Plant Genome Integrative Explorer

Abbreviation:PlantGenIE

General Information

The Plant Genome Integrative Explorer is a collection of interoperable web resources for searching, visualising and analysing genomics and transcriptomics data for different plant species. Currently, it includes dedicated web portals for enabling in-depth exploration of Poplar, Eucalyptus Norway spruce, and Arabidopsis and few more plant species. The PlantGenIE platform is based on the GenIE-Sys ( Genome Integrative Explorer System).

Homepage https://plantgenie.org

Countries that developed this resource Sweden

Created in 2008

Taxonomic range

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: PlantGenIE; Plant Genome Integrative Explorer; DOI: https://doi.org/10.25504/FAIRsharing.BnLUyq; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Apr 18 2021 7:04 p.m.

Publication for citation The Plant Genome Integrative Explorer Resource: PlantGenIE.org. Sundell D,Mannapperuma C,Netotea S,Delhomme N,Lin YC,Sjodin A,Van de Peer Y,Jansson S,Hvidsten TR,Street NR; New Phytol ; 2015; 10.1111/nph.13557;

This record is maintained by Chanaka ORCID

Record added: Dec. 4, 2019, 8:11 a.m.
Record updated: Dec. 18, 2019, 10:42 a.m. by Chanaka.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.BnLUyq' by 'Chanaka' at 10:42, 18 Dec 2019 (approved):

	'description' has been modified:
		Before: The Plant Genome Integrative Explorer is a collection of interoperable web resources for searching, visualising and analysing genomics and transcriptomics data for different plant species. Currently, it includes dedicated web portals for enabling in-depth exploration of Poplar, Eucalyptus Norway spruce, and Arabidopsis. The PlantGenIE platform uses Chado databases and is based on the GenIE-Sys ( Genome Integrative Explorer System). Within PlantGenIE are four systems, each dedicated to a different species (PopGenIE, ConGenIE, AtGenIE and EucGenIE).
		After: The Plant Genome Integrative Explorer is a collection of interoperable web resources for searching, visualising and analysing genomics and transcriptomics data for different plant species. Currently, it includes dedicated web portals for enabling in-depth exploration of Poplar, Eucalyptus Norway spruce, and Arabidopsis and few more plant species. The PlantGenIE platform is based on the GenIE-Sys ( Genome Integrative Explorer System).

Edits to 'https://fairsharing.org/FAIRsharing.BnLUyq' by 'The FAIRsharing Team' at 09:42, 05 Dec 2019 (approved):

	'description' has been modified:
		Before: The Plant Genome Integrative Explorer is a collection of interoperable web resources for searching, visualising and analysing genomics and transcriptomics data for different plant species. Currently, it includes dedicated web portals for enabling in-depth exploration of Poplar, Eucalyptus Norway spruce, and Arabidopsis. The PlantGenIE platform uses Chado databases and is based on the GenIE-Sys ( Genome Integrative Explorer System).
		After: The Plant Genome Integrative Explorer is a collection of interoperable web resources for searching, visualising and analysing genomics and transcriptomics data for different plant species. Currently, it includes dedicated web portals for enabling in-depth exploration of Poplar, Eucalyptus Norway spruce, and Arabidopsis. The PlantGenIE platform uses Chado databases and is based on the GenIE-Sys ( Genome Integrative Explorer System). Within PlantGenIE are four systems, each dedicated to a different species (PopGenIE, ConGenIE, AtGenIE and EucGenIE).

	'dataProcesses' has been modified:
		Before:
			Sequence Search
			Community Annotation
			Download (FTP)
		After:
			Sequence Search
			Community Annotation
			Download (FTP)
			PopGenIE
			AtGenIE
			ConGenIE
			EucGenIE
		Added:
			PopGenIE
			AtGenIE
			ConGenIE
			EucGenIE
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.BnLUyq' by 'Chanaka' at 09:25, 04 Dec 2019 (approved):

	'supportLinks' has been modified:
		Before:
			email|contact@plantgenie.org
			help|http://congenie.org/help
		After:
			email|contact@plantgenie.org
			help|https://plantgenie.org/help/tool_id/blast/
		Added:
			help|https://plantgenie.org/help/tool_id/blast/
		Removed:
			help|http://congenie.org/help

Edits to 'https://fairsharing.org/FAIRsharing.BnLUyq' by 'Chanaka' at 09:21, 04 Dec 2019 (approved):

	'taxonomies' has been modified:
		Before:
			Picea abies
			Picea taeda
		After:
			Arabidopsis thaliana
			Eucalyptus grandis
			Picea abies
			Picea taeda
			Populus trichocarpa
		Added:
			Arabidopsis thaliana
			Eucalyptus grandis
			Populus trichocarpa
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.BnLUyq' by 'The FAIRsharing Team' at 09:13, 04 Dec 2019 (approved):

