Edits to 'https://fairsharing.org/FAIRsharing.ad1zae' by 'The FAIRsharing Team' at 11:41, 22 Mar 2021 (approved):
'description' has been modified:
Before: Ensembl Protists holds over 240 genomes of interest covering those involved in disease and of scientific interest. This includes genomes such as Plasmodium falciparum, Dictyostelium discoideum, Phytophthora infestans and Leishmania major. A majority of these genomes are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at EMBL-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
After: Ensembl Protists stores protist genomes of interest, covering those involved in disease and of scientific interest. This includes genomes such as Plasmodium falciparum, Dictyostelium discoideum, Phytophthora infestans and Leishmania major. A majority of these genomes are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at EMBL-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
Edits to 'https://fairsharing.org/FAIRsharing.ad1zae' by 'The FAIRsharing Team' at 11:40, 22 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:
'related_databases' has been modified:
Before:
Ensembl
Ensembl Genomes
RNAcentral
After:
GenBank
DNA Data Bank of Japan
European Nucleotide Archive
Ensembl
Ensembl Genomes
RNAcentral
Added:
GenBank
DNA Data Bank of Japan
European Nucleotide Archive
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
help|https://protists.ensembl.org/info/
mailing list|http://lists.ensembl.org/mailman/listinfo/dev
twitter|@ensemblgenomes
Added:
blog|https://www.ensembl.info/
help|https://protists.ensembl.org/info/
Removed:
blog|http://www.ensembl.info/
online documentation|http://ensemblgenomes.org/info
'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://protists.ensembl.org/info/website/ftp/index.html
browse, data access, http://protists.ensembl.org/species.html
search, data access, http://protists.ensembl.org/index.html
After:
Variant Effect Predictor, data access, https://protists.ensembl.org/Plasmodium_falciparum/Tools/VEP
Download, data access, https://protists.ensembl.org/info/data/ftp/index.html
Browse, data access, https://protists.ensembl.org/species.html
Search, data access, https://protists.ensembl.org/index.html
HMMER, data access, https://protists.ensembl.org/hmmer
BLAST/BLAT, data access, https://protists.ensembl.org/Plasmodium_falciparum/Tools/Blast
Assembly Converter, data access, https://protists.ensembl.org/Plasmodium_falciparum/Tools/AssemblyConverter
ID History Converter, data access, https://protists.ensembl.org/Plasmodium_falciparum/Tools/IDMapper
BioMart, data access, https://protists.ensembl.org/biomart/martview
Added:
Variant Effect Predictor, data access, https://protists.ensembl.org/Plasmodium_falciparum/Tools/VEP
Download, data access, https://protists.ensembl.org/info/data/ftp/index.html
Browse, data access, https://protists.ensembl.org/species.html
Search, data access, https://protists.ensembl.org/index.html
HMMER, data access, https://protists.ensembl.org/hmmer
BLAST/BLAT, data access, https://protists.ensembl.org/Plasmodium_falciparum/Tools/Blast
Assembly Converter, data access, https://protists.ensembl.org/Plasmodium_falciparum/Tools/AssemblyConverter
ID History Converter, data access, https://protists.ensembl.org/Plasmodium_falciparum/Tools/IDMapper
BioMart, data access, https://protists.ensembl.org/biomart/martview
Removed:
FTP API download, data access, ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz
download, data access, http://protists.ensembl.org/info/website/ftp/index.html
browse, data access, http://protists.ensembl.org/species.html
search, data access, http://protists.ensembl.org/index.html
'taxonomies' has been modified:
Before:
Eukaryota
After:
Protozoa
Added:
Protozoa
Removed:
Eukaryota
'tools' has been modified:
Before:
Biomart||http://protists.ensembl.org/biomart
Ensembl Variant Effect Predictor||http://protists.ensembl.org/Plasmodium_falciparum/Tools/VEP?db=core
Phmmer||http://protists.ensembl.org/hmmer/index.html
Blast||http://protists.ensembl.org/Plasmodium_falciparum/Tools/Blast?db=core
Assembly Converter||http://protists.ensembl.org/Plasmodium_falciparum/Tools/AssemblyConverter?db=core
ID History Converter||http://protists.ensembl.org/Plasmodium_falciparum/Tools/IDMapper?db=core
