Integrated Microbial Genomes And Microbiomes

Abbreviation:IMG/M

General Information

The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. The IMG data warehouse integrates genome and metagenome datasets provided by IMG users with a set of publicly available genome and metagenome datasets. IMG/M is also open to scientists worldwide for the annotation, analysis, and distribution of their own genome and microbiome datasets, as long as they agree with the IMG/M data release policy and follow the metadata requirements for integrating data into IMG/M.

Homepage http://img.jgi.doe.gov/cgi-bin/m/main.cgi

Countries that developed this resource United States

Created in 2006

Taxonomic range

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: IMG/M; Integrated Microbial Genomes And Microbiomes; DOI: https://doi.org/10.25504/FAIRsharing.ae956n; Last edited: Oct. 12, 2020, 1:19 p.m.; Last accessed: Jan 24 2021 6:26 p.m.

Publication for citation IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Chen IA,Chu K,Palaniappan K,Pillay M,Ratner A,Huang J,Huntemann M,Varghese N,White JR,Seshadri R,Smirnova T,Kirton E,Jungbluth SP,Woyke T,Eloe-Fadrosh EA,Ivanova NN,Kyrpides NC; Nucleic Acids Res ; 2018; 10.1093/nar/gky901;

Record updated: Oct. 12, 2020, 1:10 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.ae956n' by 'The FAIRsharing Team' at 13:10, 12 Oct 2020 (approved):

	'user_defined_tags' has been modified:
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			SEED product name associations
			SEED subsystems
		After:
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		Removed:
			SEED product name associations
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	'related_databases' has been modified:
		Before:
			GenBank
			Genomes OnLine Database
			MetaCyc
			Integrated Microbial Genomes
			Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes
			Sequence Read Archive
			Kyoto Encyclopedia of Genes and Genomes
			US Department of Energy Systems Biology Knowledgebase
			SILVA
			Phytozome
			National Microbiome Data Collaborative
			Integrated Microbial Genomes and Microbiomes - Viral Resources
		After:
			GenBank
			GENI-ACT
			Genomes OnLine Database
			MetaCyc
			Integrated Microbial Genomes
			Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes
			Sequence Read Archive
			Kyoto Encyclopedia of Genes and Genomes
			US Department of Energy Systems Biology Knowledgebase
			SILVA
			Phytozome
			National Microbiome Data Collaborative
			Integrated Microbial Genomes and Microbiomes - Viral Resources
		Added:
			GENI-ACT
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.ae956n' by 'The FAIRsharing Team' at 13:08, 12 Oct 2020 (approved):

	'standardsImplemented' has been modified:
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			Gene Ontology
			ENA Sequence Flat File Format
			FASTA Sequence Format
			FASTQ Sequence and Sequence Quality Format
			GenBank Sequence Format
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		After:
			Gene Ontology
			ENA Sequence Flat File Format
			FASTA Sequence Format
			FASTQ Sequence and Sequence Quality Format
			GenBank Sequence Format
			Generic Feature Format Version 3
			XML for evolutionary biology and comparative genomics.
		Added:
			XML for evolutionary biology and comparative genomics.
		Removed:

	'related_databases' has been modified:
		Before:
			GenBank
			Genomes OnLine Database
			MetaCyc
			Integrated Microbial Genomes
			Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes
			Sequence Read Archive
			Kyoto Encyclopedia of Genes and Genomes
			US Department of Energy Systems Biology Knowledgebase
			Phytozome
			National Microbiome Data Collaborative
			Integrated Microbial Genomes and Microbiomes - Viral Resources
		After:
			GenBank
			Genomes OnLine Database
			MetaCyc
			Integrated Microbial Genomes
			Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes
			Sequence Read Archive
			Kyoto Encyclopedia of Genes and Genomes
			US Department of Energy Systems Biology Knowledgebase
			SILVA
			Phytozome
			National Microbiome Data Collaborative
			Integrated Microbial Genomes and Microbiomes - Viral Resources
		Added:
			SILVA
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.ae956n' by 'The FAIRsharing Team' at 12:59, 12 Oct 2020 (approved):

	'organizations' has been modified:
		Before:
			United States Department of Energy|http://www.energy.gov/|Funds
			Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA|http://www.lbl.gov|Maintains
		After:
			United States Department of Energy|http://www.energy.gov/|Funds
			Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA|http://www.lbl.gov|Maintains
			Department of Energy Joint Genome Institute (DOE JGI), Lawrence Berkeley National Laboratory, CA, USA|https://jgi.doe.gov|Maintains
		Added:
			Department of Energy Joint Genome Institute (DOE JGI), Lawrence Berkeley National Laboratory, CA, USA|https://jgi.doe.gov|Maintains
		Removed:

	'standardsImplemented' has been modified:
		Before:
			Gene Ontology
			ENA Sequence Flat File Format
			FASTA Sequence Format
			GenBank Sequence Format
			Generic Feature Format Version 3
		After:
			Gene Ontology
			ENA Sequence Flat File Format
			FASTA Sequence Format
			FASTQ Sequence and Sequence Quality Format
			GenBank Sequence Format
			Generic Feature Format Version 3
		Added:
			FASTQ Sequence and Sequence Quality Format
		Removed:

	'related_databases' has been modified:
		Before:
			MetaCyc
			Integrated Microbial Genomes
			Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes
			Kyoto Encyclopedia of Genes and Genomes
			US Department of Energy Systems Biology Knowledgebase
			National Microbiome Data Collaborative
			Integrated Microbial Genomes and Microbiomes - Viral Resources
		After:
			GenBank
			Genomes OnLine Database
			MetaCyc
			Integrated Microbial Genomes
			Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes
			Sequence Read Archive
			Kyoto Encyclopedia of Genes and Genomes
			US Department of Energy Systems Biology Knowledgebase
			Phytozome
			National Microbiome Data Collaborative
			Integrated Microbial Genomes and Microbiomes - Viral Resources
		Added:
			GenBank
			Genomes OnLine Database
			Sequence Read Archive
			Phytozome
		Removed:

	'supportLinks' has been modified:
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			FAQ|https://sites.google.com/a/lbl.gov/img-form/faq
			forum|https://groups.google.com/a/lbl.gov/forum/#!forum/img-user-forum
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		After:
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			help|https://img.jgi.doe.gov/docs/DownloadingIMGSequenceAndAnnotationData.pdf
			help|https://img.jgi.doe.gov/docs/DownloadIMGgenesAnnotated.pdf
		Added:
			FAQ|https://img.jgi.doe.gov/docs/submission/
			FAQ|https://img.jgi.doe.gov/docs/faq
			contact form|https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=Questions
			forum|https://groups.google.com/a/lbl.gov/g/img-user-forum
			help|https://img.jgi.doe.gov/help.html
			help|https://img.jgi.doe.gov/docs/DownloadingIMGSequenceAndAnnotationData.pdf
			help|https://img.jgi.doe.gov/docs/DownloadIMGgenesAnnotated.pdf
		Removed:
			FAQ|https://sites.google.com/a/lbl.gov/img-form/faq
			forum|https://groups.google.com/a/lbl.gov/forum/#!forum/img-user-forum
			online documentation|https://sites.google.com/a/lbl.gov/img-form/documents
			training|https://sites.google.com/a/lbl.gov/img-form/using-img/tutorial

	'name' has been modified:
		Before: IMG/M: the integrated metagenome data management and comparative analysis system
		After: Integrated Microbial Genomes And Microbiomes

	'onto_disciplines' has been modified:
		Before:
			Life Science
			Ontology and Terminology
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			Comparative Genomics
			Genomics
			Metagenomics
		Added:
			Comparative Genomics
			Genomics
			Metagenomics
		Removed:
			Life Science
			Ontology and Terminology

	'onto_domains' has been modified:
		Before:
			Citation
			DNA sequence
			GO-term enrichment report
			Prediction and recognition
			Protein cleavage site prediction
			Protein domain
			Protein identification
			RNA-seq assay
			Transmembrane protein prediction
			enzyme
			gene model annotation
			genome
			microbiome
			molecular interaction
			orthologous
			phenotype
			plasmid
			protein expression profiling assay
			pseudogene
			ribonucleic acid
			transport
		After:
			Citation
			DNA sequence
			GO-term enrichment report
			Genome annotation
			Prediction and recognition
			Protein cleavage site prediction
			Protein domain
			Protein identification
			RNA-seq assay
			Transmembrane protein prediction
			enzyme
			gene model annotation
			genome
			microbiome
			molecular interaction
			orthologous
			phenotype
			plasmid
			protein expression profiling assay
			pseudogene
			ribonucleic acid
			transport
		Added:
			Genome annotation
		Removed:

	'dataProcesses' has been modified:
		Before:
			FTP download, data access, 
			file download(tab-delimited,XLS), data access, 
			web interface, data access, 
			no versioning policy, data versioning, 
			automated functional prediction for IMG term assignment, pathway assertion,phenotype prediction., data curation, 
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		After:
			Downloads Available, data release, 
			Compare Genomes, data access, https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=CompareGenomes&page=compareGenomes
			Find Functions, data access, https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=FindFunctions&page=findFunctions
			Find Genes, data access, https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneSearch&page=searchForm
			Find Genomes, data access, https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GenomeSearch&page=searchForm
		Added:
			Downloads Available, data release, 
			Compare Genomes, data access, https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=CompareGenomes&page=compareGenomes
			Find Functions, data access, https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=FindFunctions&page=findFunctions
			Find Genes, data access, https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneSearch&page=searchForm
			Find Genomes, data access, https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GenomeSearch&page=searchForm
		Removed:
			FTP download, data access, 
			file download(tab-delimited,XLS), data access, 
			web interface, data access, 
			no versioning policy, data versioning, 
			automated functional prediction for IMG term assignment, pathway assertion,phenotype prediction., data curation, 
			manual curation, data curation, 
			quarterly release, data release, 

