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ToxoDB

Recommended

General Information

ToxoDB is a free online resource that provides access to genomic and functional genomic data for Toxoplasma and related organisms. The resource contains over 30 fully sequenced and annotated genomes, with genomic sequence from multiple strains available for variant detection and copy number variation analysis. In addition to genomic sequence data, ToxoDB contains functional genomic datasets including microarray, RNAseq, proteomics, ChIP-seq, and phenotypic data. In addition, results from a number of whole-genome analyses are incorporated, including mapping to orthology clusters, which allows users to leverage phylogenetic relationships in their analyses.

Homepage https://toxodb.org

Countries that developed this resource United States

Created in 2007

Taxonomic range

Toxoplasma

Knowledge Domains

Subjects

In the following recommendations:

How to cite this record FAIRsharing.org: ToxoDB; ToxoDB; DOI: https://doi.org/10.25504/FAIRsharing.a08mtc; Last edited: March 1, 2021, 4:23 p.m.; Last accessed: Nov 27 2021 11:54 p.m.

Record updated: March 1, 2021, 4:16 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.a08mtc' by 'The FAIRsharing Team' at 16:16, 01 Mar 2021 (approved):

	'organizations' has been modified:
		Before:
			National Institute of Allergy and Infectious Diseases (NIAD), Bethesda, MD, USA|http://www.niaid.nih.gov/|Funds
			National Institute of Allergy and Infectious Diseases (NIAD), Bethesda, MD, USA|http://www.niaid.nih.gov/|Funds
		After:
			Bioinformatics Resource Centers, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA|https://www.niaid.nih.gov/research/bioinformatics-resource-centers|Maintains
			National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA|https://www.niaid.nih.gov/|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
		Added:
			Bioinformatics Resource Centers, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA|https://www.niaid.nih.gov/research/bioinformatics-resource-centers|Maintains
			National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA|https://www.niaid.nih.gov/|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
		Removed:
			National Institute of Allergy and Infectious Diseases (NIAD), Bethesda, MD, USA|http://www.niaid.nih.gov/|Funds
			National Institute of Allergy and Infectious Diseases (NIAD), Bethesda, MD, USA|http://www.niaid.nih.gov/|Funds

	'related_databases' has been modified:
		Before:
			CryptoDB
			Eukaryotic Pathogen, Vector and Host Informatics Resource
			PlasmoDB
			VectorBase
			Target Pathogen
		After:
			Fungal and Oomycete genomics resource
			CryptoDB
			Eukaryotic Pathogen, Vector and Host Informatics Resource
			GiardiaDB
			MicrosporidiaDB
			PlasmoDB
			TrichDB
			TriTrypDB
			AmoebaDB
			VectorBase
			Target Pathogen
			ClinEpiDB
		Added:
			Fungal and Oomycete genomics resource
			GiardiaDB
			MicrosporidiaDB
			TrichDB
			TriTrypDB
			AmoebaDB
			ClinEpiDB
		Removed:

	'supportLinks' has been modified:
		Before:
			contact form|http://toxodb.org/toxo/contact.do
			help|https://cryptodb.org/cryptodb/app/static-content/landing.html
			help|http://toxodb.org/toxo/showXmlDataContent.do?name=XmlQuestions.Tutorials
			twitter|@EuPathDB
		After:
			contact form|https://toxodb.org/toxo/app/contact-us
			help|https://toxodb.org/toxo/app/static-content/landing.html
			twitter|@VEuPathDB
		Added:
			contact form|https://toxodb.org/toxo/app/contact-us
			help|https://toxodb.org/toxo/app/static-content/landing.html
			twitter|@VEuPathDB
		Removed:
			contact form|http://toxodb.org/toxo/contact.do
			help|https://cryptodb.org/cryptodb/app/static-content/landing.html
			help|http://toxodb.org/toxo/showXmlDataContent.do?name=XmlQuestions.Tutorials
			twitter|@EuPathDB

	'name' has been modified:
		Before: Toxoplasma Genomics Resource
		After: ToxoDB

	'licences' has been modified:
		Before:
			Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0|http://opendatacommons.org/licenses/pddl/1.0/|Data
		After:
			VEuPathDB Data Submission and Release Policies|https://static-content.veupathdb.org/documents/VEuPathDB_Data_Sub_Release_policy_rev_02April2020.pdf|Data
		Added:
			VEuPathDB Data Submission and Release Policies|https://static-content.veupathdb.org/documents/VEuPathDB_Data_Sub_Release_policy_rev_02April2020.pdf|Data
		Removed:
			Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0|http://opendatacommons.org/licenses/pddl/1.0/|Data

	'tools' has been modified:
		Before:
			BLAST||http://toxodb.org/toxo/showQuestion.do?questionFullName=UniversalQuestions.UnifiedBlast
		After:
		Added:
		Removed:
			BLAST||http://toxodb.org/toxo/showQuestion.do?questionFullName=UniversalQuestions.UnifiedBlast

	'onto_disciplines' has been modified:
		Before:
			Life Science
		After:
			Comparative Genomics
			Functional Genomics
			Genomics
			Phylogenetics
			Proteomics
		Added:
			Comparative Genomics
			Functional Genomics
			Genomics
			Phylogenetics
			Proteomics
		Removed:
			Life Science

	'onto_domains' has been modified:
		Before:
			disease
			genome
			pathogen
		After:
			ChIP-seq assay
			DNA microarray
			Gene expression data
			RNA-seq assay
			disease
			genome
			pathogen
			phenotype
			proteome
		Added:
			ChIP-seq assay
			DNA microarray
			Gene expression data
			RNA-seq assay
			phenotype
			proteome
		Removed:

