cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.g9euq2
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lamprotornis splendidus",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003696-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9dgm9s
title: Occurrence Download

description: A dataset containing 241269 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Argentina",
 "OccurrenceStatus is Present",
 "TaxonKey is Myiopsitta monachus"
 ]
}

 The dataset includes 241269 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003666-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pdq7cz
title: Occurrence Download

description: A dataset containing 51208 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Copsychus saularis",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 51208 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003634-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x4ub8k
title: Occurrence Download

description: A dataset containing 139 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Parthenium integrifolium",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 139 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003697-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.48xwap
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lamprotornis superbus",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 17 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003698-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.953p9f
title: Occurrence Download

description: A dataset containing 386 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lamprotornis superbus",
 "Country is United Arab Emirates",
 "HasCoordinate is true"
 ]
}

 The dataset includes 386 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003699-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.abhxqs
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lamprotornis superbus",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003700-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nw43jq
title: Occurrence Download

description: A dataset containing 5623 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Enicurus scouleri",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5623 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003701-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17148766
title: Life at the extremes: Maximally divergent microbes with similar genomic signatures linked to extreme environments (Dataset)

description: Dataset Description

We curated a dataset of 693 high-quality extremophile microbial genomes, spanning diverse environmental conditions defined by both temperature and pH optima. This includes psychrophiles, mesophiles, thermophiles, hyperthermophiles, acidophiles, and alkaliphiles, representing broad taxonomic coverage across bacteria and archaea. Genome assemblies were collected through a comprehensive review of primary literature and cross-referenced with the Genome Taxonomy Database to ensure accuracy and taxonomic consistency.

The dataset was organized into two subsets:





Temperature Dataset (598 genomes): 148 psychrophiles, 190 mesophiles, 183 thermophiles, and 77 hyperthermophiles.




pH Dataset (186 genomes): 100 acidophiles and 86 alkaliphiles.



A total of 91 genomes occur in both subsets, either as mesophiles adapted to acidic/alkaline conditions or as polyextremophiles capable of surviving under both temperature and pH extremes.

To ensure compatibility with downstream machine learning analyses, we applied a genome proxy approach in which each genome was represented by pseudo-concatenated, randomly selected subsequences. This alignment-free strategy enabled the calculation of canonical 𝑘-mer frequency vectors and the identification of convergent genomic signatures across maximally divergent bacteria–archaea pairs.

Technical Information





Assemblies.zip: Contains the curated set of extremophile genome assemblies in FASTA format.




Extremophiles_metadata.tsv: Provides metadata including taxonomy, environmental category (temperature/pH class), and isolation details for each genome.



General description of FASTA files:Each genome FASTA file contains sequence data where entries begin with a header line (>), followed by sequence identifiers.

Metadata linkage:Sequence identifiers in the FASTA assemblies can be directly mapped to the metadata file (Extremophiles_metadata.tsv), which contains corresponding environmental and taxonomic information.
DOI: 10.5281/zenodo.17148767
title: Life at the extremes: Maximally divergent microbes with similar genomic signatures linked to extreme environments (Dataset)

description: Dataset Description

We curated a dataset of 693 high-quality extremophile microbial genomes, spanning diverse environmental conditions defined by both temperature and pH optima. This includes psychrophiles, mesophiles, thermophiles, hyperthermophiles, acidophiles, and alkaliphiles, representing broad taxonomic coverage across bacteria and archaea. Genome assemblies were collected through a comprehensive review of primary literature and cross-referenced with the Genome Taxonomy Database to ensure accuracy and taxonomic consistency.

The dataset was organized into two subsets:





Temperature Dataset (598 genomes): 148 psychrophiles, 190 mesophiles, 183 thermophiles, and 77 hyperthermophiles.




pH Dataset (186 genomes): 100 acidophiles and 86 alkaliphiles.



A total of 91 genomes occur in both subsets, either as mesophiles adapted to acidic/alkaline conditions or as polyextremophiles capable of surviving under both temperature and pH extremes.

To ensure compatibility with downstream machine learning analyses, we applied a genome proxy approach in which each genome was represented by pseudo-concatenated, randomly selected subsequences. This alignment-free strategy enabled the calculation of canonical 𝑘-mer frequency vectors and the identification of convergent genomic signatures across maximally divergent bacteria–archaea pairs.

Technical Information





Assemblies.zip: Contains the curated set of extremophile genome assemblies in FASTA format.




Extremophiles_metadata.tsv: Provides metadata including taxonomy, environmental category (temperature/pH class), and isolation details for each genome.



General description of FASTA files:Each genome FASTA file contains sequence data where entries begin with a header line (>), followed by sequence identifiers.

