GlyGen Protein Dataset Release 2022_03
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UniProt release: 03-Aug-2022
GlyGen dataset : 22-Aug-2022

* uniprot-proteome-homo-sapiens.nt.gz
* uniprot-proteome-mus-musculus.nt.gz
* uniprot-proteome-rattus-norvegicus.nt.gz
* uniprot-proteome-drosophila-melanogaster.nt.gz
* uniprot-proteome-hepatitis-c-virus-1a.nt.gz
* uniprot-proteome-hepatitis-c-virus-1b.nt.gz
* uniprot-proteome-human-sars-coronavirus.nt.gz
* uniprot-proteome-sars-cov-2.nt.gz


Changes in this release:
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* 'Calcium binding', 'Metal' and 'Nucleotide binding' annotations have been removed. 
There are eight new qualifiers for the BINDING feature type to describe a ligand (/ligand, /ligand_id, /ligand_label, /ligand_note) and a ligand part (/ligand_part, /ligand_part_id, /ligand_part_label, /ligand_part_note). Please refer https://www.uniprot.org/help/binding for detailed structuring of 'Binding site' annotations.

* Attribute cofactorLabel has been removed

Homo Sapiens Dataset inputs:
> Homo_sapiens.GRCh38.cds.all.fa from http://ftp.ensembl.org/pub/current_fasta/homo_sapiens/cds
> UP000005640_9606_uniprot_proteome.rdf using UniProt website REST API in Aug 2022
> UP000005640_9606.coordinates.json using Proteins REST API in Aug 2022
> Isoform info using UniProt Java API in Aug 2022
> UP000005640_9606.fasta from UniProt Release 2022_03
> UP000005640_9606_additional.fasta from UniProt Release 2022_03


Mus Musculus Dataset inputs:
> Mus_musculus.GRCm39.cds.all.fa from http://ftp.ensembl.org/pub/current_fasta/mus_musculus/cds
> UP000000589_10090_uniprot_proteome.rdf using UniProt website REST API in Aug 2022
> UP000000589_10090.coordinates.json using Proteins REST API in Aug 2022
> Isoform info using UniProt Java API in Aug 2022
> UP000000589_10090.fasta from UniProt Release 2022_03
> UP000000589_10090_additional.fasta from UniProt Release 2022_03


Rattus Norvegicus Dataset inputs:
> Rattus_norvegicus.mRatBN7.2.cds.all.fa.gz from http://ftp.ensembl.org/pub/current_fasta/rattus_norvegicus/cds
> UP000002494_10116_uniprot_proteome.rdf using UniProt website REST API in Aug 2022
> UP000002494_10116.coordinates.json using Proteins REST API in Aug 2022
> Isoform info using UniProt Java API in Aug 2022
> UP000002494_10116.fasta from UniProt Release 2022_03
> UP000002494_10116_additional.fasta from UniProt Release 2022_03


Drosophila Melanogaster Dataset inputs:
> Drosophila_melanogaster.BDGP6.32.cds.all.fa.gz from http://ftp.ensembl.org/pub/current_fasta/drosophila_melanogaster/cds/
> UP000000803_7227_uniprot_proteome.rdf using UniProt website REST API in Aug 2022
> UP000000803_7227.coordinates.json using Proteins REST API in Aug 2022
> Isoform info using UniProt Java API in Aug 2022
> UP000000803_7227.fasta from UniProt Release 2022_03
> UP000000803_7227_additional.fasta from UniProt Release 2022_03


Hepatitis C Virus Genotype 1a Dataset inputs:
> UP000000518_63746_uniprot_proteome.rdf using UniProt website REST API in Aug 2022
> Isoform info using UniProt Java API in Aug 2022
> UP000000518_63746.fasta from UniProt Release 2022_03


Hepatitis C Virus Genotype 1b Dataset inputs:
> UP000008095_11116_uniprot_proteome.rdf using UniProt website REST API in Aug 2022
> Isoform info using UniProt Java API in Aug 2022
> UP000008095_11116.fasta from UniProt website in Jun 2021


Human SARS coronavirus Dataset inputs:
> UP000000354_694009_uniprot_proteome.rdf using UniProt website REST API in Aug 2022
> Isoform info using UniProt Java API in Aug 2022
> UP000000354_694009.fasta from UniProt Release 2022_03


SARS CoV 2 Dataset inputs:
> UniProt pre_release data in Aug 2022 - https://ftp.uniprot.org/pub/databases/uniprot/pre_release


Reaction info from Reactome:
> GraphDB v81 - https://reactome.org/download/current/reactome.graphdb.tgz 
> UniProt to All reactions mapping - https://reactome.org/download/current/UniProt2ReactomeReactions.txt


Rhea info from ftp://ftp.ebi.ac.uk/pub/databases/rhea/rdf/rhea.rdf.gz


Common UniProt Supporting Datasets (2022_03):
> databases.rdf.xz   Databases that are linked to from uniprot.rdf.xz
> diseases.rdf.xz    Human diseases
> enzyme.rdf.xz      Enzyme classification
> go.owl.xz          Gene Ontology
> keywords.rdf.xz    Keywords
> locations.rdf.xz   Subcellular locations
> tissues.rdf.xz     Tissues