Genes ◽  
Orsay Virus ◽  
Syndrome Protein

ABSTRACT Many fundamental biological discoveries have been made in Caenorhabditis elegans. The discovery of Orsay virus has enabled studies of host-virus interactions in this model organism. To identify host factors critical for Orsay virus infection, we designed a forward genetic screen that utilizes a virally induced green fluorescent protein (GFP) reporter. Following chemical mutagenesis, two Viro (virus induced reporter off) mutants that failed to express GFP were mapped to sid-3, a nonreceptor tyrosine kinase, and B0280.13 (renamed viro-2), an ortholog of human Wiskott-Aldrich syndrome protein (WASP). Both mutants yielded Orsay virus RNA levels comparable to that of the residual input virus, suggesting that they are not permissive for Orsay virus replication. In addition, we demonstrated that both genes affect an early prereplication stage of Orsay virus infection. Furthermore, it is known that the human ortholog of SID-3, activated CDC42-associated kinase (ACK1/TNK2), is capable of phosphorylating human WASP, suggesting that VIRO-2 may be a substrate for SID-3 in C. elegans. A targeted RNA interference (RNAi) knockdown screen further identified the C. elegans gene nck-1, which has a human ortholog that interacts with TNK2 and WASP, as required for Orsay virus infection. Thus, genetic screening in C. elegans identified critical roles in virus infection for evolutionarily conserved genes in a known human pathway. IMPORTANCE Orsay virus is the only known virus capable of naturally infecting the model organism Caenorhabditis elegans, which shares many evolutionarily conserved genes with humans. We exploited the robust genetic tractability of C. elegans to identify three host genes, sid-3, viro-2, and nck-1, which are essential for Orsay virus infection. Mutant animals that lack these three genes are highly defective in viral replication. Strikingly, the human orthologs of these three genes, activated CDC42-associated kinase (TNK2), Wiskott-Aldrich syndrome protein (WASP), and noncatalytic region of tyrosine kinase adaptor protein 1 (NCK1) are part of a known signaling pathway in mammals. These results suggest that TNK2, WASP, and NCK1 may play important roles in mammalian virus infection. IMPORTANCE Orsay virus is the only known virus capable of naturally infecting the model organism Caenorhabditis elegans, which shares many evolutionarily conserved genes with humans. We exploited the robust genetic tractability of C. elegans to identify three host genes, sid-3, viro-2, and nck-1, which are essential for Orsay virus infection. Mutant animals that lack these three genes are highly defective in viral replication. Strikingly, the human orthologs of these three genes, activated CDC42-associated kinase (TNK2), Wiskott-Aldrich syndrome protein (WASP), and noncatalytic region of tyrosine kinase adaptor protein 1 (NCK1) are part of a known signaling pathway in mammals. These results suggest that TNK2, WASP, and NCK1 may play important roles in mammalian virus infection.

scholarly journals Model organism databases are in jeopardy

Development ◽  
2021 ◽  
Vol 148 (19) ◽  
Author(s):  
Hugo J. Bellen ◽  
E. J. A. Hubbard ◽  
Ruth Lehmann ◽  
Hiten D. Madhani ◽  
Lila Solnica-Krezel ◽  
...  
Keyword(s):  
Model Organism ◽  
Model Organism Databases

SoundSpace Online: The Development of an Online Resource About Hearing Loss

2015 ◽  
Vol 24 (3) ◽  
pp. 289-292 ◽  
Author(s):  
Zheng Yen Ng ◽  
Sue Archbold ◽  
Connie Mayer ◽  
Imran Mulla
Keyword(s):  
Hearing Loss ◽  
Education Research ◽  
Developmental State ◽  
The Internet ◽  
Functional Information ◽  
Target Groups ◽  
Online Resource ◽  
Wide Range ◽  
E Learning ◽  
Near Future

Purpose The Internet has been a growing source of health information on hearing loss, but the information provided often varies in quality, readability, and usability. Additionally, the information is provided across a wide range of domains, making access challenging to those who need it. This research forum article describes the development of a new website, SoundSpace Online (Ng, Archbold, Mayer, & Mulla, 2014), which aims to tackle these issues and bring together information and resources for all those concerned with hearing loss. Method The SoundSpace Online website's current developmental state was reached through the following methods: (a) discussions with a group of individuals that included experts in e-learning, education, research, and hearing loss; (b) interviews with different target groups (e.g., users, families, and professionals); and (c) collaboration with contributors. Result The website is structured to become a go-to resource on various topics related to hearing loss, providing accurate, comprehensive, and functional information and resources at varying levels of complexity for the intended users. Conclusion The literature and the range of interest have illustrated the need for an up-to-date website providing information and resources on hearing loss. Challenges include monitoring and keeping the website up to date; in this article, a plan of action is discussed. The website is currently in development, with plans for a launch in the near future.

Model Organism Databases in Behavioral Neuroscience

2012 ◽  
pp. 25-46
Author(s):  
Mary. Shimoyama ◽  
Jennifer R. Smith ◽  
G. Thomas. Hayman ◽  
Victoria. Petri ◽  
Rajni. Nigam
Keyword(s):  
Model Organism ◽  
Behavioral Neuroscience ◽  
Model Organism Databases
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