Edits to 'https://fairsharing.org/FAIRsharing.ae956n' by 'The FAIRsharing Team' at 13:10, 12 Oct 2020 (approved):
'user_defined_tags' has been modified:
Before:
SEED product name associations
SEED subsystems
After:
Added:
Removed:
SEED product name associations
SEED subsystems
'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:
Before:
Gene Ontology
ENA Sequence Flat File Format
FASTA Sequence Format
FASTQ Sequence and Sequence Quality 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
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:
Before:
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
After:
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
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
After:
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,
manual curation, data curation,
quarterly release, data release,
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: