cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.fzw276
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year is greater than or equal to 1981",
 "Year is less than or equal to 2010",
 "HasCoordinate is true",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "ScientificName is Cryptogramma crispa (L.) R.Br.",
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters is less than or equal to 1000"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002346-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n8qdgd
title: Occurrence Download

description: A dataset containing 743 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Girella punctata Gray, 1835",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 743 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002345-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q5faq8
title: Occurrence Download

description: A dataset containing 174 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Benthic biodiversity of Campana Archipelago, Katalalixar National Reserve (Aysén, Chile)"
 ]
}

 The dataset includes 174 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002347-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hh2dck
title: Occurrence Download

description: A dataset containing 7873269 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Acipenser baerii Brandt, 1869, Acipenser ruthenus Linnaeus, 1758, Acipenser transmontanus Richardson, 1836, Carassius auratus (Linnaeus, 1758), Carassius carassius (Linnaeus, 1758), Coregonus lavaretus (Linnaeus, 1758), Ctenopharyngodon idella (Valenciennes, 1844), Cyprinus carpio Linnaeus, 1758, Esox lucius Linnaeus, 1758, Hypophthalmichthys molitrix (Valenciennes, 1844), Hypophthalmichthys nobilis (Richardson, 1845), Leuciscus idus (Linnaeus, 1758), Leuciscus leuciscus (Linnaeus, 1758), Micropterus salmoides (Lacepède, 1802), Oncorhynchus mykiss (Walbaum, 1792), Oreochromis mossambicus (Peters, 1852), Oreochromis niloticus (Linnaeus, 1758), Perca fluviatilis Linnaeus, 1758, Rutilus rutilus (Linnaeus, 1758), Salmo trutta Linnaeus, 1758, Salvelinus alpinus (Linnaeus, 1758), Salvelinus fontinalis (Mitchill, 1814), Sander lucioperca (Linnaeus, 1758), Scardinius erythrophthalmus (Linnaeus, 1758), Silurus glanis Linnaeus, 1758, Thymallus thymallus (Linnaeus, 1758), Tinca tinca (Linnaeus, 1758), Acipenser gueldenstaedtii Brandt & Ratzeburg, 1833, Carassius gibelio (Bloch, 1782), Polyodon spathula (Walbaum, 1792))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7873269 records from 1726 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002319-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rkhwt3
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leiothrix lutea",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 55 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003602-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jsjs26
title: Occurrence Download

description: A dataset containing 144 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 Oxytheca perfoliata",
 "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 144 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003603-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17172590
title: DORAnet supplementary bundle (code + datasets)

description: This archive contains the scripts and datasets used in Zhang et al., Digital Discovery (2025).
DOI: 10.5281/zenodo.17172591
title: DORAnet supplementary bundle (code + datasets)

description: This archive contains the scripts and datasets used in Zhang et al., Digital Discovery (2025).
DOI: 10.15468/dl.k2mdw2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leiothrix lutea",
 "Country is Slovenia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003604-250920141307145/datasets/export for details.
DOI: 10.15468/dl.cep7aw
title: Occurrence Download

description: A dataset containing 7845 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leiothrix lutea",
 "Country is Spain",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7845 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003605-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jk2yvw
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leiothrix lutea",
 "Country is Togo",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003606-250920141307145/datasets/export for details.
DOI: 10.5281/zenodo.17172592
title: microbetag : building a thorough database of genome-scale KO annotations

description: In this repository we keep internal data for the microbetag microbial co-occurrence network annotator.

microbetag makes use of 2-column files for each genome, indicating the KO term found and a KEGG module in which this terms takes part into. As a single KO term might participates in more than one KEGG modules, the same KO might be more than once in an annotation file. 






chem_xref.tar.gz



The MNXref namespace



The identifier of a chemical compound in an external resource [XREF]

The corresponding identifier in the MNXref namespace [MNX_ID]

The description given by the external resource [STRING]


MNXref 4.0 release notes: - The third column (evidence tag for the mapping) was suppressed - The descriptions were completed - Deprecated identifiers were moved into they own table below





gtdb_modelseed_gems.zip



for all the GTDB genomes their corresponding PATRIC annotations were gathered. Then, using modelseedpy we constructed their genome scale metabolic reconstructions





gtdb_kofam_scan_per_module.tar.gz



all representative genomes of GTDB (v.202) were parsed and their corresponding `.faa` files were retrieved from the NCBI FTP. Then the kofam_scan tool was used to annotate them and finally a manual script was used to keep KOs of each genome per module. 



SeedSet.pkl.gz


A pickle file with the seeds of each GEM included in the gtdb_modelseed_gems.zip file and related to the KEGG MODULES based on the seedId_keggId_module.tsv file you can find on microbetag's GitHub page.  Example:

PATRIC                                                                                        SeedSet373.172    [cpd00891, cpd00136, cpd00199, cpd01772, cpd00...397278.5   [cpd00891, cpd00136, cpd01772, cpd02698, cpd08...



NonSeedSet.pkl.gz


A pickle file with the non seeds of each GEM included in the gtdb_modelseed_gems.zip file and related to the KEGG MODULES based on the seedId_keggId_module.tsv file you can find on microbetag's GitHub page.  Example:

PATRIC                                                                                        NonSeedSet64187.548   [cpd00508, cpd00869, cpd00774, cpd03830, cpd00...74426.1719  [cpd00204, cpd00447, cpd20171, cpd03470, cpd00...



seeds_per_genome.pkl.gz


A pickle file with a binary representation of the seeds per genome .  Example:

                         cpd00493  cpd00296  cpd11431  cpd00063  cpd15717   ... 2162051.4          1         0         0         1         0         0         0         0         0         0  ...     





nonseeds_per_genome.pkl.gz

Like above for non-seeds.




phen_classes.zip

A list of pickle files with the re-trained classes of phenDB for the prediction of functional traits on a genome.
DOI: 10.5281/zenodo.6345382
title: microbetag : building a thorough database of genome-scale KO annotations

description: In this repository we keep internal data for the microbetag microbial co-occurrence network annotator.

microbetag makes use of 2-column files for each genome, indicating the KO term found and a KEGG module in which this terms takes part into. As a single KO term might participates in more than one KEGG modules, the same KO might be more than once in an annotation file. 






chem_xref.tar.gz



The MNXref namespace



The identifier of a chemical compound in an external resource [XREF]

The corresponding identifier in the MNXref namespace [MNX_ID]

The description given by the external resource [STRING]


MNXref 4.0 release notes: - The third column (evidence tag for the mapping) was suppressed - The descriptions were completed - Deprecated identifiers were moved into they own table below





gtdb_modelseed_gems.zip



for all the GTDB genomes their corresponding PATRIC annotations were gathered. Then, using modelseedpy we constructed their genome scale metabolic reconstructions





gtdb_kofam_scan_per_module.tar.gz



all representative genomes of GTDB (v.202) were parsed and their corresponding `.faa` files were retrieved from the NCBI FTP. Then the kofam_scan tool was used to annotate them and finally a manual script was used to keep KOs of each genome per module. 



SeedSet.pkl.gz


A pickle file with the seeds of each GEM included in the gtdb_modelseed_gems.zip file and related to the KEGG MODULES based on the seedId_keggId_module.tsv file you can find on microbetag's GitHub page.  Example:

PATRIC                                                                                        SeedSet373.172    [cpd00891, cpd00136, cpd00199, cpd01772, cpd00...397278.5   [cpd00891, cpd00136, cpd01772, cpd02698, cpd08...



NonSeedSet.pkl.gz


A pickle file with the non seeds of each GEM included in the gtdb_modelseed_gems.zip file and related to the KEGG MODULES based on the seedId_keggId_module.tsv file you can find on microbetag's GitHub page.  Example:

PATRIC                                                                                        NonSeedSet64187.548   [cpd00508, cpd00869, cpd00774, cpd03830, cpd00...74426.1719  [cpd00204, cpd00447, cpd20171, cpd03470, cpd00...



seeds_per_genome.pkl.gz


A pickle file with a binary representation of the seeds per genome .  Example:

                         cpd00493  cpd00296  cpd11431  cpd00063  cpd15717   ... 2162051.4          1         0         0         1         0         0         0         0         0         0  ...     





nonseeds_per_genome.pkl.gz

Like above for non-seeds.




phen_classes.zip

A list of pickle files with the re-trained classes of phenDB for the prediction of functional traits on a genome.
DOI: 10.15468/dl.5wd7zj
title: Occurrence Download

description: A dataset containing 337 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-122.52862 45.53194,-123.05225 45.08026,-122.97435 44.42261,-122.52862 43.19562,-120.21747 42.91819,-119.06189 43.56756,-118.29085 44.781,-118.54297 45.25237,-118.803 46.13737,-120.11923 46.16645,-121.55464 45.84331,-122.52862 45.53194))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Strix varia",
 "Year 2006-2016"
 ]
}

 The dataset includes 337 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003607-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qkspvv
title: Occurrence Download

description: A dataset containing 55 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 Oxytropis coerulea",
 "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 55 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003608-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3ea7gn
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-122.67577 45.65069,-123.00341 42.96991,-120.34135 42.54894,-117.74072 43.19426,-118.47791 45.97895,-120.68946 46.12107,-122.67577 45.65069))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Strix occidentalis",
 "Year 2006-2016"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003610-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p9gtyh
title: Occurrence Download

description: A dataset containing 192 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 Oxytropis kansuensis",
 "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 192 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003613-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fya3uy
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leiothrix lutea",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003612-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pjurms
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leiothrix lutea",
 "Country is United Arab Emirates",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003611-250920141307145/datasets/export for details.
DOI: 10.17632/wf48t9b7t6
title: Cingulate cortex shapes early postnatal development of social vocalizations

description: The common marmoset provides a unique opportunity to study the developmental trajectory of vocal behavior, and to track the consequences of early brain damage on aspects of social vocalizations. We created ACC lesions in neonatal marmosets and compared their pattern of vocalization to that of age-matched controls throughout the first 6 weeks of life. We found that while early life ACC lesions had little influence on the production of vocal calls, developmental changes to the quality of social contact calls and their associated sequential and acoustic characteristics were compromised. These animals made fewer social contact calls, and when they did, they were short, loud and monotonic. We further determined that damage to ACC in infancy results in a permanent alteration in downstream brain areas known to be involved in social vocalizations, such as the amygdala and periaqueductal gray. Namely, in the adult, these structures exhibited diminished GABA-immunoreactivity relative to control animals, likely reflecting disruption of the normal inhibitory balance following ACC deafferentation. Together, these data indicate that the normal development of social vocal behavior depends on the ACC and its interaction with other areas in the vocal network during early life.
DOI: 10.17632/wf48t9b7t6.1
title: Cingulate cortex shapes early postnatal development of social vocalizations

description: The common marmoset provides a unique opportunity to study the developmental trajectory of vocal behavior, and to track the consequences of early brain damage on aspects of social vocalizations. We created ACC lesions in neonatal marmosets and compared their pattern of vocalization to that of age-matched controls throughout the first 6 weeks of life. We found that while early life ACC lesions had little influence on the production of vocal calls, developmental changes to the quality of social contact calls and their associated sequential and acoustic characteristics were compromised. These animals made fewer social contact calls, and when they did, they were short, loud and monotonic. We further determined that damage to ACC in infancy results in a permanent alteration in downstream brain areas known to be involved in social vocalizations, such as the amygdala and periaqueductal gray. Namely, in the adult, these structures exhibited diminished GABA-immunoreactivity relative to control animals, likely reflecting disruption of the normal inhibitory balance following ACC deafferentation. Together, these data indicate that the normal development of social vocal behavior depends on the ACC and its interaction with other areas in the vocal network during early life.
DOI: 10.17632/yff7r65jzz
title: Iron sources and cycling during diagenetic transformations of Negev phosphorites (Israel)

description: The dataset comprises geochemical and mineralogical data generated in the course of this study. Table 1 summarizes iron (Fe) speciation and the concentrations of Fe, phosphorus (P), aluminum (Al), and total organic carbon (TOC) in the analyzed samples. Table 2 provides estimates of the impact of pyrite and Fe(II) oxidation on iron speciation. Table 3 reports mineral phase abundances (in wt%, normalized to 100%) of ten pristine phosphorite samples based on XRD analysis.
DOI: 10.17632/yff7r65jzz.1
title: Iron sources and cycling during diagenetic transformations of Negev phosphorites (Israel)

description: The dataset comprises geochemical and mineralogical data generated in the course of this study. Table 1 summarizes iron (Fe) speciation and the concentrations of Fe, phosphorus (P), aluminum (Al), and total organic carbon (TOC) in the analyzed samples. Table 2 provides estimates of the impact of pyrite and Fe(II) oxidation on iron speciation. Table 3 reports mineral phase abundances (in wt%, normalized to 100%) of ten pristine phosphorite samples based on XRD analysis.
DOI: 10.15468/dl.ea9anx
title: Occurrence Download

description: A dataset containing 28 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 Oxytropis latibracteata",
 "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 28 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003614-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gph954
title: Occurrence Download

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

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003615-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.espafg
title: Occurrence Download

description: A dataset containing 102773 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Motacilla tschutschensis",
 "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 102773 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003553-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.