cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.g6hnd5
title: Occurrence Download

description: A dataset containing 9318 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eugenia uniflora L."
 ]
}

 The dataset includes 9318 records from 325 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139919-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qu3yxm
title: Occurrence Download

description: A dataset containing 5985 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "or" : [
 "TaxonKey is Daucus carota Mill., 1768",
 "TaxonKey is Daucus carota L."
 ]
 }
 ]
}

 The dataset includes 5985 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0385083-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/mer99q
title: Swedish Malaise Trap Project (SMTP) - Ichneumoninae excl Phaeogenini

description: Occurrences in this dataset on Swedish Insects have been identified from specimens collected from for the Swedish Malaise Project (SMTP), an inventory funded by the Swedish Species Information Centre (ArtDatabanken). These records comprise the foundation for recent estimates on the size and composition of the Swedish insect fauna, published herein as sample-based datasets.
DOI: 10.15468/dl.6m2umd
title: Occurrence Download

description: A dataset containing 482052 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eupatorium cannabinum L."
 ]
}

 The dataset includes 482052 records from 1628 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139933-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29264663
title: PBFL

description: PBFL
DOI: 10.6084/m9.figshare.29264663.v1
title: PBFL

description: PBFL
DOI: 10.6084/m9.figshare.29261957
title: Biogeochemical dynamics of major elements in municipal solid waste landfills – drivers of environmental and health risks

description: Supplementary tables (Table S1-S8) for the manuscript "Biogeochemical dynamics of major elements in municipal solid waste landfills – drivers of environmental and health risks" submitted to <i>One Earth</i>.Table S1: Elemental compositionTable S2: Distribution of elements in different phases after degradation in landfill conditionsTable S3: Element conversion rateTable S4: Landfill-related human health risk ratioTable S5: Mined waste compositionTable S6: CWD, UCWD, WEI, and uncertainties of WEI for all administrative divisionsTable S7: Default values of WEI correction factorsTable S8: Minimum, maximum, default values, and distributions of WEI pollutant-specific parameters
DOI: 10.6084/m9.figshare.29261957.v1
title: Biogeochemical dynamics of major elements in municipal solid waste landfills – drivers of environmental and health risks

description: Supplementary tables (Table S1-S8) for the manuscript "Biogeochemical dynamics of major elements in municipal solid waste landfills – drivers of environmental and health risks" submitted to <i>One Earth</i>.Table S1: Elemental compositionTable S2: Distribution of elements in different phases after degradation in landfill conditionsTable S3: Element conversion rateTable S4: Landfill-related human health risk ratioTable S5: Mined waste compositionTable S6: CWD, UCWD, WEI, and uncertainties of WEI for all administrative divisionsTable S7: Default values of WEI correction factorsTable S8: Minimum, maximum, default values, and distributions of WEI pollutant-specific parameters
DOI: 10.15468/dl.6br9a3
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material sample)"
 ]
 }
 },
 "TaxonKey is Lepilemur scottorum Lei, Engberg, Andriantompohavana, McGuire, Mittermeier, Zaonarivelo, Brenneman & Louis Jr., 2008",
 "Continent is one of (Africa)",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029296-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10442848
title: ESCOTT Missense Mutational Effect Predictions for Entire Human Proteome

description: This dataset contains ESCOTT single point mutation predictions of about ~19000 human proteins.

Description of the data and file structure

Data of each human protein is in a folder named after its uniprotID. Inside uniprotID folder, there is a subfolder called results that contain all input and output. An example results folder for uniprotID A0A0B4J245 will contain the following files:





Raw escott predictions (output file): A0A0B4J245_normPred_evolCombi_escott.txt




Ranksorted (between 0-1) escott predictions in csv format (output file): A0A0B4J245_normPred_evolCombiTransposedRanksorted_escott.csv




Colabfold MSA file (input file): aliA0A0B4J245.fasta




Bzipped pdb file (input file): AF-A0A0B4J245-F1-model_v4.pdb.tar.bz2




JET2 file containing JET, PC and CV scores for each amino acid (output file) : A0A0B4J245_jet_escott.res




Configuration file containing default parameters (output file): default.conf




Log file (output file): escott.log
DOI: 10.5281/zenodo.10442849
title: ESCOTT Missense Mutational Effect Predictions for Entire Human Proteome

description: This dataset contains ESCOTT single point mutation predictions of about ~19000 human proteins.

