datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
sabdab_joint_sequences_uniprotuniprotkb_obsolete_entries_120000000uniprotkb_obsolete_entries_240000000-v1
uniprotkb_obsolete_entries_240000000
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_240000000.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_240000000 converted to
HuggingFace dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_240000000-v1.uniprotkb_obsolete_entries_50000000
uniprotkb_obsolete_entries_50000000
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_50000000.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_50000000 converted to HuggingFace
dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_50000000.uniprot_organisms
Dataset Details
Dataset Description
Organisms in which a amino-acid sequence can be found.
Curated by:
License: MIT
Dataset Sources
data source
Citation
BibTeX:
@article{10.1093/nar/gkac1052,
author = {The UniProt Consortium},
title = {UniProt - the Universal Protein Knowledgebase in 2023},
journal = {Nucleic Acids Research},
volume = {51},
number = {D1},
pages = {D523-D531},
year = {2022},
month = {11},
issn = {0305-1048},
doi =… See the full description on the dataset page: https://huggingface.co/datasets/jablonkagroup/uniprot_organisms.uniprotkb_obsolete_entries_250000000-v1
uniprotkb_obsolete_entries_250000000
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_250000000.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_250000000 converted to HuggingFace
dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_250000000-v1.uniprot
UniProt RDF
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_reviewed_eukaryota_opisthokonta_metazoa_33208_0.rdf.xz
Dataset Summary
This dataset contains RDF triples from UniProt RDF converted to HuggingFace
dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to HuggingFace Dataset
Size: 0.392 GB… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprot.uniprotkb_obsolete_entries_70000000
uniprotkb_obsolete_entries_70000000
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_70000000.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_70000000 converted to HuggingFace
dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_70000000.uniprot_reactions
Dataset Details
Dataset Description
Protein sequences and the reactions these can catalyze.
Curated by:
License: MIT
Dataset Sources
data source
Citation
BibTeX:
@article{10.1093/nar/gkac1052,
author = {The UniProt Consortium},
title = {UniProt - the Universal Protein Knowledgebase in 2023},
journal = {Nucleic Acids Research},
volume = {51},
number = {D1},
pages = {D523-D531},
year = {2022},
month = {11},
issn = {0305-1048},
doi =… See the full description on the dataset page: https://huggingface.co/datasets/jablonkagroup/uniprot_reactions.uniprot
Dataset Description
Dataset Summary
This dataset is a mirror of the Uniprot/SwissProt database. It contains the names and sequences of >500K proteins.
This dataset was parsed from the FASTA file at https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz.
Supported Tasks and Leaderboards: None
Languages: English
Dataset Structure
Data Instances
Data Fields: id, description, sequence
Data… See the full description on the dataset page: https://huggingface.co/datasets/damlab/uniprot.uniprot-taxonomy-splits
Bias in the Branches: A Benchmark on Phylogenetic Representation Gaps in Language Models
Abstract:
Protein and genome language models are trained on corpora that are highly taxonomically imbalanced. Yet, benchmarks seldom quantify how that imbalance affects the representations they learn.
To address this, we introduce a novel benchmark with both amino acid and nucleotide-level sequences that systematically pairs representatives from common and rare taxonomic families across all… See the full description on the dataset page: https://huggingface.co/datasets/biasinthebranches/uniprot-taxonomy-splits.uniprot_binding_sites_multiple
Dataset Details
Dataset Description
Binding sites of a molecule in protein sequences.
Curated by:
License: MIT
Dataset Sources
data source
Citation
BibTeX:
@article{10.1093/nar/gkac1052,
author = {The UniProt Consortium},
title = {UniProt - the Universal Protein Knowledgebase in 2023},
journal = {Nucleic Acids Research},
volume = {51},
number = {D1},
pages = {D523-D531},
year = {2022},
month = {11},
issn = {0305-1048},
doi =… See the full description on the dataset page: https://huggingface.co/datasets/jablonkagroup/uniprot_binding_sites_multiple.uniprotkb_obsolete_entries_0-v1
uniprotkb_obsolete_entries_0
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_0.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_0 converted to HuggingFace
dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to HuggingFace Dataset
Size:… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_0-v1.uniprotkb_obsolete_entries_10000000-v1
uniprotkb_obsolete_entries_10000000
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: https://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_10000000.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_10000000 converted to
HuggingFace dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_10000000-v1.uniprotkb_obsolete_entries_210000000-v1
uniprotkb_obsolete_entries_210000000
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_210000000.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_210000000 converted to HuggingFace
dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_210000000-v1.uniprotkb_obsolete_entries_260000000-v1
uniprotkb_obsolete_entries_260000000
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_260000000.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_260000000 converted to HuggingFace
dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_260000000-v1.uniprotkb_obsolete_entries_40000000
uniprotkb_obsolete_entries_40000000
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_40000000.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_40000000 converted to HuggingFace
dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_40000000.uniprotkb_obsolete_entries_60000000
uniprotkb_obsolete_entries_60000000
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_60000000.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_60000000 converted to HuggingFace
dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_60000000.uniprotkb_obsolete_entries_270000000-v1
uniprotkb_obsolete_entries_270000000
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_270000000.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_270000000 converted to HuggingFace
dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_270000000-v1.uniprotkb_obsolete_entries_0-vp-v1
uniprotkb_obsolete_entries_0
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_0.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_0 converted to
HuggingFace dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to HuggingFace
Dataset
Size:… See the full description on the dataset page: https://huggingface.co/datasets/vipinpalhugging/uniprotkb_obsolete_entries_0-vp-v1.uniprot-datasetuniprotkb_obsolete_entries_0-vp
uniprotkb_obsolete_entries_0
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_0.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_0 converted to
HuggingFace dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to HuggingFace
Dataset
Size:… See the full description on the dataset page: https://huggingface.co/datasets/vipinpalhugging/uniprotkb_obsolete_entries_0-vp.uniprotkb_obsolete_entries_230000000-v1
uniprotkb_obsolete_entries_230000000
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_230000000.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_230000000 converted to HuggingFace
dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_230000000-v1.protein-pairs-uniprot-swissprot
Protein Pairs and Similarity
Selected protein similarities within training, test, and validation sets.
Each protein gets two similarities selected at random and (usually) proteins within the top and bottom quintiles for similarity.
The protein is represented by its UniProt ID and its amino acid sequence (using IUPAC-IUB codes where each amino acid maps to a letter of the alphabet, see: https://en.wikipedia.org/wiki/FASTA_format ).
The distance column is cosine distance (identical =… See the full description on the dataset page: https://huggingface.co/datasets/monsoon-nlp/protein-pairs-uniprot-swissprot.uniprotkb_obsolete_entries_20000000-v1
uniprotkb_obsolete_entries_20000000
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_20000000.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_20000000 converted to HuggingFace
dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_20000000-v1.uniprotkb_obsolete_entries_220000000-v1
uniprotkb_obsolete_entries_220000000
Dataset Description
Comprehensive protein knowledgebase with functional annotations
Original Source: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/uniprotkb_obsolete_entries_220000000.rdf.xz
Dataset Summary
This dataset contains RDF triples from uniprotkb_obsolete_entries_220000000 converted to HuggingFace
dataset format for easy use in machine learning pipelines.
Format: Originally rdf, converted to… See the full description on the dataset page: https://huggingface.co/datasets/CleverThis/uniprotkb_obsolete_entries_220000000-v1.uniprot-testing-1uniprot_sprot
Dataset Card for "uniprot_sprot"
More Information needed
uniprot_sentences
Dataset Details
Dataset Description
Descriptions of the function of a protein.
Curated by:
License: MIT
Dataset Sources
data source
Citation
BibTeX:
@article{10.1093/nar/gkac1052,
author = {The UniProt Consortium},
title = {UniProt - the Universal Protein Knowledgebase in 2023},
journal = {Nucleic Acids Research},
volume = {51},
number = {D1},
pages = {D523-D531},
year = {2022},
month = {11},
issn = {0305-1048},
doi = {10.1093/nar/gkac1052}… See the full description on the dataset page: https://huggingface.co/datasets/jablonkagroup/uniprot_sentences.UniProtKB
UniProtKB Processed
The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication, we describe ongoing changes to our production pipeline to limit the sequences available in UniProtKB to high-quality, non-redundant reference proteomes. We continue to manually curate the scientific literature to add the latest… See the full description on the dataset page: https://huggingface.co/datasets/LiteFold/UniProtKB.