cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4300971
title: High-quality large curated dataset of protein sequences (1.83 million) and their corresponding Position Specific Scoring Matrices

description: As part of his master thesis at the Rostlab, which is located at the Technical University of Munich (TUM), Mr. Issar Arab developed the first language model that encodes evolutionary information of proteins explicitly. The pre-training involved the creation of a novel high-quality dataset of protein sequences (around 1.83 million proteins, or ~0.8 Billion amino acids) with their corresponding Position Specific Scoring Matrices (PSSMs).  Those matrices reflect the relative frequency of each amino acid at each position in a protein and is derived from evolutionarily related proteins.

Mr. Arab makes this work publicly available to help other researchers speed up their work to leverage AI to learn the representation of protein evolutionary information more explicitly. The set of sequences was derived by extracting all PSSMs from the PredictProtein (PP) cache, which were also part o the UniProt Reference Cluster with 50% sequence identity (uniref50 2019_12). The overlap between PP and uniref50 was further filtered to only include high-quality samples, e.g. only multiple sequence alignments with a certain number of aligned sequences were considered. The processing led to a training set of 1.83 Million sequences, a validation set of 879 instances, and a test set of 879 entries. The training data of proteins is reduced to 40% sequence identity, with respect to the validation/test sets, and contains sequences ranging between 18 and 9858 residues in length.

Refer to the Jupyter notebook for a detailed description of the files' structure and a Python code snippet to correctly manipulate this data.

To access the full original work, please visit the following link:  Manuscript Note: The dataset was recently used to fine tune a protein sequence language model (PEvoLM). The work was presented at the CIBCB'23 conference. If you use PEvoLM or this dataset in your work, please cite the following publication:

- Issar Arab, PEvoLM: Protein Sequence Evolutionary Information Language Model, IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), Eindhoven, Netherlands, (2023), pp. 1-8, doi:10.1109/CIBCB56990.2023.10264890
DOI: 10.15468/dl.b2d3t2
title: Occurrence Download

description: A dataset containing 8482 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Crotalus scutulatus Kennicott, 1861"
 ]
}

 The dataset includes 8482 records from 103 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017244-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11249494
title: Sion 1840 - Building 444 (LoD-1)

description: Coordinates: N/A Length: 11.96 mWidth: 14.23 mHeight: 10.29 mVertices: 36 Primitives: 20  The Length, Width, Height, Vertices and Primitives listed above have been derived directly from the OBJ file.Main Files:
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DOI: 10.5281/zenodo.11249495
title: Sion 1840 - Building 444 (LoD-1)

description: Coordinates: N/A Length: 11.96 mWidth: 14.23 mHeight: 10.29 mVertices: 36 Primitives: 20  The Length, Width, Height, Vertices and Primitives listed above have been derived directly from the OBJ file.
DOI: 10.5281/zenodo.11486733
title: Sion 1840 - Building 444 (LoD-1)

description: Coordinates: N/A Length: 11.96 mWidth: 14.23 mHeight: 10.29 mVertices: 36 Primitives: 20  The Length, Width, Height, Vertices and Primitives listed above have been derived directly from the OBJ file.Main Files:
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DOI: 10.5281/zenodo.12692511
title: Sion 1840 - Building 444 (LoD-1)

description: Coordinates: N/A Length: 11.96 mWidth: 14.23 mHeight: 10.29 mVertices: 36 Primitives: 20  The Length, Width, Height, Vertices and Primitives listed above have been derived directly from the OBJ file.Main Files:
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DOI: 10.5281/zenodo.11564070
title: Trento 1851 - Building 480

description: Coordinates: N/A Length: 12.73 mWidth: 12.06 mHeight: 9.18 mPoints: 10 Vertices: 48 Primitives: 16 Main Files:
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DOI: 10.5281/zenodo.11564071
title: Trento 1851 - Building 480

description: Coordinates: N/A Length: 12.73 mWidth: 12.06 mHeight: 9.18 mPoints: 10 Vertices: 48 Primitives: 16
DOI: 10.5281/zenodo.11579963
title: Trento 1936 - Building 429

description: Coordinates: N/A Length: 13.06 mWidth: 13.52 mHeight: 11.33 mPoints: 14 Vertices: 72 Primitives: 24
DOI: 10.5281/zenodo.12530647
title: Trento 1851 - Building 480

description: Coordinates: N/A Length: 12.73 mWidth: 12.06 mHeight: 9.18 mPoints: 10 Vertices: 48 Primitives: 16 Main Files:
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DOI: 10.5281/zenodo.12552440
title: Trento 1936 - Building 429

description: Coordinates: N/A Length: 13.06 mWidth: 13.52 mHeight: 11.33 mPoints: 14 Vertices: 72 Primitives: 24 Main Files:
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DOI: 10.5281/zenodo.12692518
title: Trento 1851 - Building 480