Description of the data and file structure

Data of each human protein is in a folder named after its uniprotID. Inside uniprotID folder, there is a subfolder called results that contain all input and output. An example results folder for uniprotID A0A0B4J245 will contain the following files:





Raw escott predictions (output file): A0A0B4J245_normPred_evolCombi_escott.txt




Ranksorted (between 0-1) escott predictions in csv format (output file): A0A0B4J245_normPred_evolCombiTransposedRanksorted_escott.csv




Colabfold MSA file (input file): aliA0A0B4J245.fasta




Bzipped pdb file (input file): AF-A0A0B4J245-F1-model_v4.pdb.tar.bz2




JET2 file containing JET, PC and CV scores for each amino acid (output file) : A0A0B4J245_jet_escott.res




Configuration file containing default parameters (output file): default.conf




Log file (output file): escott.log
DOI: 10.5281/zenodo.10577421
title: ESCOTT Missense Mutational Effect Predictions for Entire Human Proteome

description: This dataset contains ESCOTT single point mutation predictions of about ~19000 human proteins.

Description of the data and file structure

Data of each human protein is in a folder named after its uniprotID. Inside uniprotID folder, there is a subfolder called results that contain all input and output. An example results folder for uniprotID A0A0B4J245 will contain the following files:





Raw escott predictions (output file): A0A0B4J245_normPred_evolCombi_escott.txt




Ranksorted (between 0-1) escott predictions in csv format (output file): A0A0B4J245_normPred_evolCombiTransposedRanksorted_escott.csv




Colabfold MSA file (input file): aliA0A0B4J245.fasta




Bzipped pdb file (input file): AF-A0A0B4J245-F1-model_v4.pdb.tar.bz2




JET2 file containing JET, PC and CV scores for each amino acid (output file) : A0A0B4J245_jet_escott.res




Configuration file containing default parameters (output file): default.conf




Log file (output file): escott.log
DOI: 10.5281/zenodo.10670914
title: ESCOTT Missense Mutational Effect Predictions for Entire Human Proteome

description: This dataset contains ESCOTT single point mutation predictions of about ~19000 human proteins.

Description of the data and file structure

Data of each human protein is in a folder named after its uniprotID. Inside uniprotID folder, there is a subfolder called results that contain all input and output. An example results folder for uniprotID A0A0B4J245 will contain the following files:





Raw escott predictions (output file): A0A0B4J245_normPred_evolCombi_escott.txt




Ranksorted (between 0-1) escott predictions in csv format (output file): A0A0B4J245_normPred_evolCombiTransposedRanksorted_escott.csv




Colabfold MSA file (input file): aliA0A0B4J245.fasta




Bzipped pdb file (input file): AF-A0A0B4J245-F1-model_v4.pdb.tar.bz2




JET2 file containing JET, PC and CV scores for each amino acid (output file) : A0A0B4J245_jet_escott.res




Configuration file containing default parameters (output file): default.conf




Log file (output file): escott.log
DOI: 10.15468/dl.36debv
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (India, China, Myanmar, Nepal, Bhutan, Bangladesh, Pakistan, Afghanistan)",
 "TaxonKey is Baltia butleri (Moore, 1882)"
 ]
}

 The dataset includes 38 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029298-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ytq97v
title: Occurrence Download

description: A dataset containing 710 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ephedra pseudodistachya Pachom., Ephedra regeliana Florin, Ephedra rhytidosperma Pachom., Ephedra rituensis Y.Yang, D.Z.Fu & G.H.Zhu, Ephedra sarcocarpa Aitch. & Hemsl., Ephedra saxatilis (Stapf) Royle ex Florin, Ephedra sinaica Riedl, Ephedra sinica Stapf, Ephedra strobilacea Bunge, Ephedra transitoria Riedl)",
 "HasCoordinate is true",
 "Year is greater than 1900"
 ]
}

 The dataset includes 710 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029297-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15619522
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS250608p Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS250608p Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.5281/zenodo.15619523
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS250608p Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS250608p Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.15468/dl.b3bmmz
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material sample)"
 ]
 }
 },
 "TaxonKey is Lepilemur seali Louis Jr., Engberg, Lei, Geng, Sommer, Randriamampionona, Randriamanana, Zaonarivelo et al., 2006",
 "Continent is one of (Africa)",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029299-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sgxqyu
title: Occurrence Download

description: A dataset containing 170808 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((128.49097 -2.96561,132.31872 -2.96561,132.31872 1.59747,128.49097 1.59747,128.49097 -2.96561))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 170808 records from 264 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029283-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10435331
title: PRESCOTT/ESCOTT/iGEMME mutational effect predictions of all single point mutations for ~3000 proteins

description: This dataset contains all necessary data to reproduce our analyses on ~3000 proteins:

It is made up of 4 compressed datasets. 