	'grants' has been modified:
		Before:
			HHSN266200400037C
		After:
			212929/Z/18/Z
			218288/Z/19/Z
			HHSN266200400037C
		Added:
			212929/Z/18/Z
			218288/Z/19/Z
		Removed:

	'publications' has been modified:
		Before:
			ToxoDB: an integrated Toxoplasma gondii database resource.|Gajria B., Bahl A., Brestelli J., Dommer J., Fischer S., Gao X., Heiges M., Iodice J., Kissinger JC., Mackey AJ., Pinney DF., Roos DS., Stoeckert CJ., Wang H., Brunk BP., |Nucleic Acids Res.|2008
		After:
			ToxoDB: an integrated Toxoplasma gondii database resource.|Gajria B., Bahl A., Brestelli J., Dommer J., Fischer S., Gao X., Heiges M., Iodice J., Kissinger JC., Mackey AJ., Pinney DF., Roos DS., Stoeckert CJ., Wang H., Brunk BP., |Nucleic Acids Res.|2008
			ToxoDB: Functional Genomics Resource for Toxoplasma and Related Organisms.|Harb OS,Roos DS|Methods Mol Biol|2019
		Added:
			ToxoDB: Functional Genomics Resource for Toxoplasma and Related Organisms.|Harb OS,Roos DS|Methods Mol Biol|2019
		Removed:

	'dataProcesses' has been modified:
		Before:
			Download, data access, http://toxodb.org/common/downloads/
			Browse, data access, http://toxodb.org/cgi-bin/gbrowse/toxodb/
		After:
			Download, data release, https://toxodb.org/toxo/app/downloads/
			Search by Gene ID, data access, https://toxodb.org/toxo/app/search/transcript/GeneByLocusTag
			Submit, data curation, https://toxodb.org/toxo/app/static-content/dataSubmission.html
		Added:
			Download, data release, https://toxodb.org/toxo/app/downloads/
			Search by Gene ID, data access, https://toxodb.org/toxo/app/search/transcript/GeneByLocusTag
			Submit, data curation, https://toxodb.org/toxo/app/static-content/dataSubmission.html
		Removed:
			Download, data access, http://toxodb.org/common/downloads/
			Browse, data access, http://toxodb.org/cgi-bin/gbrowse/toxodb/

	'accessPoints' has been modified:
		Before:
			Other|http://toxodb.org/toxo/serviceList.jsp|WADLs web services
		After:
			REST|https://toxodb.org/toxo/app/static-content/content/ToxoDB/webServices.html|ToxoDB Web Services Documentation
		Added:
			REST|https://toxodb.org/toxo/app/static-content/content/ToxoDB/webServices.html|ToxoDB Web Services Documentation
		Removed:
			Other|http://toxodb.org/toxo/serviceList.jsp|WADLs web services

	'homepage' has been modified:
		Before: http://www.toxodb.org/toxo/home.jsp
		After: https://toxodb.org

	'description' has been modified:
		Before: ToxoDB is a genome database for the genus Toxoplasma, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including toxoplasmosis.
		After: ToxoDB is a free online resource that provides access to genomic and functional genomic data for Toxoplasma and related organisms. The resource contains over 30 fully sequenced and annotated genomes, with genomic sequence from multiple strains available for variant detection and copy number variation analysis. In addition to genomic sequence data, ToxoDB contains functional genomic datasets including microarray, RNAseq, proteomics, ChIP-seq, and phenotypic data. In addition, results from a number of whole-genome analyses are incorporated, including mapping to orthology clusters, which allows users to leverage phylogenetic relationships in their analyses.

Edits to 'https://fairsharing.org/FAIRsharing.a08mtc' by 'The FAIRsharing Team' at 18:13, 15 Sep 2016 (approved):

	'contactName' has been modified:
		Before:
			
		After:
			Michael Gottlieb
		Added:
		Removed:

Support

General

contact form	Contact Form
help	How to Use
twitter	@VEuPathDB

Additional Information

Contact

Michael Gottlieb

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

VEuPathDB Data Submission and Release Policies

Data Release

Download

https://toxodb.org/toxo/app/downloads/

Data Curation

Submit

https://toxodb.org/toxo/app/static-content/dataSubmission.html

Data Access

Search by Gene ID

https://toxodb.org/toxo/app/search/transcript/GeneByLocusTag

REST Web Services

ToxoDB Web Services Documentation

https://toxodb.org/toxo/app/static-content/content/ToxoDB/webServices. ...

Publications

ToxoDB: an integrated Toxoplasma gondii database resource.

Gajria B., Bahl A., Brestelli J., Dommer J., Fischer S., Gao X., Heiges M., Iodice J., Kissinger JC., Mackey AJ., Pinney DF., Roos DS., Stoeckert CJ., Wang H., Brunk BP.,
Nucleic Acids Res. 2008

View Paper (PubMed) View Publication

ToxoDB: Functional Genomics Resource for Toxoplasma and Related Organisms.

Harb OS,Roos DS
Methods Mol Biol 2019

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

Credit

Record Maintainer

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Funds

National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA (Government body)
The Wellcome Trust, UK (Charitable foundation)

Maintains

Bioinformatics Resource Centers, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA (Government body) Lead

Grant Number(s)

212929/Z/18/Z (The Wellcome Trust, UK)
218288/Z/19/Z (The Wellcome Trust, UK)
HHSN266200400037C (National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA)

ToxoDB

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