cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.4ys37a
title: Occurrence Download

description: A dataset containing 788 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Ursus americanus Pallas, 1780",
 "Year 2000-2024"
 ]
}

 The dataset includes 788 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003956-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.24355/dbbs.084-202411180831-0
title: Gene Expression of Theobroma cacao

description: Gene expression of Theobroma cacao was analyzed based on various reference sequences. All available paired-end RNA-seq datasets were downloaded from the Sequence Read Archive and processed with kallisto. Final count tables were generated with customized Python scripts.
DOI: 10.5281/zenodo.13382835
title: All_2DIR_data
DOI: 10.15468/dl.97ub83
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Malcolmia orsiniana (Ten.) Ten., Hesperis orsiniana Ten., Wilckia orsiniana (Ten.) Degen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 19 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003957-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z7gm9d
title: Occurrence Download

description: A dataset containing 161 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Centre for Australian National Biodiversity Research (CANB) AVH data",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Duma florulenta (Meisn.) T.M.Schust."
 ]
}

 The dataset includes 161 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003958-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.whwcf3
title: Occurrence Download

description: A dataset containing 4297 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Saccharum officinarum L."
 ]
}

 The dataset includes 4297 records from 352 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003959-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3xgam4
title: Occurrence Download

description: A dataset listing the 444 species recorded in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Laccaria Berk. & Broome, 1883"
 ]
}

 The dataset's 444 records were derived from 599 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003938-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mspprm
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Malva unguiculata (Desf.) Alef., Lavatera unguiculata Desf., Lavatera olbia Sibth. & Sm., Lavatera bryoniifolia Mill., Lavatera sphaciotica Gand., Lavatera tomentosa Dum.Cours., Lavatera olbia var. unguiculata (Desf.) Arcang., 1882, Althaea unguiculata (Desf.) Kuntze)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 63 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003961-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vzfzpb
title: Occurrence Download

description: A dataset containing 9178 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Ligyrus sallaei Bates, 1888, Cyclocephala lunulata Burmeister, 1847, Coelosis biloba (Linnaeus, 1767), Coelosis sylvanus (Fabricius, 1775), Coelosis inermis Sternberg, 1908)"
 ]
}

 The dataset includes 9178 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003960-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zpjnek
title: Occurrence Download

description: A dataset containing 295 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Marrubium incanum Desr.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 295 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003963-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11225486
title: Working Species List and Sources for Maine eDNA Reference Library

description: These files are part of an (as of May 2023) ongoing effort to create a reference library database and database creation tools for use by Maine-eDNA, and include a species list with genus-only entries, duplicates, and special characters mostly removed (though some issues may still persist) and a source list for each collected species/genus entry with the last date of accession and the link to the source and search criteria. All sources without a link were made available as separate files and are hosted elsewhere. Species list sources are courtesy of Maine eDNA researchers and public datasets.

Contact Beth Davis - bethyd@hawaii.edu for questions

 

July 11, 2023 - Did additional cleaning to the MaineSpeciesList_Clean file and uploaded the new version - July2023_SpeciesList

May 20, 2024 - Additional cleaning to correct deduplication errors and ran taxize's gnr_resolve to resolve names and fill out taxonomy. The version update adds two files, GNRMaineSpecies_May2024.csv containing the full result of gnr_resolve, and GNRMaineTaxonomiedSpecies_May2024.csv contains only those species from the original list that could be resolved with taxonomy. The SpeciesListMeta_Shareable.csv has not been updated but is still an accurate tracker of the sources from which the species names were gained from.
description: Supported by National Science Foundation award #OIA-1849227 to Maine EPSCoR at the University of Maine, and National Science Foundation award 2104147
DOI: 10.5281/zenodo.14232801
title: Reference Sequence Library Resources - Maine-eDNA

description: The following files and resources are associated with the Maine-eDNA Reference Library Research Group - aiming to create reference sequence library resources for researchers part of Maine-eDNA or otherwise interested in leveraging eDNA tools for research in the Gulf of Maine.

These include:





RoughWorkflow.zip






contains a NCBI scraping script to build reference databases based on an input species list, a configuration file for the script, and genbankr version - most useful for shorter species lists (time-intensive)





12S_REFDB.fasta






A DADA2-compliant reference library for 12S sequences, built with the RoughWorkflow based on the GNRMaineSpecies_May2024 species list





COI_REFDB.fasta






A DADA2-compliant reference library for COI sequences, built with the RoughWorkflow based on the GNRMaineSpecies_May2024 species list





GitHub Repo - referee - https://github.com/BigelowLab/referee






Scripts for building reference databases for the Maine-eDNA project through downloading GenBank - this workflow is suggested especially for large species lists