After:
Variant Effect Predictor (Download Script)||https://github.com/Ensembl/ensembl-tools/archive/release/103.zip
ID History Converter||https://github.com/Ensembl/ensembl-tools/tree/release/103/scripts/id_history_converter
Added:
Variant Effect Predictor (Download Script)||https://github.com/Ensembl/ensembl-tools/archive/release/103.zip
ID History Converter||https://github.com/Ensembl/ensembl-tools/tree/release/103/scripts/id_history_converter
Removed:
Biomart||http://protists.ensembl.org/biomart
Ensembl Variant Effect Predictor||http://protists.ensembl.org/Plasmodium_falciparum/Tools/VEP?db=core
Phmmer||http://protists.ensembl.org/hmmer/index.html
Blast||http://protists.ensembl.org/Plasmodium_falciparum/Tools/Blast?db=core
Assembly Converter||http://protists.ensembl.org/Plasmodium_falciparum/Tools/AssemblyConverter?db=core
ID History Converter||http://protists.ensembl.org/Plasmodium_falciparum/Tools/IDMapper?db=core
Edits to 'https://fairsharing.org/FAIRsharing.ad1zae' by 'The FAIRsharing Team' at 10:07, 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.ad1zae' by 'ensembl_fair' at 15:37, 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 27 release onwards, all protist 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) are now available in Ensembl Protists. The release now consists of a total of over 150 genomes, of which over 100 have been taken directly from the INSDC archives and the remainder taken from other sources. The new genomes have been functionally annotated with InterPro entries and GO terms using InterPro v53.
After: Ensembl Protists holds over 240 genomes of interest covering those involved in disease and of scientific interest. This includes genomes such as Plasmodium falciparum, Dictyostelium discoideum, Phytophthora infestans and Leishmania major. A majority of these genomes are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at EMBL-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
'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://protists.ensembl.org/info/website/ftp/index.html
browse, data access, http://protists.ensembl.org/species.html
search, data access, http://protists.ensembl.org/index.html
After:
FTP API download, data access, ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz
download, data access, http://protists.ensembl.org/info/website/ftp/index.html
browse, data access, http://protists.ensembl.org/species.html
search, data access, http://protists.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
After:
Other|https://github.com/Ensembl|Ensembl Perl API
REST|https://rest.ensembl.org|Ensembl REST API
Added:
REST|https://rest.ensembl.org|Ensembl REST API
Removed:
Other|ftp://ftp.ensemblgenomes.org/pub/release-34/virtual_machines|Ensembl Genomes Virtual Machine
'tools' has been modified:
Before:
Biomart||http://protists.ensembl.org/biomart/martview/60424d446335b1d4a15a89ddc650ded3
Variant effect predictor||http://protists.ensembl.org/Plasmodium_falciparum/Tools/VEP?db=core
Phmmer||http://protists.ensembl.org/hmmer/index.html
Blast||http://protists.ensembl.org/Plasmodium_falciparum/Tools/Blast?db=core
Assembly Converter||http://protists.ensembl.org/Plasmodium_falciparum/Tools/AssemblyConverter?db=core
ID History Converter||http://protists.ensembl.org/Plasmodium_falciparum/Tools/IDMapper?db=core
After:
Biomart||http://protists.ensembl.org/biomart
Ensembl Variant Effect Predictor||http://protists.ensembl.org/Plasmodium_falciparum/Tools/VEP?db=core
Phmmer||http://protists.ensembl.org/hmmer/index.html
Blast||http://protists.ensembl.org/Plasmodium_falciparum/Tools/Blast?db=core
Assembly Converter||http://protists.ensembl.org/Plasmodium_falciparum/Tools/AssemblyConverter?db=core
ID History Converter||http://protists.ensembl.org/Plasmodium_falciparum/Tools/IDMapper?db=core
Added:
Biomart||http://protists.ensembl.org/biomart
Ensembl Variant Effect Predictor||http://protists.ensembl.org/Plasmodium_falciparum/Tools/VEP?db=core
Removed:
Biomart||http://protists.ensembl.org/biomart/martview/60424d446335b1d4a15a89ddc650ded3
Variant effect predictor||http://protists.ensembl.org/Plasmodium_falciparum/Tools/VEP?db=core
Edits to 'https://fairsharing.org/FAIRsharing.ad1zae' 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:
Ensembl Protists
