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== Supported Species ==
== Supported species ==
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.
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.


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* [[Asterias rubens]] (Sugar star)
* [[Asterias rubens]] (Sugar star)


== Software, Hardware and Platform ==
== Software, hardware and platform ==
Echinobase runs in a cloud environment.<ref name="kv2014">K. Karimi and P.D. Vize (2014). [https://academic.oup.com/database/article-lookup/doi/10.1093/database/bau108 The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud], Database, doi: 10.1093/database/bau108</ref> Its virtual machines are running in a [[VMware]] [[vSphere]] environment on two servers, with automatic [[load balancing (computing)|load balancing]] and [[fault tolerance]]. Its software uses [[Java (programming language)|Java]], [[JavaServer Pages|JSP]], [[JavaScript]], [[AJAX]], [[XML]], and [[CSS]]. It also uses [[Apache Tomcat]] and the [[IBM Db2]] database. Echinobase is developed in tandem with [[Xenbase]].
Echinobase runs in a cloud environment.<ref name="kv2014">K. Karimi and P.D. Vize (2014). [https://academic.oup.com/database/article-lookup/doi/10.1093/database/bau108 The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud], Database, doi: 10.1093/database/bau108</ref> Its virtual machines are running in a [[VMware]] [[vSphere]] environment on two servers, with automatic [[load balancing (computing)|load balancing]] and [[fault tolerance]]. Its software uses [[Java (programming language)|Java]], [[JavaServer Pages|JSP]], [[JavaScript]], [[AJAX]], [[XML]], and [[CSS]]. It also uses [[Apache Tomcat]] and the [[IBM Db2]] database. Echinobase is developed in tandem with [[Xenbase]].


== Functional Genomics ==
== Functional genomics ==
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.
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.


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*'''Echinoderm Anatomical Ontology''' - Standardized anatomy terms are used to describe developmental stages
*'''Echinoderm Anatomical Ontology''' - Standardized anatomy terms are used to describe developmental stages


== Literature, Resources and Community ==
== Literature, resources and community ==
Literature on Echinobase is collected by automatically searching published papers using echinoderm query terms and retrieved articles are then manually curated.
Literature on Echinobase is collected by automatically searching published papers using echinoderm query terms and retrieved articles are then manually curated.
*'''Literature Search''' - Users can search for papers based on title, author, journal, etc.
*'''Literature Search''' - Users can search for papers based on title, author, journal, etc.

Revision as of 00:08, 13 August 2024

Echinobase
Content
DescriptionEchinobase: The Echinoderm Knowledgebase.
Data types
captured		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
Organismsechinoderms
Contact
Research centerCarnegie Mellon University, University of Calgary
LaboratoryEttensohn lab, Hinman lab, Vize lab
Primary citationPMID 38262680
Release date2009
Access
Websitehttps://www.echinobase.org/
Download URLhttps://download.echinobase.org/echinobase/
Tools
StandaloneBLAST, JBrowse
Miscellaneous
LicensePublic domain
Data release
frequency		Continuous
Version6.x
Curation policyProfessionally curated
Bookmarkable
entities		Yes

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.


Supported species

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:

Software, hardware and platform

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.

Functional genomics

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.

  • Gene search - Search genes by name, symbol or synonym directly from the landing page
  • Gene nomenclature guidelines - Echinobase is the official body responsible for echinoderm gene naming
  • Genome browser with tracks for RNA-seq and ATAC-seq data - Echinobase uses JBrowse
  • BLAST - Users can BLAST against supported genomes, RNA, and protein sequences
  • RNA-seq data visualization - Plots of temporal expression profiles and spatial (anatomy) expression heatmaps for S. purpuratus
  • Diseases - Users can search for both Disease Ontology and OMIM diseases to find relevant genes and publications

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".

  • Echinoderm Anatomical Ontology - Standardized anatomy terms are used to describe developmental stages

Literature, resources and community

Literature on Echinobase is collected by automatically searching published papers using echinoderm query terms and retrieved articles are then manually curated.

  • Literature Search - Users can search for papers based on title, author, journal, etc.

The data download site makes GFF genome files available and Gene Page Reports provide files for bioinformatic analyses.

  • EchinoWiki -The Echinobase Resources serve to support the community by collecting data, protocols, reagents and other resources that are then shared using the EchinoWiki.
  • Reagents - Echinobase has reagent search tools for antibodies (Ab), morpholinos (MO), and guide RNAs (gRNA) used in published studies.

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.

  • Community Link - People, jobs, labs which study echinoderms

Other Model Organism Databases (MODs)

References

  1. ^ Telmer CA, Karimi K, Chess MM, Agalakov S, Arshinoff BI, Lotay V, Wang DZ, Chu S, Pells TJ, Vize PD, Hinman VF, Ettensohn CA, Echinobase: a resource to support the echinoderm research community, Genetics, 2024, doi:10.1093/genetics/iyae002
  2. ^ K. Karimi and P.D. Vize (2014). The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud, Database, doi: 10.1093/database/bau108
  3. ^ S. Foley et al. Integration of 1: 1 orthology maps and updated datasets into Echinobase, Database, Volume 2021, 2021, baab030

Gene regulatory networks

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