Edits to 'https://fairsharing.org/FAIRsharing.bg5xqs' by 'The FAIRsharing Team' at 11:29, 22 Mar 2021 (approved):
'related_databases' has been modified:
Before:
Ensembl
Ensembl Genomes
RNAcentral
After:
GenBank
European Nucleotide Archive
Ensembl
Ensembl Genomes
RNAcentral
DDBJ BioProject
Added:
GenBank
European Nucleotide Archive
DDBJ BioProject
Removed:
Edits to 'https://fairsharing.org/FAIRsharing.bg5xqs' by 'The FAIRsharing Team' at 20:58, 19 Mar 2021 (approved):
'organizations' has been modified:
Before:
European Commission FP7|https://ec.europa.eu/research/fp7/index_en.cfm|Funds
European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
After:
European Commission FP7|https://ec.europa.eu/research/fp7/index_en.cfm|Funds
European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
Added:
European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
Removed:
European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
'standardsImplemented' has been modified:
Before:
NCBI Taxonomy
Gene Ontology
After:
NCBI Taxonomy
Gene Ontology
Bioschemas
Added:
Bioschemas
Removed:
'supportLinks' has been modified:
Before:
blog|http://www.ensembl.info/
email|helpdesk@ensemblgenomes.org
mailing list|http://lists.ensembl.org/mailman/listinfo/dev
online documentation|http://ensemblgenomes.org/info
twitter|@ensemblgenomes
After:
blog|https://www.ensembl.info/
email|helpdesk@ensemblgenomes.org
mailing list|http://lists.ensembl.org/mailman/listinfo/dev
online documentation|http://fungi.ensembl.org/info/index.html
twitter|@ensemblgenomes
Added:
blog|https://www.ensembl.info/
online documentation|http://fungi.ensembl.org/info/index.html
Removed:
blog|http://www.ensembl.info/
online documentation|http://ensemblgenomes.org/info
'description' has been modified:
Before: Ensembl Fungi is a browser for fungal genomes. A majority of these are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan); in some cases, the annotation has been taken directly from the websites of the data generators. As of release 47, Ensembl Fungi contained over 1000 genomes of interest.
After: Ensembl Fungi is a browser for fungal genomes. A majority of these are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan); in some cases, the annotation has been taken directly from the websites of the data generators.
'onto_disciplines' has been modified:
Before:
Comparative Genomics
Life Science
After:
Comparative Genomics
Genomics
Added:
Genomics
Removed:
Life Science
'dataProcesses' has been modified:
Before:
FTP API download, data access, ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz
Download, data access, http://fungi.ensembl.org/info/website/ftp/index.html
Browse, data access, http://fungi.ensembl.org/species.html
Search, data access, http://fungi.ensembl.org/index.html
After:
Download, data release, https://fungi.ensembl.org/info/data/ftp/index.html
Browse, data access, https://fungi.ensembl.org/species.html
Search, data access, http://fungi.ensembl.org/index.html
BLAST, data access, https://fungi.ensembl.org/Multi/Tools/Blast
Variant Predictor, data access, https://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/VEP?db=core
phmmer, data access, https://fungi.ensembl.org/hmmer/index.html
Assembly Converter, data access, https://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/AssemblyConverter?db=core
ID History Converter, data access, https://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/IDMapper?db=core
Added:
Download, data release, https://fungi.ensembl.org/info/data/ftp/index.html
Browse, data access, https://fungi.ensembl.org/species.html
BLAST, data access, https://fungi.ensembl.org/Multi/Tools/Blast
Variant Predictor, data access, https://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/VEP?db=core
phmmer, data access, https://fungi.ensembl.org/hmmer/index.html
Assembly Converter, data access, https://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/AssemblyConverter?db=core
ID History Converter, data access, https://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/IDMapper?db=core
Removed:
FTP API download, data access, ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz
Download, data access, http://fungi.ensembl.org/info/website/ftp/index.html
Browse, data access, http://fungi.ensembl.org/species.html
'accessPoints' has been modified:
Before:
Other|https://github.com/Ensembl|Ensembl Perl API
