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PLAZA

General Information

PLAZA is a platform for comparative, evolutionary, and functional genomics. The platform consists of multiple instances, where each instance contains additional genomes, improved genome annotations, new software tools, etc.

Homepage https://bioinformatics.psb.ugent.be/plaza/

Countries that developed this resource Belgium

Created in 2008

Taxonomic range

Eukaryota

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: PLAZA; PLAZA; DOI: https://doi.org/10.25504/FAIRsharing.wBOua0; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 29 2022 1:44 p.m.

Publication for citation PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. Van Bel M,Diels T,Vancaester E,Kreft L,Botzki A,Van de Peer Y,Coppens F,Vandepoele K; Nucleic Acids Res ; 2017; 10.1093/nar/gkx1002;

This record is maintained by MichielVanBel ORCID

Record added: May 9, 2019, 3:46 p.m.
Record updated: May 14, 2019, 10:18 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.wBOua0' by 'The FAIRsharing Team' at 10:18, 14 May 2019 (approved):

	'supportLinks' has been modified:
		Before:
		After:
			FAQ|https://bioinformatics.psb.ugent.be/plaza_development/documentation/faq
			online documentation|https://bioinformatics.psb.ugent.be/plaza_development/pages/fair_data
			online documentation|https://bioinformatics.psb.ugent.be/plaza_development/documentation
			online documentation|https://bioinformatics.psb.ugent.be/plaza_development/news
			tess training|https://tess.elixir-europe.org/materials/plant-bioinformatics
			tess training|https://tess.elixir-europe.org/materials/plaza-is-a-plant-oriented-online-resource-for-comparative-evolutionary-and-functional-genomics
			training|https://bioinformatics.psb.ugent.be/plaza_development/documentation/tutorial
		Added:
			FAQ|https://bioinformatics.psb.ugent.be/plaza_development/documentation/faq
			online documentation|https://bioinformatics.psb.ugent.be/plaza_development/pages/fair_data
			online documentation|https://bioinformatics.psb.ugent.be/plaza_development/documentation
			online documentation|https://bioinformatics.psb.ugent.be/plaza_development/news
			tess training|https://tess.elixir-europe.org/materials/plant-bioinformatics
			tess training|https://tess.elixir-europe.org/materials/plaza-is-a-plant-oriented-online-resource-for-comparative-evolutionary-and-functional-genomics
			training|https://bioinformatics.psb.ugent.be/plaza_development/documentation/tutorial
		Removed:

	'onto_disciplines' has been modified:
		Before:
			Life Sciences
			Phylogenetics
		After:
			Communication Science
			Evolutionary Biology
			Functional Genomics
			Genomics
			Life Sciences
			Phylogenetics
		Added:
			Communication Science
			Evolutionary Biology
			Functional Genomics
			Genomics
		Removed:

	'tools' has been modified:
		Before:
			PhyD3|v1.0|https://phyd3.bits.vib.be
		After:
			PhyD3|v1.0|https://phyd3.bits.vib.be
			PLAZA Tool Listing||https://bioinformatics.psb.ugent.be/plaza_development/documentation/intro_tutorial#navigation_table_tools
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			PLAZA Tool Listing||https://bioinformatics.psb.ugent.be/plaza_development/documentation/intro_tutorial#navigation_table_tools
		Removed:

	'dataProcesses' has been modified:
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			Main website for data access
		After:
			Main website for data access
			Locate Instances by Species
			Download available for all instances
		Added:
			Locate Instances by Species
			Download available for all instances
		Removed:

	'onto_domains' has been modified:
		Before:
			Classification
			Function analysis
			GO-term enrichment report
			Protein analysis
			Protein domain
			Protein sequence
		After:
			Classification
			FAIR
			Function analysis
			GO-term enrichment report
			Genome annotation
			Protein analysis
			Protein domain
			Protein sequence
			genome
		Added:
			FAIR
			Genome annotation
			genome
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.wBOua0' by 'MichielVanBel' at 15:52, 09 May 2019 (approved):

	'licences' has been modified:
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		After:
			Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)|https://creativecommons.org/licenses/by-nc-sa/4.0/|Data
		Added:
			Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)|https://creativecommons.org/licenses/by-nc-sa/4.0/|Data
		Removed:

	'accessPoints' has been modified:
		Before:
		After:
			REST|https://bioinformatics.psb.ugent.be/plaza/api/get_species_data_links|Retrieve the links to the API calls of the various PLAZA instances
			REST|https://bioinformatics.psb.ugent.be/plaza/api/get_species_data|This API call performs the /api/get_species_data for all available PLAZA instances, merges the results, removes double entries, and returns the data and meta-data for the species in the available PLAZA instances.
			REST|https://bioinformatics.psb.ugent.be/plaza/api/available_instances|Retrieve the available PLAZA instances
		Added:
			REST|https://bioinformatics.psb.ugent.be/plaza/api/get_species_data_links|Retrieve the links to the API calls of the various PLAZA instances
			REST|https://bioinformatics.psb.ugent.be/plaza/api/get_species_data|This API call performs the /api/get_species_data for all available PLAZA instances, merges the results, removes double entries, and returns the data and meta-data for the species in the available PLAZA instances.
			REST|https://bioinformatics.psb.ugent.be/plaza/api/available_instances|Retrieve the available PLAZA instances
		Removed:

	'dataProcesses' has been modified:
		Before:
		After:
			Main website for data access
		Added:
			Main website for data access
		Removed:

In Collections

RDA Covid-19 WG Resources

Support

General

FAQ	FAQ
online documentation	PLAZA and FAIR data
online documentation	PLAZA Documentation
online documentation	News
training	PLAZA Tutorials

Additional Information

Contact

Klaas Vandepoele ORCID

TeSS training resources

Plant Bioinformatics

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics

Tools

PhyD3	https://phyd3.bits.vib.be	v1.0
PLAZA Tool Listing	https://bioinformatics.psb.ugent.be/plaza_development/documentation/in ...

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)

Data Release

Download available for all instances

No link recorded

Data Access

Main website for data access	https://bioinformatics.psb.ugent.be/plaza
Locate Instances by Species	https://bioinformatics.psb.ugent.be/plaza/instance/instances_locate

REST Web Services

Retrieve the links to the API calls of the various PLAZA instances	https://bioinformatics.psb.ugent.be/plaza/api/get_species_data_links
This API call performs the /api/get_species_data for all available PLAZA instances, merges the results, removes double entries, and returns the data and meta-data for the species in the available PLAZA instances.	https://bioinformatics.psb.ugent.be/plaza/api/get_species_data
Retrieve the available PLAZA instances	https://bioinformatics.psb.ugent.be/plaza/api/available_instances

Publications

PLAZA: a comparative genomics resource to study gene and genome evolution in plants.

Proost S,Van Bel M,Sterck L,Billiau K,Van Parys T,Van de Peer Y,Vandepoele K
Plant Cell 2009

View Paper (PubMed) View Publication

Dissecting plant genomes with the PLAZA comparative genomics platform.

Van Bel M,Proost S,Wischnitzki E,Movahedi S,Scheerlinck C,Van de Peer Y,Vandepoele K
Plant Physiol 2011

View Paper (PubMed) View Publication

PLAZA 3.0: an access point for plant comparative genomics.

Proost S,Van Bel M,Vaneechoutte D,Van de Peer Y,Inze D,Mueller-Roeber B,Vandepoele K
Nucleic Acids Res 2014

View Paper (PubMed) View Publication

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics.

Van Bel M,Diels T,Vancaester E,Kreft L,Botzki A,Van de Peer Y,Coppens F,Vandepoele K
Nucleic Acids Res 2017

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

JavaScript Object Notation

Identifier Schemas

No identifier schema standards defined

Metrics

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Related Databases

No related databases defined

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by MichielVanBel ORCID

Maintains

VIB, Belgium (Research institute)
Ghent University, Gent, Belgium (University)
VIB-UGent Center for Plant Systems Biology, Ghent, Belgium (Research institute) Lead

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