cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.66s7ed
title: Occurrence Download

description: A dataset containing 67418 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Poland",
 "DatasetKey is Observation.org, Nature data from around the World"
 ]
}

 The dataset includes 67418 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023068-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.crq4mc
title: Occurrence Download

description: A dataset containing 107 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Brachyuromys ramirohitra Forsyth Major, 1896"
 ]
}

 The dataset includes 107 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008685-150615163101818/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mlpfbg
title: Occurrence Download

description: A dataset containing 155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cyprinella lutrensis (Baird & Girard, 1853)",
 "Geometry POLYGON((-82.77 33.57,-82.77 37.14,-75.88 37.14,-75.88 33.57,-82.77 33.57))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 155 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055870-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6frqx7
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepanthes synema Luer & Hirtz"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0172241-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.l9eaex
title: Occurrence Download

description: A dataset containing 137 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Meriania involucrata (Desr.) Naudin"
 ]
}

 The dataset includes 137 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008685-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9gnh6j
title: Occurrence Download

description: A dataset containing 11726 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantago lanceolata L.",
 {
 "or" : [
 "Country is Uruguay",
 "Country is Korea (Democratic People’s Republic of)",
 "Country is India",
 "Country is Japan",
 "Country is South Africa",
 "Country is Lesotho",
 "Country is Korea, Republic of",
 "Country is Chile",
 "Country is Mexico",
 "Country is China",
 "Country is Colombia",
 "Country is New Zealand",
 "Country is Bolivia (Plurinational State of)",
 "Country is Argentina",
 "Country is Australia",
 "Country is Peru",
 "Country is Canada",
 "Country is United States of America"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 11726 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055872-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ykz1ix
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Allophylus peduncularis Radlk."
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008686-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fmhitf
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cuculiformes",
 "Country is Norfolk Island",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "Month is greater than or equal to January"
 ]
}

 The dataset includes 14 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055879-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ys29wn
title: Occurrence Download

description: A dataset containing 510 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lepisanthes tetraphylla (Vahl) Radlk.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 510 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039529-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nrrqox
title: Occurrence Download

description: A dataset containing 1515 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is CERMES Barbados Lionfish Derby Data"
 ]
}

 The dataset includes 1515 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008686-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v9xmlp
title: Occurrence Download

description: A dataset containing 1020 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantago lanceolata L.",
 "Geometry POLYGON((20.65 19.50,20.65 66.52,130.87 66.52,130.87 19.50,20.65 19.50))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1020 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055883-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xth8jj
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Presbytis hosei sabana (Thomas, 1893)",
 "DatasetKey is Natural History Museum (London) Collection Specimens"
 ]
}

 The dataset includes 10 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008690-150615163101818/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.i0qgi1
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gordonia Ellis",
 "Geometry POLYGON((-80.28 13.08,-80.28 29.35,-52.72 29.35,-52.72 13.08,-80.28 13.08))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 73 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055885-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4tpsab
title: Occurrence Download

description: A dataset containing 272637 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Brunei Darussalam, Myanmar, Cambodia, Timor-Leste, Indonesia, Lao People’s Democratic Republic, Malaysia, Philippines, Singapore, Thailand, Viet Nam)",
 "IucnRedListCategory is one of (CR, EN, VU)",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 272637 records from 120 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028969-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dulex2
title: Occurrence Download

description: A dataset containing 3031 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Anniella Gray, 1852",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3031 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008690-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k5f3wy
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Falconiformes",
 "Country is Norfolk Island",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "Month is greater than or equal to January"
 ]
}

 The dataset includes 78 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055887-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6yigsf
title: Occurrence Download

description: A dataset containing 774 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carpobrotus edulis (L.) N.E.Br.",
 "Geometry POLYGON((-20.64 49.73,-20.64 59.31,5.43 59.31,5.43 49.73,-20.64 49.73))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 774 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008691-160118175350007/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ca2qzr
title: Occurrence Download

description: A dataset containing 3251 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Centropus sinensis (Stephens, 1815)"
 ]
}

 The dataset includes 3251 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027790-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a7up94
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lobelia gladiaria McVaugh"
 ]
}

 The dataset includes 4 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0172243-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mtrrpb
title: Occurrence Download

description: A dataset containing 471 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amaranthus quitensis Kunth",
 "HasCoordinate is true"
 ]
}

 The dataset includes 471 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061283-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zyjb9k
title: Occurrence Download

description: A dataset containing 97578 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Tilia platyphyllos Scop.)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Geometry POLYGON ((-15 75, -15 25, 60 25, 60 75, -15 75))"
 ]
}

 The dataset includes 97578 records from 962 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034046-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rwsn76
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Masdevallia excelsior Luer & Andreetta"
 ]
}

 The dataset includes 12 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0172242-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.l1uwhz
title: Occurrence Download

description: A dataset containing 43678 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Bromus tectorum L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 43678 records from 386 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008693-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kc4uvc
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "OccurrenceStatus is Present",
 "TaxonKey is Sargassum trichocarpum J.Agardh"
 ]
}

 The dataset includes 18 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002018-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s9jthm
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-7.16577 43.42164,-4.68447 43.37344,-4.70643 43.96476,-7.33023 44.17512,-7.16577 43.42164))",
 "OccurrenceStatus is Present",
 "TaxonKey is Holocephali"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002020-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10473310
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. 






gtdb_modelseed_gems.zip
md5:e3e62b305e64b27da7b80655d7f92f2c 

 



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
md5:cbcc9aa1a28a5bd5f6661f832d27bcbf 

 



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.
DOI: 10.5281/zenodo.10474664
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. 






gtdb_modelseed_gems.zip
md5:e3e62b305e64b27da7b80655d7f92f2c 

 



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
md5:cbcc9aa1a28a5bd5f6661f832d27bcbf 

 



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. 





updated_seedsets_of_interest.pckl

md5:2a49534b52169daa4f96157b15d1b01c 




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...





updated_non_seedsets_of_interest.pckl

md5:75c435a69b183ea23aa58d43c1e051ba 




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...
DOI: 10.5281/zenodo.10537295
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. 






gtdb_modelseed_gems.zip
md5:e3e62b305e64b27da7b80655d7f92f2c 

 



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
md5:cbcc9aa1a28a5bd5f6661f832d27bcbf 

 



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. 





updated_seedsets_of_interest.pckl

md5:2a49534b52169daa4f96157b15d1b01c 




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...





updated_non_seedsets_of_interest.pckl

md5:75c435a69b183ea23aa58d43c1e051ba 




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...





phen_classes.zip
md5:9e3f7a84fe7409ef0282ca5424797976 

 

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.10562677
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. 






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. 



updated_seedsets_of_interest.pckl


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...



updated_non_seedsets_of_interest.pckl


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...





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.15102937
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. 



updated_seedsets_of_interest.pckl


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...



updated_non_seedsets_of_interest.pckl


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...





phen_classes.zip

A list of pickle files with the re-trained classes of phenDB for the prediction of functional traits on a genome.