REST|http://rest.ensembl.org/|Ensembl Genomes REST API Endpoints
After:
Other|https://github.com/Ensembl|Ensembl Perl API
REST|https://rest.ensembl.org/|Ensembl Genomes REST API Endpoints
Added:
REST|https://rest.ensembl.org/|Ensembl Genomes REST API Endpoints
Removed:
REST|http://rest.ensembl.org/|Ensembl Genomes REST API Endpoints
'tools' has been modified:
Before:
Biomart||http://fungi.ensembl.org/biomart
Blast||http://fungi.ensembl.org/Multi/Tools/Blast?db=core
Ensembl Variant Effect Predictor||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/VEP?db=core
Phmmer||http://fungi.ensembl.org/hmmer/index.html
Assembly Converter||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/AssemblyConverter?db=core
ID History Converter||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/IDMapper?db=core
After:
Added:
Removed:
Biomart||http://fungi.ensembl.org/biomart
Blast||http://fungi.ensembl.org/Multi/Tools/Blast?db=core
Ensembl Variant Effect Predictor||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/VEP?db=core
Phmmer||http://fungi.ensembl.org/hmmer/index.html
Assembly Converter||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/AssemblyConverter?db=core
ID History Converter||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/IDMapper?db=core
Edits to 'https://fairsharing.org/FAIRsharing.bg5xqs' by 'The FAIRsharing Team' at 10:08, 23 Jul 2020 (approved):
'licences' has been modified:
Before:
EMBL-EBI Terms of Use|http://www.ebi.ac.uk/about/terms-of-use|Data
Apache 2.0|https://www.apache.org/licenses/LICENSE-2.0|Software
After:
EMBL-EBI Terms of Use|http://www.ebi.ac.uk/about/terms-of-use|Data
Apache License 2.0|http://www.apache.org/licenses/LICENSE-2.0|Software
Added:
Apache License 2.0|http://www.apache.org/licenses/LICENSE-2.0|Software
Removed:
Apache 2.0|https://www.apache.org/licenses/LICENSE-2.0|Software
Edits to 'https://fairsharing.org/FAIRsharing.bg5xqs' by 'ensembl_fair' at 15:41, 21 Jul 2020 (approved):
'organizations' has been modified:
Before:
European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
European Commission FP7|https://ec.europa.eu/research/fp7/index_en.cfm|Funds
After:
European Commission FP7|https://ec.europa.eu/research/fp7/index_en.cfm|Funds
European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
Added:
European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
Removed:
'description' has been modified:
Before: From release 28 forward, all fungal genomes whose sequence and annotation has been completed and submitted to the the International Nucleotide Sequence Database Collaboration (i.e. the ENA, GenBank and DDBJ databases) is available in Ensembl Fungi. The release now consists of a total of 589 genomes, of which 536 have been taken from the archives and 53 taken directly from other sources.
After: Ensembl Fungi is a browser for fungal genomes. A majority of these are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan); in some cases, the annotation has been taken directly from the websites of the data generators. As of release 47, Ensembl Fungi contained over 1000 genomes of interest.
'licences' has been modified:
Before:
EMBL-EBI Terms of Use|http://www.ebi.ac.uk/about/terms-of-use|Data
After:
EMBL-EBI Terms of Use|http://www.ebi.ac.uk/about/terms-of-use|Data
Apache 2.0|https://www.apache.org/licenses/LICENSE-2.0|Software
Added:
Apache 2.0|https://www.apache.org/licenses/LICENSE-2.0|Software
Removed:
'dataProcesses' has been modified:
Before:
FTP download, data access, ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz
Download, data access, http://fungi.ensembl.org/info/website/ftp/index.html
Browse, data access, http://fungi.ensembl.org/species.html
Search, data access, http://fungi.ensembl.org/index.html
After:
FTP API download, data access, ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz
Download, data access, http://fungi.ensembl.org/info/website/ftp/index.html
Browse, data access, http://fungi.ensembl.org/species.html
Search, data access, http://fungi.ensembl.org/index.html
Added:
FTP API download, data access, ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz
Removed:
FTP download, data access, ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz
'contactEmail' has been modified:
Before: pkersey@ebi.ac.uk
After: flicek@ebi.ac.uk
'contact' has been modified:
Before: Paul Julian Kersey
After: Paul Flicek
'publications' has been modified:
Before:
