| Echinobase | |
| Description: | Echinobase: The Echinoderm Knowledgebase. |
| Scope: | Literature, Nucleotide Sequence, RNA sequence, Protein sequence, Structure, Genomics, Morpholinos, Metabolic and Signaling Pathways, Human and other Vertebrate Genomes, Human Genes and Diseases, Microarray Data and other Gene Expression, Proteomics Resources, Other Molecular Biology, Organelle |
| Organism: | echinoderms |
| Center: | Carnegie Mellon University, University of Calgary |
| Laboratory: | Ettensohn lab, Hinman lab, Vize lab |
| Pmid: | 38262680 |
| Released: | 2009 |
| Url: | https://www.echinobase.org/ |
| Download: | https://download.echinobase.org/echinobase/ |
| Standalone: | BLAST, JBrowse |
| License: | Public domain |
| Frequency: | Continuous |
| Curation: | Professionally curated |
| Bookmark: | Yes |
| Version: | 6.x |
Echinobase is a Model Organism Database (MOD). It supports the international research community by providing a centralized, integrated web based resource to access the diverse and rich, functional genomics data of echinoderm evolution, development and gene regulatory networks. [1]
Genomic research data and tools are available for searching, browsing and bioinformatic analysis of genomes, genes, and transcripts.
Echinobase provides a critical data sharing infrastructure for other NIH-funded projects and enhances the availability and visibility of echinoderm data to the broader biomedical research community.
Echinobase offers two levels of integration for supported echinoderm species. Full support includes full genome integration in the database, including gene pages, as well as availability of the genomes to BLAST, browsing via JBrowse, and genome download. Partial support provides BLAST, JBrowse, and download options, but no gene page integration.
Current level one supported species (at various stages of integration) are:
Current level two supported species (at various stages of integration) are:
Echinobase runs in a cloud environment.[2] Its virtual machines are running in a VMware vSphere environment on two servers, with automatic load balancing and fault tolerance. Its software uses Java, JSP, JavaScript, AJAX, XML, and CSS. It also uses Apache Tomcat and the IBM Db2 database. Echinobase is developed in tandem with Xenbase.
Echinobase is a resource for genomics research that is organized by gene models and represented using gene pages. Each gene page has a tremendous amount of gene specific information.
Genomics - Search and BLAST tools are available directly or through the gene pages that display gene model HGNC compliant names, orthology,[3] 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.
The Echinoderm Anatomical Ontology (ECAO) uses standardized terms to refer to anatomical cell types and structures and relates these to developmental stages. Numerous echinoderm species are included in the ontology so that some terms are present in all echinoderms while others are species specific. The ECAO contains thousands of anatomical terms for cell types, structures and tissues and anatomical systems such as the nervous system or skeletal system. Relationships between entities are defined using "develops_from" or "develops_into" and "is_a" or "part_of".
Literature on Echinobase is collected by automatically searching published papers using echinoderm query terms and retrieved articles are then manually curated.
The data download site makes GFF genome files available and Gene Page Reports provide files for bioinformatic analyses.
In order to support the Community and to enable interdisciplinary and collaborative studies, research, descriptions and contact information of community members, labs and organizations are available and searchable. New Job Openings are also posted on Echinobase.