cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12671237
title: Protein haplotype sequences obtained by ProHap from the 1000 Genomes Project data set

description: Database of protein sequences obtained using ProHap (https://github.com/ProGenNo/ProHap) on the data set of phased genotypes published by the 1000 Genomes Project, aligned with the GRCh38 genome build (https://www.internationalgenome.org/data-portal/data-collection/grch38). We used Ensembl v.110 for the mapping of coordinates between genes, exons, and transcripts. The complete configuration file for each ProHap run is attached to this repository.

This data set contains six compressed directories, five representing the superpopulations included in the 1000 Genomes Project (https://catalog.coriell.org/1/NHGRI/Collections/1000-Genomes-Project-Collection/1000-Genomes-Project), and one created using all the samples included in the 1000 Genomes data set:



AFR - African

AMR - American

EUR - European

SAS - South Asian

EAS - East Asian

ALL - all participants in the 1000 Genomes Project


Each of the directories contains the following files:



F1: The concatenated fasta file ready to be used with search engines, contains the following:



Protein haplotype sequences obtained by ProHap, using alleles with at least 1 % frequency within the selected population

Reference proteome as per Ensembl v. 110

Contaminant sequences from the cRAP project (https://www.thegpm.org/crap/)

The file is provided in two formats - full and simplified. The simplified fasta contains only the artificial protein identifier and the matching gene name, and is optimised for compatibility with a wide range of tools. For annotation of peptides using the PeptideAnnotator, please provide the header (F1.2) in addition to the simplified fasta file. 



F2: Additional information about the haplotype sequences, to be used for mapping identified peptides to the original haplotypes

F3: Translations of haplotype cDNA sequences, before merging with the reference proteome


For further description of the files, please refer to https://github.com/ProGenNo/ProHap/wiki/Output-files.

For the usage of these databases with search engines, and downstream anaylsis of identified peptides, please refer to the project's wiki page: https://github.com/ProGenNo/ProHap/wiki/Using-the-database-for-proteomic-searches.

When using these databases in your publication, please cite: Vašíček, J., Kuznetsova, K.G., Skiadopoulou, D. et al. ProHap enables human proteomic database generation accounting for population diversity. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02506-0
DOI: 10.5281/zenodo.12671301
title: Protein haplotype sequences obtained by ProHap from the Haplotype Reference Consortium Release 1.1 dataset

description: Database of protein sequences obtained using ProHap (https://github.com/ProGenNo/ProHap) on the data set of phased genotypes published by the Haplotype Reference Consortium, Release 1.1 (https://ega-archive.org/datasets/EGAD00001002729). We used Ensembl v.110 for the mapping of coordinates between genes, exons, and transcripts.

Release 1.1 of the HRC is provided aligned with the GRCh37 reference genome. We have performed a liftover to the GRCh38 reference using GeneBe (https://genebe.net/tools/liftover). Variants for which the reported alternative allele is considered as reference in GRCh38 were removed. A threshold of 1% minor allele frequency was applied to filter the remaining variants. After translation, a frequency threshold of 0.5% was applied to filter the resulting unique non-canonical sequences. The complete configuration file for the ProHap run is attached to this repository.

This dataset contains one compressed directory, contains the following files:



F1: The concatenated fasta file ready to be used with search engines, contains the following:



Protein haplotype sequences obtained by ProHap

Reference proteome as per Ensembl v. 110

Contaminant sequences from the cRAP project (https://www.thegpm.org/crap/)

The file is provided in two formats - full and simplified. The simplified fasta contains only the artificial protein identifier and the matching gene name, and is optimised for compatibility with a wide range of tools. For annotation of peptides using the PeptideAnnotator, please provide the header (F1.2) in addition to the fasta file. 



F2: Additional information about the haplotype sequences, to be used for mapping identified peptides to the original haplotypes

F3: Translations of haplotype cDNA sequences, before merging with the reference proteome


For further description of the files, please refer to https://github.com/ProGenNo/ProHap/wiki/Output-files.

For the usage of these databases with search engines, and downstream anaylsis of identified peptides, please refer to the project's wiki page: https://github.com/ProGenNo/ProHap/wiki/Using-the-database-for-proteomic-searches.