Ensembl Genomes 2016: more genomes, more complexity.|Kersey PJ,Allen JE,Armean I,Boddu S,Bolt BJ,Carvalho-Silva D,Christensen M,Davis P,Falin LJ,Grabmueller C,Humphrey J,Kerhornou A,Khobova J,Aranganathan NK,Langridge N,Lowy E,McDowall MD,Maheswari U,Nuhn M,Ong CK,Overduin B,Paulini M,Pedro H,Perry E,Spudich G,Tapanari E,Walts B,Williams G,Tello-Ruiz M,Stein J,Wei S,Ware D,Bolser DM,Howe KL,Kulesha E,Lawson D,Maslen G,Staines DM|Nucleic Acids Res|2015
After:
Ensembl Genomes 2016: more genomes, more complexity.|Kersey PJ et al.|Nucleic Acids Res|2015
Ensembl Genomes 2020-enabling non-vertebrate genomic research.|Howe KL et al.|Nucleic Acids Res|2019
Added:
Ensembl Genomes 2016: more genomes, more complexity.|Kersey PJ et al.|Nucleic Acids Res|2015
Ensembl Genomes 2020-enabling non-vertebrate genomic research.|Howe KL et al.|Nucleic Acids Res|2019
Removed:
Ensembl Genomes 2016: more genomes, more complexity.|Kersey PJ,Allen JE,Armean I,Boddu S,Bolt BJ,Carvalho-Silva D,Christensen M,Davis P,Falin LJ,Grabmueller C,Humphrey J,Kerhornou A,Khobova J,Aranganathan NK,Langridge N,Lowy E,McDowall MD,Maheswari U,Nuhn M,Ong CK,Overduin B,Paulini M,Pedro H,Perry E,Spudich G,Tapanari E,Walts B,Williams G,Tello-Ruiz M,Stein J,Wei S,Ware D,Bolser DM,Howe KL,Kulesha E,Lawson D,Maslen G,Staines DM|Nucleic Acids Res|2015
'accessPoints' has been modified:
Before:
Other|https://github.com/Ensembl|Ensembl Perl API
Other|ftp://ftp.ensemblgenomes.org/pub/release-34/virtual_machines|Ensembl Genomes Virtual Machine
REST|http://rest.ensemblgenomes.org/|Ensembl Genomes REST API Endpoints
After:
Other|https://github.com/Ensembl|Ensembl Perl API
REST|http://rest.ensembl.org/|Ensembl Genomes REST API Endpoints
Added:
REST|http://rest.ensembl.org/|Ensembl Genomes REST API Endpoints
Removed:
Other|ftp://ftp.ensemblgenomes.org/pub/release-34/virtual_machines|Ensembl Genomes Virtual Machine
REST|http://rest.ensemblgenomes.org/|Ensembl Genomes REST API Endpoints
'tools' has been modified:
Before:
Biomart||http://fungi.ensembl.org/biomart/martview/340f05d598b005573f40eebf6cffaaaa
Blast||http://fungi.ensembl.org/Multi/Tools/Blast?db=core
Variant Effect Predictor||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/VEP?db=core
Phmmer||http://fungi.ensembl.org/hmmer/index.html
Assembly Converter||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/AssemblyConverter?db=core
ID History Converter||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/IDMapper?db=core
After:
Biomart||http://fungi.ensembl.org/biomart
Blast||http://fungi.ensembl.org/Multi/Tools/Blast?db=core
Ensembl Variant Effect Predictor||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/VEP?db=core
Phmmer||http://fungi.ensembl.org/hmmer/index.html
Assembly Converter||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/AssemblyConverter?db=core
ID History Converter||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/IDMapper?db=core
Added:
Biomart||http://fungi.ensembl.org/biomart
Ensembl Variant Effect Predictor||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/VEP?db=core
Removed:
Biomart||http://fungi.ensembl.org/biomart/martview/340f05d598b005573f40eebf6cffaaaa
Variant Effect Predictor||http://fungi.ensembl.org/Saccharomyces_cerevisiae/Tools/VEP?db=core
Edits to 'https://fairsharing.org/FAIRsharing.bg5xqs' by 'The FAIRsharing Team' at 10:50, 21 Nov 2018 (approved):
'domains' has been modified:
Before:
Comparative genomics
Genome annotation
Life Science
After:
Comparative genomics
DNA sequence data
Genome annotation
Life Science
Added:
DNA sequence data
Removed:
'description' has been modified:
Before: From release 28 forward, all fungal genomes whose sequence and annotation has been completed and submitted to the the International Nucleotide Sequence Database Collaboration (i.e. the ENA, GenBank and DDBJ databases) is available in Ensembl Fungi. The release now consists of a total of 589 genomes, of which 536 have been taken from the archives and 53 taken directly from other sources.
After: From release 28 forward, all fungal genomes whose sequence and annotation has been completed and submitted to the the International Nucleotide Sequence Database Collaboration (i.e. the ENA, GenBank and DDBJ databases) is available in Ensembl Fungi. The release now consists of a total of 589 genomes, of which 536 have been taken from the archives and 53 taken directly from other sources.
Ensembl Fungi