	'miriam_id' has been modified:
		Before: None
		After: 

	'publications' has been modified:
		Before:
			An experimental metagenome data management and analysis system.|Markowitz VM., Ivanova N., Palaniappan K., Szeto E., Korzeniewski F., Lykidis A., Anderson I., Mavromatis K., Mavrommatis K., Kunin V., Garcia Martin H., Dubchak I., Hugenholtz P., Kyrpides NC., |Bioinformatics|2006
			IMG/M: a data management and analysis system for metagenomes.|Markowitz VM., Ivanova NN., Szeto E., Palaniappan K., Chu K., Dalevi D., Chen IM., Grechkin Y., Dubchak I., Anderson I., Lykidis A., Mavromatis K., Hugenholtz P., Kyrpides NC., |Nucleic Acids Res.|2008
			IMG 4 version of the integrated microbial genomes comparative analysis system.|Markowitz VM,Chen IM,Palaniappan K,Chu K,Szeto E,Pillay M,Ratner A,Huang J,Woyke T,Huntemann M,Anderson I,Billis K,Varghese N,Mavromatis K,Pati A,Ivanova NN,Kyrpides NC|Nucleic Acids Res|2013
		After:
			An experimental metagenome data management and analysis system.|Markowitz VM., Ivanova N., Palaniappan K., Szeto E., Korzeniewski F., Lykidis A., Anderson I., Mavromatis K., Mavrommatis K., Kunin V., Garcia Martin H., Dubchak I., Hugenholtz P., Kyrpides NC., |Bioinformatics|2006
			IMG/M: a data management and analysis system for metagenomes.|Markowitz VM., Ivanova NN., Szeto E., Palaniappan K., Chu K., Dalevi D., Chen IM., Grechkin Y., Dubchak I., Anderson I., Lykidis A., Mavromatis K., Hugenholtz P., Kyrpides NC., |Nucleic Acids Res.|2008
			IMG 4 version of the integrated microbial genomes comparative analysis system.|Markowitz VM,Chen IM,Palaniappan K,Chu K,Szeto E,Pillay M,Ratner A,Huang J,Woyke T,Huntemann M,Anderson I,Billis K,Varghese N,Mavromatis K,Pati A,Ivanova NN,Kyrpides NC|Nucleic Acids Res|2013
			IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes.|Chen IA,Chu K,Palaniappan K,Pillay M,Ratner A,Huang J,Huntemann M,Varghese N,White JR,Seshadri R,Smirnova T,Kirton E,Jungbluth SP,Woyke T,Eloe-Fadrosh EA,Ivanova NN,Kyrpides NC|Nucleic Acids Res|2018
		Added:
			IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes.|Chen IA,Chu K,Palaniappan K,Pillay M,Ratner A,Huang J,Huntemann M,Varghese N,White JR,Seshadri R,Smirnova T,Kirton E,Jungbluth SP,Woyke T,Eloe-Fadrosh EA,Ivanova NN,Kyrpides NC|Nucleic Acids Res|2018
		Removed:

	'shortname' has been modified:
		Before: IMG/M: the integrated metagenome data management and comparative analysis system
		After: IMG/M

	'description' has been modified:
		Before: The Integrated Microbial Genomes (IMG) system serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. The IMG data warehouse integrates genome and metagenome datasets provided by IMG users with a comprehensive set of publicly available genome and metagenome datasets.
		After: The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. The IMG data warehouse integrates genome and metagenome datasets provided by IMG users with a set of publicly available genome and metagenome datasets. IMG/M is also open to scientists worldwide for the annotation, analysis, and distribution of their own genome and microbiome datasets, as long as they agree with the IMG/M data release policy and follow the metadata requirements for integrating data into IMG/M.

Edits to 'https://fairsharing.org/FAIRsharing.ae956n' by 'The FAIRsharing Team' at 11:02, 21 Nov 2018 (approved):