Metadata linkage:Sequence identifiers in the FASTA assemblies can be directly mapped to the metadata file (Extremophiles_metadata.tsv), which contains corresponding environmental and taxonomic information.
DOI: 10.15468/dl.j3k953
title: Occurrence Download

description: A dataset containing 335 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Pascopyrum smithii",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 335 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003702-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13130529
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.sm4zjd
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Onychognathus tristramii",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003703-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4vyxsm
title: Occurrence Download

description: A dataset containing 11642 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ficedula hyperythra",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 11642 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003704-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gdpr5e
title: Occurrence Download

description: A dataset containing 15850436 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia",
 "Year is 2003"
 ]
}

 The dataset includes 15850436 records from 2438 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003670-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k9ta8f
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cosmianthemum melinhense D.V.Hai, Z.L.Lin & Y.F.Deng"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006912-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m9ynbg
title: Occurrence Download

description: A dataset containing 3967776 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caryophyllaceae",
 "HasCoordinate is true",
 "Continent is Europe",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 3967776 records from 2451 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013011-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.633m9c
title: Occurrence Download

description: A dataset containing 260 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Torula fici"
 ]
}

 The dataset includes 260 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063882-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rkq6h6
title: Occurrence Download

description: A dataset containing 6601 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhizophora apiculata Blume"
 ]
}

 The dataset includes 6601 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0056590-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w5e5t7
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Glochidion punctatum Pax & K.Hoffm."
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012920-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fu9z5j
title: Occurrence Download

description: A dataset containing 2700 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Emmotum nitens (Benth.) Miers"
 ]
}

 The dataset includes 2700 records from 103 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000672-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qnwax7
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Setoeolis Baba, 1965"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0325143-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rv34u5
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Dipsas bicolor (Günther, 1895)"
 ]
}

 The dataset includes 29 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076882-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0lzj63
title: Occurrence Download

description: A dataset containing 1262261 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-59.80957 -13.26561,-45.83496 -15.22483,-43.5498 1.29188,-58.93066 2.25821,-59.80957 -13.26561))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1262261 records from 751 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000676-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rj4qm7
title: Occurrence Download

description: A dataset containing 133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cirsium alatum (S.G.Gmel.) Bobrov",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 133 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079080-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yzhr6q
title: Occurrence Download

description: A dataset containing 14448 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coronopus didymus (L.) Sm."
 ]
}

 The dataset includes 14448 records from 286 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0265836-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hvcrfr
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Natural History Museum (London) Collection Specimens",
 "TaxonKey is Brachiones przewalskii (Büchner, 1889)"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009683-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kq6a36
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-76.50755 2.15644,-76.25023 2.15644,-76.25023 2.54915,-76.50755 2.54915,-76.50755 2.15644))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Araceae"
 ]
}

 The dataset includes 27 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079075-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t464jf
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepidoblepharis colombianus Mechler, 1968"
 ]
}

 The dataset includes 21 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012950-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2e2kj8
title: Occurrence Download

description: A dataset containing 981985 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Ranunculus alpestris L., Ranunculus aconitifolius L., Pyrus pyraster (L.) Burgsd., Pulicaria vulgaris Gaertn., Pulicaria dysenterica (L.) Bernh., Puccinellia maritima (Huds.) Parl., Prunus virginiana L., Prunus tenella Batsch, Prunus fruticosa Pall., Prunella laciniata (L.) L., Prunella grandiflora (L.) Turra, Primula vulgaris Hill, Primula veris L., Primula scotica Hook., Primula minima L., Primula hirsuta All., Primula glutinosa Wulfen, Primula farinosa L., Potentilla sterilis (L.) Garcke)"
 ]
}

 The dataset includes 981985 records from 1840 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061160-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9svmj4
title: Occurrence Download

description: A dataset containing 138 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Clelia scytalina (Cope, 1867)"
 ]
}

 The dataset includes 138 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012796-241024112534372/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.27360612
title: Gene-sets

description: List of gene-sets used in the paper: <br>Huguet et al 2024
DOI: 10.6084/m9.figshare.27360612.v1
title: Gene-sets

description: List of gene-sets used in the paper: <br>Huguet et al 2024
DOI: 10.15468/dl.kvgu6r
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"TAXON_KEY","value":"2514411","matchCase":false},{"type":"equals","key":"OCCURRENCE_STATUS","value":"PRESENT","matchCase":false},{"type":"equals","key":"HAS_COORDINATE","value":"true","matchCase":false},{"type":"equals","key":"HAS_GEOSPATIAL_ISSUE","value":"false","matchCase":false},{"type":"lessThan","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"in","key":"YEAR","values":["2008","2009","2010","2011","2012","2013","2014","2015","2016","2017","2018","2019","2020","2021","2022","2023","2024"],"matchCase":false},{"type":"in","key":"BASIS_OF_RECORD","values":["LIVING_SPECIMEN","HUMAN OBSERVATION","OBSERVATION","OCCURRENCE","MACHINE_OBSERVATION"],"matchCase":false}]}

 The dataset includes 14 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012798-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8qc9z2
title: Occurrence Download

description: A dataset containing 2755 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"TAXON_KEY","value":"1747141","matchCase":false},{"type":"equals","key":"OCCURRENCE_STATUS","value":"PRESENT","matchCase":false},{"type":"equals","key":"HAS_COORDINATE","value":"true","matchCase":false},{"type":"equals","key":"HAS_GEOSPATIAL_ISSUE","value":"false","matchCase":false},{"type":"lessThan","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"in","key":"YEAR","values":["2008","2009","2010","2011","2012","2013","2014","2015","2016","2017","2018","2019","2020","2021","2022","2023","2024"],"matchCase":false},{"type":"in","key":"BASIS_OF_RECORD","values":["LIVING_SPECIMEN","HUMAN OBSERVATION","OBSERVATION","OCCURRENCE","MACHINE_OBSERVATION"],"matchCase":false}]}

 The dataset includes 2755 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012797-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.