All colabfold MSAs and structures for ~3000 proteins: colabfold-sequences-structures-3000-proteins.tar.bz2

All escott prediction: escott-v-1-6-0-max-two-components-colabfold-msas-entire-single-point-mutations-cvRC7.tgz

All igemme predictions: escott-v-1-6-0-tjet-only-colabfold-msas-entire-single-point-mutations.tgz

All gnomad v4.0.0 csv files used for prescott predictions: gnomadv4-0-0-csv-files.tgz


The dataset contains list of 500 proteins used in determining PRESCOTT coefficients in TRAINING-all_gene_names_v4_set1_no_acmg.txt. 

Furthermore, the list of 1883 proteins used to measure for testing purpose is given in TESTING-all_gene_names_v4_set1_with_acmg.txt.
DOI: 10.5281/zenodo.10435332
title: PRESCOTT/ESCOTT/iGEMME mutational effect predictions of all single point mutations for ~3000 proteins

description: This dataset contains all necessary data to reproduce our analyses on ~3000 proteins:

It is made up of 4 compressed datasets. 



All colabfold MSAs and structures for ~3000 proteins: colabfold-sequences-structures-3000-proteins.tar.bz2

All escott prediction: escott-v-1-6-0-max-two-components-colabfold-msas-entire-single-point-mutations-cvRC7.tgz

All igemme predictions: escott-v-1-6-0-tjet-only-colabfold-msas-entire-single-point-mutations.tgz

All gnomad v4.0.0 csv files used for prescott predictions: gnomadv4-0-0-csv-files.tgz
DOI: 10.5281/zenodo.10438640
title: PRESCOTT/ESCOTT/iGEMME mutational effect predictions of all single point mutations for ~3000 proteins

description: This dataset contains all necessary data to reproduce our analyses on ~3000 proteins:

It is made up of 4 compressed datasets. 



All colabfold MSAs and structures for ~3000 proteins: colabfold-sequences-structures-3000-proteins.tar.bz2

All escott prediction: escott-v-1-6-0-max-two-components-colabfold-msas-entire-single-point-mutations-cvRC7.tgz

All igemme predictions: escott-v-1-6-0-tjet-only-colabfold-msas-entire-single-point-mutations.tgz

All gnomad v4.0.0 csv files used for prescott predictions: gnomadv4-0-0-csv-files.tgz
DOI: 10.5281/zenodo.15087512
title: PRESCOTT/ESCOTT/iGEMME mutational effect predictions of all single point mutations for ~3000 proteins

description: This dataset contains all necessary data to reproduce our analyses on ~3000 proteins:

It is made up of 4 compressed datasets. 



All colabfold MSAs and structures for ~3000 proteins: colabfold-sequences-structures-3000-proteins.tar.bz2

All escott prediction: escott-v-1-6-0-max-two-components-colabfold-msas-entire-single-point-mutations-cvRC7.tgz

All igemme predictions: escott-v-1-6-0-tjet-only-colabfold-msas-entire-single-point-mutations.tgz

All gnomad v4.0.0 csv files used for prescott predictions: gnomadv4-0-0-csv-files.tgz


The dataset contains list of 500 proteins used in determining PRESCOTT coefficients in TRAINING-all_gene_names_v4_set1_no_acmg.txt. 