GitHub Repo - refdbtools - https://github.com/BigelowLab/refdbtools 






R language package to assist in making eDNA reference databases





SpeciesListMeta_Shareable.xlsx






Describes the sources from which the GNRMaineSpecies_May2024.csv and GNRMaineTaxonomiedSpecies_May2024.csv species lists were compiled - sources not associated with a link were found as separate files and are hosted elsewhere. Species list sources are courtesy of public datasets, Maine-eDNA researchers, and collaborators





GNRMaineSpecies_May2024.csv






A Maine (and surrounding area) species list ran through taxize’s gnr_resolve to resolve species names and fill out taxonomy (full results)





GNRMaineTaxonomiedSpecies_May2024.csv






A Maine (and surrounding area) species list ran through taxize’s gnr_resolve to resolve species names and fill out taxonomy (only species results that could be resolved with taxonomy)




 

Contact Beth Y. Davis - bethy.davis4@gmail.com for questions

 

###

Changelog:

May 16, 2023 (Version 1.0) - Initial upload

July 11, 2023 (Version 1.1) - Did additional cleaning to the MaineSpeciesList_Clean file and uploaded the new version - July2023_SpeciesList

May 20, 2024 (Version v3) -  Additional cleaning to correct deduplication errors and ran taxize's gnr_resolve to resolve names and fill out taxonomy. The version update adds two files, GNRMaineSpecies_May2024.csv containing the full result of gnr_resolve, and GNRMaineTaxonomiedSpecies_May2024.csv contains only those species from the original list that could be resolved with taxonomy. The SpeciesListMeta_Shareable.csv has not been updated but is still an accurate tracker of the sources from which the species names were gained from.

November 27, 2024 (Version 4.0) - Updated Zenodo description and added the RoughWorkflow R files, 12S and COI files
description: Supported by National Science Foundation award #OIA-1849227 to Maine EPSCoR at the University of Maine, and National Science Foundation award 2104147
DOI: 10.5281/zenodo.7942246
title: Reference Sequence Library Resources - Maine-eDNA

description: The following files and resources are associated with the Maine-eDNA Reference Library Research Group - aiming to create reference sequence library resources for researchers part of Maine-eDNA or otherwise interested in leveraging eDNA tools for research in the Gulf of Maine.

These include:





RoughWorkflow.zip






contains a NCBI scraping script to build reference databases based on an input species list, a configuration file for the script, and genbankr version - most useful for shorter species lists (time-intensive)





12S_REFDB.fasta






A DADA2-compliant reference library for 12S sequences, built with the RoughWorkflow based on the GNRMaineSpecies_May2024 species list





COI_REFDB.fasta






A DADA2-compliant reference library for COI sequences, built with the RoughWorkflow based on the GNRMaineSpecies_May2024 species list





GitHub Repo - referee - https://github.com/BigelowLab/referee






Scripts for building reference databases for the Maine-eDNA project through downloading GenBank - this workflow is suggested especially for large species lists





GitHub Repo - refdbtools - https://github.com/BigelowLab/refdbtools 






R language package to assist in making eDNA reference databases





SpeciesListMeta_Shareable.xlsx






Describes the sources from which the GNRMaineSpecies_May2024.csv and GNRMaineTaxonomiedSpecies_May2024.csv species lists were compiled - sources not associated with a link were found as separate files and are hosted elsewhere. Species list sources are courtesy of public datasets, Maine-eDNA researchers, and collaborators





GNRMaineSpecies_May2024.csv






A Maine (and surrounding area) species list ran through taxize’s gnr_resolve to resolve species names and fill out taxonomy (full results)





GNRMaineTaxonomiedSpecies_May2024.csv






A Maine (and surrounding area) species list ran through taxize’s gnr_resolve to resolve species names and fill out taxonomy (only species results that could be resolved with taxonomy)




 

Contact Beth Y. Davis - bethy.davis4@gmail.com for questions

 

###

Changelog:

May 16, 2023 (Version 1.0) - Initial upload

July 11, 2023 (Version 1.1) - Did additional cleaning to the MaineSpeciesList_Clean file and uploaded the new version - July2023_SpeciesList

May 20, 2024 (Version v3) -  Additional cleaning to correct deduplication errors and ran taxize's gnr_resolve to resolve names and fill out taxonomy. The version update adds two files, GNRMaineSpecies_May2024.csv containing the full result of gnr_resolve, and GNRMaineTaxonomiedSpecies_May2024.csv contains only those species from the original list that could be resolved with taxonomy. The SpeciesListMeta_Shareable.csv has not been updated but is still an accurate tracker of the sources from which the species names were gained from.

