UniProt

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/uniprot-dataset")

fs.listdir("s3://aws-open-data-uniprot-rdf/2022-05/")

Description:

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt consortium and host institutions EMBL-EBI, SIB Swiss Institute of Bioinformatics and PIR are committed to the long-term preservation of the UniProt databases.

Contact:

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt consortium and host institutions EMBL-EBI, SIB Swiss Institute of Bioinformatics and PIR are committed to the long-term preservation of the UniProt databases.

Update Frequency:

Under 1 months after a new UniProt release.

Managed By:

https://sp.sib.swiss/

Resources:

1. resource:

   • Description: UniProt 2022_05
   • ARN: arn:aws:s3:::aws-open-data-uniprot-rdf/2022-05/
   • Region: eu-west-3
   • Type: S3 Bucket

2. resource:

   • Description: UniProt 2022_04
   • ARN: arn:aws:s3:::aws-open-data-uniprot-rdf/2022-04/
   • Region: eu-west-3
   • Type: S3 Bucket

3. resource:

   • Description: UniProt 2022_03
   • ARN: arn:aws:s3:::aws-open-data-uniprot-rdf/2022-03/
   • Region: eu-west-3
   • Type: S3 Bucket

4. resource:

   • Description: UniProt 2022_02
   • ARN: arn:aws:s3:::aws-open-data-uniprot-rdf/2022-02/
   • Region: eu-west-3
   • Type: S3 Bucket

5. resource:

   • Description: UniProt 2022_01
   • ARN: arn:aws:s3:::aws-open-data-uniprot-rdf/2022-01/
   • Region: eu-west-3
   • Type: S3 Bucket

6. resource:

   • Description: UniProt 2021_04
   • ARN: arn:aws:s3:::aws-open-data-uniprot-rdf/2021-04/
   • Region: eu-west-3
   • Type: S3 Bucket

7. resource:

   • Description: UniProt 2021_03
   • ARN: arn:aws:s3:::aws-open-data-uniprot-rdf/2021-03/
   • Region: eu-west-3
   • Type: S3 Bucket

8. resource:

   • Description: UniProt 2021_02
   • ARN: arn:aws:s3:::aws-open-data-uniprot-rdf/2021-02/
   • Region: eu-west-3
   • Type: S3 Bucket

9. resource:

   • Description: UniProt 2021_01
   • ARN: arn:aws:s3:::aws-open-data-uniprot-rdf/2021-01/
   • Region: eu-west-3
   • Type: S3 Bucket

Tags:

aws-pds, chemistry, protein, enzyme, molecule, life sciences, bioinformatics, biology, RDF, graph, SPARQL

Tutorials:

1. tutorial:

   • Title: UniProt SPARQL
   • URL: https://github.com/sib-swiss/sparql-training/tree/master/uniprot
   • AuthorName: Swiss-Prot Group at SIB Swiss Institute of Bioinformatics

2. tutorial:

   • Title: Exploring the UniProt protein knowledgebase with AWS Open Data and Amazon Neptune
   • URL: https://aws.amazon.com/blogs/industries/exploring-the-uniprot-protein-knowledgebase-with-aws-open-data-and-amazon-neptune/
   • AuthorName: Eric Greene, Rafa Xu, Yuan Shi (AWS)
   • Services: Neptune