When using these databases in your publication, please cite: Vašíček, J., Kuznetsova, K.G., Skiadopoulou, D. et al. ProHap enables human proteomic database generation accounting for population diversity. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02506-0
DOI: 10.5281/zenodo.12671302
title: Protein haplotype sequences obtained by ProHap from the Haplotype Reference Consortium Release 1.1 dataset

description: Database of protein sequences obtained using ProHap (https://github.com/ProGenNo/ProHap) on the data set of phased genotypes published by the Haplotype Reference Consortium, Release 1.1 (https://ega-archive.org/datasets/EGAD00001002729). We used Ensembl v.110 for the mapping of coordinates between genes, exons, and transcripts.

Release 1.1 of the HRC is provided aligned with the GRCh37 reference genome. We have performed a liftover to the GRCh38 reference using GeneBe (https://genebe.net/tools/liftover). Variants for which the reported alternative allele is considered as reference in GRCh38 were removed. A threshold of 1% minor allele frequency was applied to filter the remaining variants. After translation, a frequency threshold of 0.5% was applied to filter the resulting unique non-canonical sequences. The complete configuration file for the ProHap run is attached to this repository.

This dataset contains one compressed directory, contains the following files:



F1: The concatenated fasta file ready to be used with search engines, contains the following:



Protein haplotype sequences obtained by ProHap

Reference proteome as per Ensembl v. 110

Contaminant sequences from the cRAP project (https://www.thegpm.org/crap/)

The file is provided in two formats - full and simplified. The simplified fasta contains only the artificial protein identifier and the matching gene name, and is optimised for compatibility with a wide range of tools. For annotation of peptides using the PeptideAnnotator, please provide the header (F1.2) in addition to the fasta file. 



F2: Additional information about the haplotype sequences, to be used for mapping identified peptides to the original haplotypes

F3: Translations of haplotype cDNA sequences, before merging with the reference proteome


For further description of the files, please refer to https://github.com/ProGenNo/ProHap/wiki/Output-files.

For the usage of these databases with search engines, and downstream anaylsis of identified peptides, please refer to the project's wiki page: https://github.com/ProGenNo/ProHap/wiki/Using-the-database-for-proteomic-searches.

When using these databases in your publication, please cite: Vašíček, J., Kuznetsova, K.G., Skiadopoulou, D. et al. ProHap enables human proteomic database generation accounting for population diversity. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02506-0
DOI: 10.5281/zenodo.12686819
title: Protein haplotype sequences obtained by ProHap from the Human Pangenome Reference Consotruim dataset

description: Database of protein sequences obtained using ProHap (https://github.com/ProGenNo/ProHap) on the data set of phased genotypes published by the Human Pangenome Reference Consotruim (HPRC), first release (https://github.com/human-pangenomics/hpp_pangenome_resources), 44 samples. We used Ensembl v.110 for the mapping of coordinates between genes, exons, and transcripts.

This repository contains one database created using all 43 samples of the HPRC release (the haplotypes of the sample NA21309 did not encode any non-canonical sequences), and then a database for each of the 43 samples separately. No filtering on allele frequency or haplotype frequency was applied in any of the databases. The complete configuration file for the ProHap run is attached to this repository.

There is one compressed directory for each of the databases, containing the following files:



F1: The concatenated fasta file ready to be used with search engines, contains the following:



Protein haplotype sequences obtained by ProHap

Reference proteome as per Ensembl v. 110

Contaminant sequences from the cRAP project (https://www.thegpm.org/crap/)

For this dataset, only the simplified format is provided. The simplified fasta contains only the artificial protein identifier and the matching gene name, and is optimised for compatibility with a wide range of tools. For annotation of peptides using the PeptideAnnotator, please provide the header (F1.2) in addition to the fasta file. 



F2: Additional information about the haplotype sequences, to be used for mapping identified peptides to the original haplotypes

F3: Translations of haplotype cDNA sequences, before merging with the reference proteome


For further description of the files, please refer to https://github.com/ProGenNo/ProHap/wiki/Output-files.

For the usage of these databases with search engines, and downstream anaylsis of identified peptides, please refer to the project's wiki page: https://github.com/ProGenNo/ProHap/wiki/Using-the-database-for-proteomic-searches.

When using these databases in your publication, please cite: Vašíček, J., Kuznetsova, K.G., Skiadopoulou, D. et al. ProHap enables human proteomic database generation accounting for population diversity. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02506-0
DOI: 10.15468/dl.d6t6b8
title: Occurrence Download

description: A dataset containing 598 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((35.32942 36.17352,54.40626 36.17352,54.40626 47.31234,35.32942 47.31234,35.32942 36.17352))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is Heracleum mantegazzianum Sommier & Levier"
 ]
}

 The dataset includes 598 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029552-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12686818
title: Protein haplotype sequences obtained by ProHap from the Human Pangenome Reference Consotruim dataset

description: Database of protein sequences obtained using ProHap (https://github.com/ProGenNo/ProHap) on the data set of phased genotypes published by the Human Pangenome Reference Consotruim (HPRC), first release (https://github.com/human-pangenomics/hpp_pangenome_resources), 44 samples. We used Ensembl v.110 for the mapping of coordinates between genes, exons, and transcripts.

This repository contains one database created using all 43 samples of the HPRC release (the haplotypes of the sample NA21309 did not encode any non-canonical sequences), and then a database for each of the 43 samples separately. No filtering on allele frequency or haplotype frequency was applied in any of the databases. The complete configuration file for the ProHap run is attached to this repository.

There is one compressed directory for each of the databases, containing the following files:



F1: The concatenated fasta file ready to be used with search engines, contains the following:



Protein haplotype sequences obtained by ProHap

Reference proteome as per Ensembl v. 110

Contaminant sequences from the cRAP project (https://www.thegpm.org/crap/)

For this dataset, only the simplified format is provided. The simplified fasta contains only the artificial protein identifier and the matching gene name, and is optimised for compatibility with a wide range of tools. For annotation of peptides using the PeptideAnnotator, please provide the header (F1.2) in addition to the fasta file. 



F2: Additional information about the haplotype sequences, to be used for mapping identified peptides to the original haplotypes

F3: Translations of haplotype cDNA sequences, before merging with the reference proteome


For further description of the files, please refer to https://github.com/ProGenNo/ProHap/wiki/Output-files.

For the usage of these databases with search engines, and downstream anaylsis of identified peptides, please refer to the project's wiki page: https://github.com/ProGenNo/ProHap/wiki/Using-the-database-for-proteomic-searches.

When using these databases in your publication, please cite: Vašíček, J., Kuznetsova, K.G., Skiadopoulou, D. et al. ProHap enables human proteomic database generation accounting for population diversity. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02506-0
DOI: 10.15468/dl.57bdpc
title: Occurrence Download

description: A dataset containing 1382504 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is India",
 "GadmGid is IND.4_1",
 "OccurrenceStatus is Present",
 "Year 2000-2024"
 ]
}

 The dataset includes 1382504 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029553-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v69kuv
title: Occurrence Download

description: A dataset containing 1382504 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is India",
 "GadmGid is IND.4_1",
 "OccurrenceStatus is Present",
 "Year 2000-2024"
 ]
}

 The dataset includes 1382504 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029554-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.55qvp8
title: Occurrence Download

description: A dataset containing 725 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((35.32942 36.17352,54.40626 36.17352,54.40626 47.31234,35.32942 47.31234,35.32942 36.17352))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Heracleum mantegazzianum Sommier & Levier, Heracleum sosnowskyi Manden.)"
 ]
}

 The dataset includes 725 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029556-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7xjs4e
title: Occurrence Download

description: A dataset containing 212 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Larix gmelinii (Rupr.) Rupr."
 ]
}