	'supportLinks' has been modified:
		Before:
			email|contact@plantgenie.org
		After:
			email|contact@plantgenie.org
			help|http://congenie.org/help
		Added:
			help|http://congenie.org/help
		Removed:

	'taxonomies' has been modified:
		Before:
			RNA-Seq
		After:
			Picea abies
			Picea taeda
		Added:
			Picea abies
			Picea taeda
		Removed:
			RNA-Seq

	'tools' has been modified:
		Before:
		After:
			BLAST||http://congenie.org/blast
			Gene List||http://congenie.org/citation?genelist=enable
			GBrowse||http://congenie.org/gbrowse
			JBrowse||http://congenie.org/jbrowse
			Random Gene List||http://congenie.org/random_gene_list
			exImage||http://congenie.org/eximage
			exNet||http://congenie.org/exnet
			exPlot||http://congenie.org/explot
			exHeatmap||http://congenie.org/exheatmap
			Enrichment||http://congenie.org/enrichment
			ComPlEx||http://complex.plantgenie.org/
			Galaxy||http://galaxy.plantgenie.org:8080/
		Added:
			BLAST||http://congenie.org/blast
			Gene List||http://congenie.org/citation?genelist=enable
			GBrowse||http://congenie.org/gbrowse
			JBrowse||http://congenie.org/jbrowse
			Random Gene List||http://congenie.org/random_gene_list
			exImage||http://congenie.org/eximage
			exNet||http://congenie.org/exnet
			exPlot||http://congenie.org/explot
			exHeatmap||http://congenie.org/exheatmap
			Enrichment||http://congenie.org/enrichment
			ComPlEx||http://complex.plantgenie.org/
			Galaxy||http://galaxy.plantgenie.org:8080/
		Removed:

	'dataProcesses' has been modified:
		Before:
		After:
			Sequence Search
			Community Annotation
			Download (FTP)
		Added:
			Sequence Search
			Community Annotation
			Download (FTP)
		Removed:

	'onto_domains' has been modified:
		Before:
			Genome visualisation
			QTL
			RNA sequence
			Sequence alignment
			coexpression
			gene expression
		After:
			GO-term enrichment report
			Genome annotation
			Genome assembly
			Genome visualisation
			QTL
			RNA sequence
			RNA-seq assay
			Sequence alignment
			coexpression
			gene expression
			protein
		Added:
			GO-term enrichment report
			Genome annotation
			Genome assembly
			RNA-seq assay
			protein
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.BnLUyq' by 'Chanaka' at 08:43, 04 Dec 2019 (approved):

	'licences' has been modified:
		Before:
			Chanaka Mannapperuma|https://opensource.org/licenses/BSD-3-Clause|Data
		After:
			BSD-3-Clause License (Modified BSD License) (New BSD License)|https://opensource.org/licenses/BSD-3-Clause|Data
		Added:
			BSD-3-Clause License (Modified BSD License) (New BSD License)|https://opensource.org/licenses/BSD-3-Clause|Data
		Removed:
			Chanaka Mannapperuma|https://opensource.org/licenses/BSD-3-Clause|Data

Edits to 'https://fairsharing.org/FAIRsharing.BnLUyq' by 'Chanaka' at 08:35, 04 Dec 2019 (approved):

	'licences' has been modified:
		Before:
			BSD-3-Clause License (Modified BSD License) (New BSD License)|https://opensource.org/licenses/BSD-3-Clause|Data
		After:
			Chanaka Mannapperuma|https://opensource.org/licenses/BSD-3-Clause|Data
		Added:
			Chanaka Mannapperuma|https://opensource.org/licenses/BSD-3-Clause|Data
		Removed:
			BSD-3-Clause License (Modified BSD License) (New BSD License)|https://opensource.org/licenses/BSD-3-Clause|Data

	'organizations' has been modified:
		Before:
		After:
			Ume Plant Science Centre|https://upsc.se|Maintains
		Added:
			Ume Plant Science Centre|https://upsc.se|Maintains
		Removed:

	'taxonomies' has been modified:
		Before:
			Gene Expression
			Gene Ontology Enrichment
			Genome Annotation
			Genome Assembly
			RNA-Seq
			Visualisation
		After:
			Gene Expression
			Gene Ontology Enrichment
			Genome Annotation
			Genome Assembly
			Protein Analysis
			RNA-Seq
			Visualisation
		Added:
			Protein Analysis
		Removed:

	'onto_disciplines' has been modified:
		Before:
		After:
			Bioinformatics
			Data Visualization
			Functional Genomics
			Genomics
			Life Science
			Phylogenetics
		Added:
			Bioinformatics
			Data Visualization
			Functional Genomics
			Genomics
			Life Science
			Phylogenetics
		Removed:

	'onto_domains' has been modified:
		Before:
		After:
			Genome visualisation
			QTL
			RNA sequence
			Sequence alignment
			coexpression
			gene expression
		Added:
			Genome visualisation
			QTL
			RNA sequence
			Sequence alignment
			coexpression
			gene expression
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.BnLUyq' by 'Chanaka' at 08:25, 04 Dec 2019 (approved):

	'licences' has been modified:
		Before:
		After:
			BSD-3-Clause License (Modified BSD License) (New BSD License)|https://opensource.org/licenses/BSD-3-Clause|Data
		Added:
			BSD-3-Clause License (Modified BSD License) (New BSD License)|https://opensource.org/licenses/BSD-3-Clause|Data
		Removed:

	'supportLinks' has been modified:
		Before:
		After:
			email|contact@plantgenie.org
		Added:
			email|contact@plantgenie.org
		Removed:

	'taxonomies' has been modified:
		Before:
		After:
			Gene Expression
			Gene Ontology Enrichment
			Genome Annotation
			Genome Assembly
			RNA-Seq
			Visualisation
		Added:
			Gene Expression
			Gene Ontology Enrichment
			Genome Annotation
			Genome Assembly
			RNA-Seq
			Visualisation
		Removed:

	'tools' has been modified:
		Before:
			exImage|v1.0|https://eucgenie.org/eximage
		After:
		Added:
		Removed:
			exImage|v1.0|https://eucgenie.org/eximage

Edits to 'https://fairsharing.org/FAIRsharing.BnLUyq' by 'Chanaka' at 08:15, 04 Dec 2019 (approved):

	'accessPoints' has been modified:
		Before:
		After:
			REST|https://api.plantgenie.org|Pubic API to query PlantGenIE databases
		Added:
			REST|https://api.plantgenie.org|Pubic API to query PlantGenIE databases
		Removed:

	'tools' has been modified:
		Before:
		After:
			exImage|v1.0|https://eucgenie.org/eximage
		Added:
			exImage|v1.0|https://eucgenie.org/eximage
		Removed:

	'publications' has been modified:
		Before:
		After:
			The Plant Genome Integrative Explorer Resource: PlantGenIE.org.|Sundell D,Mannapperuma C,Netotea S,Delhomme N,Lin YC,Sjodin A,Van de Peer Y,Jansson S,Hvidsten TR,Street NR|New Phytol|2015
		Added:
			The Plant Genome Integrative Explorer Resource: PlantGenIE.org.|Sundell D,Mannapperuma C,Netotea S,Delhomme N,Lin YC,Sjodin A,Van de Peer Y,Jansson S,Hvidsten TR,Street NR|New Phytol|2015
		Removed:

Support

General

support email	Contact PlantGenIE
help	Help

Additional Information

Contact

Nathaniel Street ORCID

Tools

BLAST	http://congenie.org/blast
Gene List	http://congenie.org/citation?genelist=enable
GBrowse	http://congenie.org/gbrowse
JBrowse	http://congenie.org/jbrowse
Random Gene List	http://congenie.org/random_gene_list
exImage	http://congenie.org/eximage
exNet	http://congenie.org/exnet
exPlot	http://congenie.org/explot
exHeatmap	http://congenie.org/exheatmap
Enrichment	http://congenie.org/enrichment
ComPlEx	http://complex.plantgenie.org/
Galaxy	http://galaxy.plantgenie.org:8080/

Access / Retrieve Data

Conditions of Use

Applies to: Data use

BSD-3-Clause License (Modified BSD License) (New BSD License)

Data Curation

Community Annotation

http://congenie.org/start_webapollo

Data Access

Sequence Search	http://congenie.org/sequence_search
Download (FTP)	ftp://plantgenie.org/Data
PopGenIE	https://popgenie.org/
AtGenIE	http://atgenie.org/
ConGenIE	http://congenie.org/
EucGenIE	http://eucgenie.org/

REST Web Services

Pubic API to query PlantGenIE databases

https://api.plantgenie.org

Publications

The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

Sundell D,Mannapperuma C,Netotea S,Delhomme N,Lin YC,Sjodin A,Van de Peer Y,Jansson S,Hvidsten TR,Street NR
New Phytol 2015

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

No syntax standards defined

Identifier Schemas

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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 Chanaka ORCID

Maintains

Umea Plant Science Centre (Research institute) Lead

Plant Genome Integrative Explorer

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