Resources, Community, Literature and Genomics

Here is a brief overview of Echinobase and terms used to refer to components.

At the Landing page you will find: 

• Carousel
• Side bar
• Content
• Announcements
• Statistics
• Videos
• Images
• Blocks
• Drop down menus

There are tutorials available about naming and downloadable files.

Resources, Community, Literature and Genomics content on Echinobase will be outlined here and is available in the video.

The new Echinobase is designed to take you to the information that you are searching for quickly and easily.

The search can be used directly from the landing page to search for: 

• Genes
• People
• Labs
• Organizations
• Paper Authors
• Paper Titles
• Echinobase Accession
• Clones
• Anatomy Items
• Disease Ontology
• OMIM Diseases
• GO terms
• GEO Data Sets

or use the drop-down menus take you to the specific searches related to:

• BLAST
• Genomes
• Genes
• Expression
• Anatomy & Development
• Resources
• Literature
• Community
• Downloads 

Resources

The Echinobase Resources serve to support the community by collecting data, protocols and other resources that are then shared using the EchinoWiki and FTP site.

EchinoWiki

• Protocols 
• Reagents

FTP Download 

• Genomes
• Gene Page Reports

Community

In order to support the Community and to enable interdisciplinary and collaborative studies, research, descriptions and contact information of community members and groups are available and searchable.

• Members
• Labs 
• Organizations
• Job openings 

Literature

Literature on Echinobase is collected by automatically searching published papers using echinoderm query terms.

Retrieved articles are then manually curated.

• Collected automatically
• Curated manually

Genomics

Echinobase is a resource for genomics research that is organized by Gene models and represented using Genepages. Each genepage has a tremendous amount of gene specific information that I will overview here. 

Genomics - Search and BLAST tools are available directly or through the GENEPAGES.

GENEPAGES display gene model HGNC compliant names, orthology, GO terms and link to BLAST, the JBrowse genome browser, and a gene expression plotting tool.

Tabs beyond the summary provide gene specific literature, transcripts, expression data, protein sequences and interactants.

Genomic research tools are implemented to assist browsing, search and analysis and visualization of genomic sequence assemblies, annotations and features.  Additionally, gene expression data collection, search and visualization is provided.

• GENEPAGE
• BLAST
• Genomes
• Genes
• Expression