 The dataset includes 212 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029558-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fd4pq5
title: Occurrence Download

description: A dataset containing 55762 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Greenland",
 "Geometry POLYGON((-47.12997 60.579,-46.60425 60.79781,-46.21777 60.95127,-45.85687 61.14735,-45.64942 61.34627,-45.39082 61.56224,-44.82247 61.48267,-44.66618 61.1303,-44.68323 60.69835,-44.32232 60.33745,-44.16603 60.05896,-44.08078 59.87709,-43.92481 59.61441,-43.00908 59.82192,-42.71135 60.21438,-42.51738 60.76923,-42.40009 61.04891,-41.97155 61.51354,-41.84524 62.40221,-41.07837 62.96157,-40.76711 63.43522,-40.52352 63.61566,-40.18971 63.94046,-39.98671 64.369,-39.86943 64.81108,-39.12511 65.37044,-37.72671 65.44262,-36.72527 65.41104,-36.7388 65.69072,-36.46363 65.73583,-35.44866 65.98845,-34.94342 66.13731,-33.43675 66.63352,-32.79619 67.46354,-32.00226 67.80638,-28.27618 68.25296,-25.54703 68.62738,-23.00609 69.46533,-22.21666 69.71344,-21.21974 70.13747,-21.17914 70.71037,-21.17011 71.55843,-20.20025 73.27712,-17.02451 74.80184,-16.50547 77.57076,-15.34375 79.96255,-12.43944 80.4409,-8.57842 82.59351,-19.33097 83.64226,-25.34459 84.15478,-29.99148 84.29145,-36.6543 84.53063,-45.53806 84.05227,-58.59036 83.74476,-60.19315 82.23622,-62.41615 81.61157,-65.85171 81.09715,-68.64425 80.2153,-71.03261 79.24158,-73.89864 78.3781,-73.34748 76.88997,-70.22424 75.98975,-65.48427 75.23649,-61.5343 75.18138,-57.93339 74.28115,-56.39015 70.71699,-55.1776 68.43886,-54.27737 65.99539,-50.87856 62.41286,-49.39043 60.79612,-47.35114 60.26334,-47.12997 60.579))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 55762 records from 191 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029557-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/5gk-r1b-rn9
title: †Hesperorthidae Schuchert & Cooper, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/aar-kxq-42y
title: †Hesperorthidae Schuchert & Cooper, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/f93-xcf-5wt
title: †Hesperorthidae Schuchert & Cooper, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/jrh-y6c-qva
title: †Hesperorthidae Schuchert & Cooper, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/r8c-3fv-92r
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/v75-12t-3ww
title: †Hesperorthidae Schuchert & Cooper, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/fwf-wzp-cm9
title: †Hesperorthidae Schuchert & Cooper, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/l9a-n97-v03
title: †Parastrophina Schuchert & LeVene, 1929

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/nnr-8rb-mw5
title: †Hesperorthidae Schuchert & Cooper, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/fkj-tpp-0pl
title: †Sowerbyella Jones, 1928

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/hm4-kjl-3fs
title: †Hesperorthidae Schuchert & Cooper, 1931

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5fq-9z7-dmx
title: †Sowerbyella Jones, 1928

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/mw1-963-rdj
title: †Sowerbyella Jones, 1928

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.15468/dl.mv8gdj
title: Occurrence Download

description: A dataset containing 1342084 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Peru",
 "OccurrenceStatus is Present",
 "StateProvince is Loreto"
 ]
}

 The dataset includes 1342084 records from 568 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010837-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/4vx-25d-rk2
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/hcb-5t0-ara
title: †Sowerbyella Jones, 1928

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/av2-qxz-l6j
title: †Sowerbyella Jones, 1928

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ztg-qgt-41j
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/387-pxt-fam
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/c14-8mm-9ad
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/brh-yby-h6m
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/m91-eze-nq1
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/735-2c7-2wb
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wh6-xgz-ffz
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/96k-9kh-d7r
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vdq-22h-ap5
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/efb-efa-3gc
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/mqz-k52-ak9
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vhq-q37-hqk
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xxw-k2q-xe8
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1gc-k6t-h27
title: †Eoplectodonta Kozlowski, 1929

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/r4b-k6l-q6n
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/rbx-26v-8pq
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/tqk-grn-6vv
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bxs-np1-8az
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/x1d-m9w-nsd
title: †Eoplectodonta Kozlowski, 1929

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/3ay-zsg-a6t
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/pgm-qac-7h0
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/z61-mx9-657
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.