description: Coordinates: N/A Length: 12.73 mWidth: 12.06 mHeight: 9.18 mPoints: 10 Vertices: 48 Primitives: 16 Main Files:
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DOI: 10.5281/zenodo.11579962
title: Trento 1936 - Building 429

description: Coordinates: N/A Length: 13.06 mWidth: 13.52 mHeight: 11.33 mPoints: 14 Vertices: 72 Primitives: 24 Main Files:
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DOI: 10.5281/zenodo.12692526
title: Trento 1936 - Building 429

description: Coordinates: N/A Length: 13.06 mWidth: 13.52 mHeight: 11.33 mPoints: 14 Vertices: 72 Primitives: 24 Main Files:
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DOI: 10.5281/zenodo.11562771
title: Trento 1851 - Building 418

description: Coordinates: N/A Length: 5.93 mWidth: 10.58 mHeight: 9.83 mPoints: 8 Vertices: 36 Primitives: 12 Main Files:
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DOI: 10.5281/zenodo.11562772
title: Trento 1851 - Building 418

description: Coordinates: N/A Length: 5.93 mWidth: 10.58 mHeight: 9.83 mPoints: 8 Vertices: 36 Primitives: 12
DOI: 10.5281/zenodo.11565437
title: Trento 1851 - Building 1022

description: Coordinates: N/A Length: 8.55 mWidth: 13.98 mHeight: 19.33 mPoints: 8 Vertices: 36 Primitives: 12 Main Files:
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DOI: 10.5281/zenodo.11565438
title: Trento 1851 - Building 1022

description: Coordinates: N/A Length: 8.55 mWidth: 13.98 mHeight: 19.33 mPoints: 8 Vertices: 36 Primitives: 12
DOI: 10.5281/zenodo.12528554
title: Trento 1851 - Building 418

description: Coordinates: N/A Length: 5.93 mWidth: 10.58 mHeight: 9.83 mPoints: 8 Vertices: 36 Primitives: 12 Main Files:
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DOI: 10.5281/zenodo.12533096
title: Trento 1851 - Building 1022

description: Coordinates: N/A Length: 8.55 mWidth: 13.98 mHeight: 19.33 mPoints: 8 Vertices: 36 Primitives: 12 Main Files:
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DOI: 10.5281/zenodo.12692628
title: Trento 1851 - Building 418

description: Coordinates: N/A Length: 5.93 mWidth: 10.58 mHeight: 9.83 mPoints: 8 Vertices: 36 Primitives: 12 Main Files:
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DOI: 10.5281/zenodo.12692630
title: Trento 1851 - Building 1022

description: Coordinates: N/A Length: 8.55 mWidth: 13.98 mHeight: 19.33 mPoints: 8 Vertices: 36 Primitives: 12 Main Files:
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DOI: 10.5281/zenodo.11248977
title: Sion 1840 - Building 213 (LoD-1)

description: Coordinates: N/A Length: 10.15 mWidth: 9.05 mHeight: 7.16 mVertices: 30 Primitives: 16  The Length, Width, Height, Vertices and Primitives listed above have been derived directly from the OBJ file.
DOI: 10.5281/zenodo.11251826
title: Sion 1760 - Building 102 (LoD-1)

description: Coordinates: N/A Length: 12.55 mWidth: 10.47 mHeight: 4.44 mVertices: 30 Primitives: 16  The Length, Width, Height, Vertices and Primitives listed above have been derived directly from the OBJ file.
DOI: 10.5281/zenodo.11485465
title: Sion 1840 - Building 213 (LoD-1)

description: Coordinates: N/A Length: 10.15 mWidth: 9.05 mHeight: 7.16 mVertices: 30 Primitives: 16  The Length, Width, Height, Vertices and Primitives listed above have been derived directly from the OBJ file.Main Files:
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DOI: 10.5281/zenodo.11572300
title: Trento 1936 - Building 2097

description: Coordinates: N/A Length: 5.98 mWidth: 6.99 mHeight: 5.87 mPoints: 8 Vertices: 36 Primitives: 12 Main Files:
Filename.glb.xml.objbuilding_2097.objLinkbuilding_2097.glbLink11572300_metsmods.xmlLink11572300_edm.xmlLinkThumbnails:
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DOI: 10.5281/zenodo.11572301
title: Trento 1936 - Building 2097

description: Coordinates: N/A Length: 5.98 mWidth: 6.99 mHeight: 5.87 mPoints: 8 Vertices: 36 Primitives: 12
DOI: 10.5281/zenodo.11573736
title: Trento 1936 - Building 48

description: Coordinates: N/A Length: 33.68 mWidth: 16.17 mHeight: 53.01 mPoints: 25 Vertices: 138 Primitives: 46
DOI: 10.5281/zenodo.12540302
title: Trento 1936 - Building 2097