Furthermore, the list of 1883 proteins used to measure for testing purpose is given in TESTING-all_gene_names_v4_set1_with_acmg.txt.
DOI: 10.15468/dl.c2smkr
title: Occurrence Download

description: A dataset containing 593 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (India, China, Myanmar, Nepal, Bhutan, Bangladesh, Pakistan, Afghanistan)",
 "TaxonKey is Pieris brassicae (Linnaeus, 1758)"
 ]
}

 The dataset includes 593 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029302-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7zj4nc
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material sample)"
 ]
 }
 },
 "TaxonKey is Lepilemur septentrionalis Rumpler & Albignac, 1975",
 "Continent is one of (Africa)",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029303-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15619525
title: Parental  exposure to wet and dry conditions shapes the viability and thermotolerance of eggs in Aedes aegypti
DOI: 10.5281/zenodo.10441520
title: iGEMME Missense Mutational Effect Predictions for Entire Human Proteome

description: This dataset contains iGEMME single point mutation predictions of about ~19000 human proteins. In iGEMME predictions, only evolutionary data coming from multiple sequence alignment files is used. 

Description of the data and file structure

This dataset contains iGEMME predictions for all human proteins. 

Data of each human protein is in a folder named after its uniprotID. Inside uniprotID folder, there is a subfolder called results that contain all input and output. An example results folder for uniprotID A0A0B4J245 will contain the following files:





Raw igemme predictions (output file): A0A0B4J245_normPred_evolCombi_igemme.txt




Ranksorted (between 0-1) igemme predictions in csv format (output file): A0A0B4J245_normPred_evolCombiTransposedRanksorted_igemme.csv




Colabfold MSA file (input file): aliA0A0B4J245.fasta




JET2 file containing JET scores for each amino acid (output file) : A0A0B4J245_jet_igemme.res




Configuration file containing default parameters (output file): default.conf




Log file (output file): igemme.log
DOI: 10.5281/zenodo.10441521
title: iGEMME Missense Mutational Effect Predictions for Entire Human Proteome

description: This dataset contains iGEMME single point mutation predictions of about ~19000 human proteins. In iGEMME predictions, only evolutionary data coming from multiple sequence alignment files is used. 

Description of the data and file structure

This dataset contains iGEMME predictions for all human proteins. 

Data of each human protein is in a folder named after its uniprotID. Inside uniprotID folder, there is a subfolder called results that contain all input and output. An example results folder for uniprotID A0A0B4J245 will contain the following files:





Raw igemme predictions (output file): A0A0B4J245_normPred_evolCombi_igemme.txt




Ranksorted (between 0-1) igemme predictions in csv format (output file): A0A0B4J245_normPred_evolCombiTransposedRanksorted_igemme.csv




Colabfold MSA file (input file): aliA0A0B4J245.fasta




JET2 file containing JET scores for each amino acid (output file) : A0A0B4J245_jet_igemme.res




Configuration file containing default parameters (output file): default.conf




Log file (output file): igemme.log
DOI: 10.5281/zenodo.10671864
title: iGEMME Missense Mutational Effect Predictions for Entire Human Proteome

description: This dataset contains iGEMME single point mutation predictions of about ~19000 human proteins. In iGEMME predictions, only evolutionary data coming from multiple sequence alignment files is used. 

Description of the data and file structure

This dataset contains iGEMME predictions for all human proteins. 

Data of each human protein is in a folder named after its uniprotID. Inside uniprotID folder, there is a subfolder called results that contain all input and output. An example results folder for uniprotID A0A0B4J245 will contain the following files:





Raw igemme predictions (output file): A0A0B4J245_normPred_evolCombi_igemme.txt




Ranksorted (between 0-1) igemme predictions in csv format (output file): A0A0B4J245_normPred_evolCombiTransposedRanksorted_igemme.csv




Colabfold MSA file (input file): aliA0A0B4J245.fasta




JET2 file containing JET scores for each amino acid (output file) : A0A0B4J245_jet_igemme.res




Configuration file containing default parameters (output file): default.conf




Log file (output file): igemme.log
DOI: 10.15468/dl.qac43r
title: Occurrence Download

description: A dataset containing 483 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is one of (Ethiopia, Kenya)",
 "OccurrenceStatus is Present",
 "TaxonKey is Prosopis juliflora (Sw.) DC.",
 "Year 1950-2024"
 ]
}

 The dataset includes 483 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029307-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8rhbeg
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material sample)"
 ]
 }
 },
 "TaxonKey is Lepilemur tymerlachsoni Louis Jr., Engberg, Lei, Geng, Sommer, Randriamampionona, Randriamanana, Zaonarivelo et al., 2006",
 "Continent is one of (Africa)",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 39 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029305-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15619538
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS250608p Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS250608p Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.5281/zenodo.15619539
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS250608p Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS250608p Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract