CryptoDB

Recommended

General Information

CryptoDB serves as the functional genomics database for Cryptosporidium and related species. CryptoDB is a free, online resource for accessing and exploring genome sequence and annotation, functional genomics data, isolate sequences, and orthology profiles across organisms. It also includes supplemental bioinformatics analyses and a web interface for data-mining.

Homepage https://cryptodb.org/cryptodb/app

Countries that developed this resource United States

Created in 2005

Taxonomic range

Cryptosporidium

Knowledge Domains

Subjects

In the following recommendations:

How to cite this record FAIRsharing.org: CryptoDB; CryptoDB; DOI: https://doi.org/10.25504/FAIRsharing.t3nprm; Last edited: March 1, 2021, 4:24 p.m.; Last accessed: Jun 19 2021 4:46 a.m.

Record updated: March 1, 2021, 4:22 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.t3nprm' by 'The FAIRsharing Team' at 16:22, 01 Mar 2021 (approved):

	'organizations' has been modified:
		Before:
			National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA|https://www.niaid.nih.gov/|Funds
			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
			Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA, USA|https://ctegd.uga.edu/|Maintains
		After:
			National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA|https://www.niaid.nih.gov/|Funds
			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
			Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA, USA|https://ctegd.uga.edu/|Maintains
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
		Added:
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
		Removed:

	'grants' has been modified:
		Before:
		After:
			212929/Z/18/Z
			218288/Z/19/Z
			HHSN75N93019C00077
		Added:
			212929/Z/18/Z
			218288/Z/19/Z
			HHSN75N93019C00077
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.t3nprm' by 'The FAIRsharing Team' at 14:23, 01 Mar 2021 (approved):

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

	'name' has been modified:
		Before: Cryptosporidum Genomics Resource
		After: CryptoDB

Edits to 'https://fairsharing.org/FAIRsharing.t3nprm' by 'The FAIRsharing Team' at 14:22, 01 Mar 2021 (approved):

	'organizations' has been modified:
		Before:
			Computational Biology and Informatics Laboratory (CBIL), University of Pennsylvania, Philadelphia, PA, USA|http://www.cbil.upenn.edu/|Maintains
			Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA, USA|https://ctegd.uga.edu/|Maintains
			National Institute of Allergy and Infectious Diseases (NIAD), Bethesda, MD, USA|http://www.niaid.nih.gov/|Funds
		After:
			National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA|https://www.niaid.nih.gov/|Funds
			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
			Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA, USA|https://ctegd.uga.edu/|Maintains
		Added:
			National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA|https://www.niaid.nih.gov/|Funds
			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
		Removed:
			Computational Biology and Informatics Laboratory (CBIL), University of Pennsylvania, Philadelphia, PA, USA|http://www.cbil.upenn.edu/|Maintains
			National Institute of Allergy and Infectious Diseases (NIAD), Bethesda, MD, USA|http://www.niaid.nih.gov/|Funds

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

	'supportLinks' has been modified:
		Before:
			contact form|http://cryptodb.org/cryptodb/contact.do
			help|https://tritrypdb.org/tritrypdb/app/static-content/landing.html
			twitter|@eupathdb
		After:
			contact form|https://cryptodb.org/cryptodb/app/contact-us
			help|https://cryptodb.org/cryptodb/app/static-content/landing.html
			online documentation|https://cryptodb.org/cryptodb/app/search/organism/GenomeDataTypes/result
			twitter|@VEuPathDB
		Added:
			contact form|https://cryptodb.org/cryptodb/app/contact-us
			help|https://cryptodb.org/cryptodb/app/static-content/landing.html
			online documentation|https://cryptodb.org/cryptodb/app/search/organism/GenomeDataTypes/result
			twitter|@VEuPathDB
		Removed:
			contact form|http://cryptodb.org/cryptodb/contact.do
			help|https://tritrypdb.org/tritrypdb/app/static-content/landing.html
			twitter|@eupathdb

	'description' has been modified:
		Before: CryptoDB is an integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers, it also includes supplemental bioinformatics analyses and a web interface for data-mining.
		After:  CryptoDB serves as the functional genomics database for Cryptosporidium and related species. CryptoDB is a free, online resource for accessing and exploring genome sequence and annotation, functional genomics data, isolate sequences, and orthology profiles across organisms. It also includes supplemental bioinformatics analyses and a web interface for data-mining.