description: Coordinates: N/A Length: 5.98 mWidth: 6.99 mHeight: 5.87 mPoints: 8 Vertices: 36 Primitives: 12 Main Files:
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DOI: 10.5281/zenodo.12692631
title: Trento 1936 - Building 2097

description: Coordinates: N/A Length: 5.98 mWidth: 6.99 mHeight: 5.87 mPoints: 8 Vertices: 36 Primitives: 12 Main Files:
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DOI: 10.5281/zenodo.12692707
title: Trento 1936 - Building 48

description: Coordinates: N/A Length: 33.68 mWidth: 16.17 mHeight: 53.01 mPoints: 25 Vertices: 138 Primitives: 46 Main Files:
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DOI: 10.5281/zenodo.11248976
title: Sion 1840 - Building 213 (LoD-1)

description: Coordinates: N/A Length: 10.15 mWidth: 9.05 mHeight: 7.16 mVertices: 30 Primitives: 16  The Length, Width, Height, Vertices and Primitives listed above have been derived directly from the OBJ file.Main Files:
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DOI: 10.5281/zenodo.11492349
title: Sion 1760 - Building 102 (LoD-1)

description: Coordinates: N/A Length: 12.55 mWidth: 10.47 mHeight: 4.44 mVertices: 30 Primitives: 16  The Length, Width, Height, Vertices and Primitives listed above have been derived directly from the OBJ file.Main Files:
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DOI: 10.5281/zenodo.11564081
title: Trento 1851 - Building 899

description: Coordinates: N/A Length: 10.96 mWidth: 10.95 mHeight: 7.49 mPoints: 8 Vertices: 36 Primitives: 12
DOI: 10.5281/zenodo.11564759
title: Trento 1851 - Building 306

description: Coordinates: N/A Length: 25.28 mWidth: 13.21 mHeight: 6.79 mPoints: 14 Vertices: 72 Primitives: 24
DOI: 10.5281/zenodo.11566990
title: Trento 1886 - Building 289

description: Coordinates: N/A Length: 0.01 mWidth: 14.81 mHeight: 0.01 mPoints: 6 Vertices: 24 Primitives: 8
DOI: 10.5281/zenodo.11573735
title: Trento 1936 - Building 48

description: Coordinates: N/A Length: 33.68 mWidth: 16.17 mHeight: 53.01 mPoints: 25 Vertices: 138 Primitives: 46 Main Files:
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DOI: 10.5281/zenodo.11574999
title: Trento 1936 - Building 2380

description: Coordinates: N/A Length: 12.8 mWidth: 6.54 mHeight: 11.02 mPoints: 8 Vertices: 36 Primitives: 12 Main Files:
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DOI: 10.5281/zenodo.11575000
title: Trento 1936 - Building 2380

description: Coordinates: N/A Length: 12.8 mWidth: 6.54 mHeight: 11.02 mPoints: 8 Vertices: 36 Primitives: 12
DOI: 10.5281/zenodo.11577045
title: Trento 1936 - Building 2376

description: Coordinates: N/A Length: 15.12 mWidth: 9.87 mHeight: 24.81 mPoints: 22 Vertices: 120 Primitives: 40 Main Files:
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DOI: 10.5281/zenodo.11577046
title: Trento 1936 - Building 2376

description: Coordinates: N/A Length: 15.12 mWidth: 9.87 mHeight: 24.81 mPoints: 22 Vertices: 120 Primitives: 40
DOI: 10.5281/zenodo.12531962
title: Trento 1851 - Building 306

description: Coordinates: N/A Length: 25.28 mWidth: 13.21 mHeight: 6.79 mPoints: 14 Vertices: 72 Primitives: 24 Main Files:
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DOI: 10.5281/zenodo.12535211
title: Trento 1886 - Building 289

description: Coordinates: N/A Length: 0.01 mWidth: 14.81 mHeight: 0.01 mPoints: 6 Vertices: 24 Primitives: 8 Main Files:
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DOI: 10.5281/zenodo.12541801
title: Trento 1936 - Building 48

description: Coordinates: N/A Length: 33.68 mWidth: 16.17 mHeight: 53.01 mPoints: 25 Vertices: 138 Primitives: 46 Main Files:
Filename.glb.objbuilding_48.objLinkbuilding_48.glbLinkThumbnails:
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DOI: 10.5281/zenodo.12543836
title: Trento 1936 - Building 2380

description: Coordinates: N/A Length: 12.8 mWidth: 6.54 mHeight: 11.02 mPoints: 8 Vertices: 36 Primitives: 12 Main Files:
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DOI: 10.5281/zenodo.12547740
title: Trento 1936 - Building 2376

description: Coordinates: N/A Length: 15.12 mWidth: 9.87 mHeight: 24.81 mPoints: 22 Vertices: 120 Primitives: 40 Main Files:
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