	'domains' has been modified:
		Before:
			Citation
			DNA sequence data
			Enzyme
			Gene Ontology (GO) enrichment
			Gene model annotation
			Genome
			Life Science
			Microbiome
			Molecular interaction
			Ontology and terminology
			Orthologous
			Phenotype
			Plasmid
			Prediction and recognition
			Protein cleavage site prediction
			Protein domain
			Protein expression profiling
			Protein identification
			Pseudogene
			RNA sequencing (RNA-Seq)
			Ribonucleic acid (RNA)
			SEED product name associations
			SEED subsystems
			Transmembrane protein prediction
			Transport
		After:
			Citation
			Computational predictions
			DNA sequence data
			Enzyme
			Gene Ontology (GO) enrichment
			Gene model annotation
			Genome
			Life Science
			Microbiome
			Molecular interaction
			Ontology and terminology
			Orthologous
			Phenotype
			Plasmid
			Protein cleavage site prediction
			Protein domain
			Protein expression profiling
			Protein identification
			Pseudogene
			RNA sequencing (RNA-Seq)
			Ribonucleic acid (RNA)
			SEED product name associations
			SEED subsystems
			Transmembrane protein prediction
			Transport
		Added:
			Computational predictions
		Removed:
			Prediction and recognition

Edits to 'https://fairsharing.org/FAIRsharing.ae956n' by 'The FAIRsharing Team' at 10:57, 21 Nov 2018 (approved):

	'domains' has been modified:
		Before:
			Citation
			Enzyme
			Gene Ontology (GO) enrichment
			Gene model annotation
			Genome
			Life Science
			Microbiome
			Molecular interaction
			Ontology and terminology
			Orthologous
			Phenotype
			Plasmid
			Prediction and recognition
			Protein cleavage site prediction
			Protein domain
			Protein expression profiling
			Protein identification
			Pseudogene
			RNA sequencing (RNA-Seq)
			Ribonucleic acid (RNA)
			SEED product name associations
			SEED subsystems
			Transmembrane protein prediction
			Transport
		After:
			Citation
			DNA sequence data
			Enzyme
			Gene Ontology (GO) enrichment
			Gene model annotation
			Genome
			Life Science
			Microbiome
			Molecular interaction
			Ontology and terminology
			Orthologous
			Phenotype
			Plasmid
			Prediction and recognition
			Protein cleavage site prediction
			Protein domain
			Protein expression profiling
			Protein identification
			Pseudogene
			RNA sequencing (RNA-Seq)
			Ribonucleic acid (RNA)
			SEED product name associations
			SEED subsystems
			Transmembrane protein prediction
			Transport
		Added:
			DNA sequence data
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.ae956n' by 'The FAIRsharing Team' at 21:19, 19 Aug 2016 (approved):

	'contactName' has been modified:
		Before:
			
		After:
			Victor M. Markowitz
		Added:
		Removed:

In Collections

RDA Covid-19 WG Resources

Support

General

FAQ	Submission FAQ
FAQ	General FAQ
contact form	Contact Form
forum	IMG User Forum
help	Help
help	Download IMG Sequence & Annotation Data ...
help	Download IMG Genes Annotated with Specif ...

Additional Information

Contact

Victor M. Markowitz

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Release

Downloads Available

No link recorded

Data Access

Compare Genomes	https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=CompareGenomes&page ...
Find Functions	https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=FindFunctions&page= ...
Find Genes	https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneSearch&page=sea ...
Find Genomes	https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GenomeSearch&page=s ...

Publications

An experimental metagenome data management and analysis system.

Markowitz VM., Ivanova N., Palaniappan K., Szeto E., Korzeniewski F., Lykidis A., Anderson I., Mavromatis K., Mavrommatis K., Kunin V., Garcia Martin H., Dubchak I., Hugenholtz P., Kyrpides NC.,
Bioinformatics 2006

View Paper (PubMed)

IMG/M: a data management and analysis system for metagenomes.

Markowitz VM., Ivanova NN., Szeto E., Palaniappan K., Chu K., Dalevi D., Chen IM., Grechkin Y., Dubchak I., Anderson I., Lykidis A., Mavromatis K., Hugenholtz P., Kyrpides NC.,
Nucleic Acids Res. 2008

View Paper (PubMed) View Publication

IMG 4 version of the integrated microbial genomes comparative analysis system.

Markowitz VM,Chen IM,Palaniappan K,Chu K,Szeto E,Pillay M,Ratner A,Huang J,Woyke T,Huntemann M,Anderson I,Billis K,Varghese N,Mavromatis K,Pati A,Ivanova NN,Kyrpides NC
Nucleic Acids Res 2013

View Paper (PubMed) View Publication

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes.

Chen IA,Chu K,Palaniappan K,Pillay M,Ratner A,Huang J,Huntemann M,Varghese N,White JR,Seshadri R,Smirnova T,Kirton E,Jungbluth SP,Woyke T,Eloe-Fadrosh EA,Ivanova NN,Kyrpides NC
Nucleic Acids Res 2018

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Gene Ontology

Models and Formats

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Metrics

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Funds

United States Department of Energy (Government body)

Maintains

Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA (University)
Department of Energy Joint Genome Institute (DOE JGI), Lawrence Berkeley National Laboratory, CA, USA (Research institute) Lead

Grant Number(s)

DE-AC02-05CH11231 (United States Department of Energy)

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