	'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://cryptodb.org/cryptodb/showQuestion.do
		After:
		Added:
		Removed:
			BLAST||http://cryptodb.org/cryptodb/showQuestion.do

	'onto_disciplines' has been modified:
		Before:
		After:
			Functional Genomics
			Genomics
			Parasitology
		Added:
			Functional Genomics
			Genomics
			Parasitology
		Removed:

	'onto_domains' has been modified:
		Before:
			genome
		After:
			Gene functional annotation
			Genome annotation
			genome
			parasite
		Added:
			Gene functional annotation
			Genome annotation
			parasite
		Removed:

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

	'publications' has been modified:
		Before:
			CryptoDB: a Cryptosporidium bioinformatics resource update.|Heiges M., Wang H., Robinson E., Aurrecoechea C., Gao X., Kaluskar N., Rhodes P., Wang S., He CZ., Su Y., Miller J., Kraemer E., Kissinger JC., |Nucleic Acids Res.|2006
		After:
			CryptoDB: a Cryptosporidium bioinformatics resource update.|Heiges M., Wang H., Robinson E., Aurrecoechea C., Gao X., Kaluskar N., Rhodes P., Wang S., He CZ., Su Y., Miller J., Kraemer E., Kissinger JC., |Nucleic Acids Res.|2006
			Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org.|Warrenfeltz S,Kissinger JC|Methods Mol Biol|2019
		Added:
			Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org.|Warrenfeltz S,Kissinger JC|Methods Mol Biol|2019
		Removed:

	'accessPoints' has been modified:
		Before:
		After:
			REST|https://cryptodb.org/cryptodb/app/static-content/content/CryptoDB/webServices.html|Web Services
		Added:
			REST|https://cryptodb.org/cryptodb/app/static-content/content/CryptoDB/webServices.html|Web Services
		Removed:

	'homepage' has been modified:
		Before: http://cryptodb.org/cryptodb/
		After: https://cryptodb.org/cryptodb/app

Edits to 'https://fairsharing.org/FAIRsharing.t3nprm' by 'The FAIRsharing Team' at 17:19, 15 Sep 2016 (approved):

	'contactName' has been modified:
		Before:
			
		After:
			Jessica Kissinger
		Added:
		Removed:

Support

General

contact form	Contact Form
help	How to Use
online documentation	Statistics
twitter	@VEuPathDB

Additional Information

Contact

Jessica Kissinger ORCID

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

VEuPathDB Data Submission and Release Policies

Data Release

Download

https://cryptodb.org/cryptodb/app/downloads/

Data Curation

Submit Data

https://cryptodb.org/cryptodb/app/static-content/dataSubmission.html

Data Access

Search by Gene ID

https://cryptodb.org/cryptodb/app/search/transcript/GeneByLocusTag

REST Web Services

Web Services

https://cryptodb.org/cryptodb/app/static-content/content/CryptoDB/webS ...

Publications

CryptoDB: a Cryptosporidium bioinformatics resource update.

Heiges M., Wang H., Robinson E., Aurrecoechea C., Gao X., Kaluskar N., Rhodes P., Wang S., He CZ., Su Y., Miller J., Kraemer E., Kissinger JC.,
Nucleic Acids Res. 2006

View Paper (PubMed)

Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org.

Warrenfeltz S,Kissinger JC
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

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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

Grant Number(s)

212929/Z/18/Z (The Wellcome Trust, UK)
218288/Z/19/Z (The Wellcome Trust, UK)
HHSN75N93019C00077 (National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA)

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