November 27, 2024 (Version 4.0) - Updated Zenodo description and added the RoughWorkflow R files, 12S and COI files
description: Supported by National Science Foundation award #OIA-1849227 to Maine EPSCoR at the University of Maine, and National Science Foundation award 2104147
DOI: 10.5281/zenodo.7942247
title: Working Species List and Sources for Maine eDNA Reference Library

description: These files are part of an (as of May 2023) ongoing effort to create a reference library database and database creation tools for use by Maine-eDNA, and include a species list with genus-only entries, duplicates, and special characters mostly removed (though some issues may still persist) and a source list for each collected species/genus entry with the last date of accession and the link to the source and search criteria. All sources without a link were made available as separate files and are hosted elsewhere. Species list sources are courtesy of Maine eDNA researchers and public datasets. Contact Beth Davis - beth.davis@maine.edu for questions
description: Supported by National Science Foundation award #OIA-1849227 to Maine EPSCoR at the University of Maine, and National Science Foundation award 2104147
DOI: 10.5281/zenodo.8136534
title: Working Species List and Sources for Maine eDNA Reference Library

description: These files are part of an (as of May 2023) ongoing effort to create a reference library database and database creation tools for use by Maine-eDNA, and include a species list with genus-only entries, duplicates, and special characters mostly removed (though some issues may still persist) and a source list for each collected species/genus entry with the last date of accession and the link to the source and search criteria. All sources without a link were made available as separate files and are hosted elsewhere. Species list sources are courtesy of Maine eDNA researchers and public datasets. Contact Beth Davis - beth.davis@maine.edu for questions July 11, 2023 - Did additional cleaning to the MaineSpeciesList_Clean file and uploaded the new version - July2023_SpeciesList
description: Supported by National Science Foundation award #OIA-1849227 to Maine EPSCoR at the University of Maine, and National Science Foundation award 2104147
DOI: 10.15468/dl.cxruzp
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Mcneillia graminifolia subsp. rosanoi (Ten.) F.Conti, Bartolucci, Iamonico & Del Guacchio, Arenaria rosanoi Ten., Alsine graminifolia J.F.Gmel., Alsine graminifolia var. rosanoi (Ten.) Bég., Mcneillia rosanoi (Ten.) F.Conti & Del Guacchio, Alsine rosanoi (Ten.) Guss., Minuartia graminifolia subsp. rosanoi (Ten.) Mattf.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003964-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q5zeub
title: Occurrence Download

description: A dataset containing 1432 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Fallopia aubertii (L.Henry) Holub"
 ]
}

 The dataset includes 1432 records from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003965-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n358bv
title: Occurrence Download

description: A dataset containing 2005 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Diplotaxis cribriceps Bates, 1889, Diplotaxis bifida Vaurie, 1960, Strategus tarsalis Casey, 1915, Phileurus valgus (Olivier, 1789), Phileurus carinatus declivis Prell, 1914)"
 ]
}

 The dataset includes 2005 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003966-241126133413365/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.27924030.v1
title: 1111

description: 111111
DOI: 10.6084/m9.figshare.27924030
title: 1111

description: 111111
DOI: 10.15468/dl.q58mkr
title: Occurrence Download

description: A dataset containing 10483 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Medicago arborea L., Medicago arborea var. citrina FontQuer, Trigonella arborea (L.) Vassilcz., Medica arborea (L.) Mill., Rhodusia arborea (L.) Vassilcz.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 10483 records from 114 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003969-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t625m9
title: Occurrence Download

description: A dataset containing 18689 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "GadmGid is CHN.3_1",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 18689 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003970-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cgzw8k
title: Occurrence Download

description: A dataset containing 84787 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "GadmGid is CHN.7_1",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 84787 records from 257 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003968-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gmcrm4
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Malaysia, Indonesia, Singapore)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Mustela nudipes Desmarest, 1822"
 ]
}

 The dataset includes 36 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052261-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yv2z2g
title: Occurrence Download

description: A dataset containing 10625 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Spain",
 "Country is Portugal"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Epidalea calamita (Laurenti, 1768)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 10625 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015943-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u9jr4x
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "HasCoordinate is true",
 "TaxonKey is Planorbella occidentalis (J.G.Cooper, 1870)"
 ]
}

 The dataset includes 26 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0090770-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7ekc7k
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Murbeckiella omissa B.P.R.Chéron"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063794-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hr3a63
title: Occurrence Download

description: A dataset containing 198 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-90.77748 18.53127,-90.72937 18.52445,-90.72052 18.60261,-90.76716 18.60796,-90.77748 18.53127))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (April, March, February, January, October, May, June, July, August, September)",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata",
 "Year 2020-2024"
 ]
}

 The dataset includes 198 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041857-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0hi8z9
title: Occurrence Download

description: A dataset containing 5487330 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Observation",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 5487330 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008708-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.asrcp8
title: Occurrence Download

description: A dataset containing 1221 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Murbeckiella boryi (Boiss.) Rothm."
 ]
}

 The dataset includes 1221 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063791-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gwk2f4
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acontia viridisquama Guenée, 1852"
 ]
}

 The dataset includes 14 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0090774-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lywtsx
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Spain",
 "Country is Portugal"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Hyla molleri Bedriaga, 1889",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 59 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015948-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.