cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.5sr2pf
title: Occurrence Download

description: A dataset containing 1268 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trifolium pallescens Schreb.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1268 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009452-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fsr7yg
title: Occurrence Download

description: A dataset containing 1106 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1883-2002",
 "HasCoordinate is true",
 "TaxonKey is Holochilus Brandt, 1835",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1106 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002846-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xxpvhu
title: Occurrence Download

description: A dataset containing 547861 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caltha palustris L."
 ]
}

 The dataset includes 547861 records from 1458 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074893-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3e9zma
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingCountry is Canada",
 "TaxonKey is one of (Vicia sativa var. angustifolia (L.) H.T.Ho, 1988)"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001645-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u8tlf5
title: Occurrence Download

description: A dataset containing 4006 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gaga Pryer, Fay W.Li & Windham"
 ]
}

 The dataset includes 4006 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002903-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ruttvf
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "DatasetKey is one of (Computarización de las colecciones de vertebrados terrestres de la Escuela Nacional de Ciencias Biológicas, IPN Fase 4 (Anfibios y reptiles), LACM Vertebrate Collection, Herpetofauna del Estado de Veracruz, University of Michigan Museum of Zoology, Division of Reptiles & Amphibians, Anfibios y reptiles del estado de Tamaulipas, México, Digitalización y Sistematización de las Colecciones Biológicas Nacionales del Instituto de Biología, UNAM (vertebrados), Southeastern Louisiana University Herpetology Collection, Actualización de la taxonomía y distribución de los anfibios y reptiles de San Luis Potosí, Formación de una base de datos y elaboración de un atlas de la herpetofauna de México (Anfibiosreptiles), Anfibios y reptiles del estado de Querétaro)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "PublishingOrg is one of (ff90b050-c256-11db-b71b-b8a03c50a862, 493fe050-055d-11d8-b84f-b8a03c50a862, 19456090-b49a-11d8-abeb-b8a03c50a862, bc092ff0-02e4-11dc-991f-b8a03c50a862, ccd1ddc0-6c21-11de-8224-b8a03c50a862, 2b8e48b0-812d-11de-86fe-b8a03c50a862, 7b8aff00-a9f8-11d8-944b-b8a03c50a862, c361e830-181e-11da-9544-b8a03c50a862, 4200d851-2340-4411-bda9-126613424633, 6ea87510-0561-11d8-b851-b8a03c50a862)",
 "TaxonKey is Ficimia olivacea Gray, 1849",
 "Year 1950-2024"
 ]
}

 The dataset includes 37 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042776-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12175913
title: Scorpio Gene-Taxa Benchmark Dataset

description:  
















We used the Woltka pipeline to compile the complete Basic genome dataset, consisting of 4634 genomes, with each genus represented by a single genome. After downloading all coding sequences (CDS) from the NCBI database, we extracted 8 million distinct CDS, focusing on bacteria and archaea and excluding viruses and fungi due to inadequate gene information.

To maintain accuracy, we excluded hypothetical proteins, uncharacterized proteins, and sequences without gene labels. We addressed issues with gene name inconsistencies in NCBI by keeping only genes with more than 1000 samples and ensuring each phylum had at least 350 sequences. This resulted in a curated dataset of 800,318 gene sequences from 497 genes across 2046 genera.

We created four datasets to evaluate our model: a training set (Train_set), a test set (Test_set) with different samples but the same genus and gene as the training set, a Taxa_out_set excluding 18 phyla present in the training set but from different phyla, and a Gene_out_set excluding 60 genes from the training set but from the same phyla. We ensured each CDS had only one representation per genome, removing genes with multiple representations within the same species.
description: test.fasta :  Contains sequences for model testing.




gene_out.fasta: Includes sequences excluded based on gene criteria for model evaluation.




taxa_out.fasta :Includes sequences excluded based on taxonomic criteria for model evaluation.




train.fasta: Contains sequences for model training.




metadata.csv: Contains metadata information for sequences in the FASTA files.




hierarchical-level.txt : Determines hierarchical levels for triplet training and hierarchical sampling required for Scorpio training.



General Description of FASTA Files:

FASTA files contain sequence data where each sequence entry begins with a header line, starting with ">" followed by a sequence identifier (seqid). 

Retrieving Information from Metadata:

To retrieve metadata information based on the sequence ID (seqid) from the FASTA files:



Extract the seqid from the header of the FASTA file

Use the extracted seqid to look up the corresponding row in the metadata.csv file.
DOI: 10.15468/dl.vaczfs
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Viet Nam",
 "GadmGid is VNM.43.1.1_1",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 36 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042777-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.97rqcp
title: Occurrence Download

description: A dataset containing 696236 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-31.21697 19.21704,31.77315 19.21704,31.77315 57.68301,-31.21697 57.68301,-31.21697 19.21704))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Quercus suber L."
 ]
}

 The dataset includes 696236 records from 334 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042765-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.euw5az
title: Occurrence Download

description: A dataset containing 152 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "DatasetKey is MEXU/Colección de Briofitas"
 ]
}

 The dataset includes 152 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042778-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gtkek6
title: Occurrence Download

description: A dataset containing 5422112 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 5422112 records from 1417 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042771-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uwk2hd
title: Occurrence Download

description: A dataset containing 652634 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Centaurea L.",
 "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 652634 records from 1643 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012881-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5jt6u9
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cleistanthus morii Kaneh."
 ]
}

 The dataset includes 9 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006505-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7sb2hm
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Regenwasserabfangbecken"
 ]
}

 The dataset includes 31 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010661-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ds9jh9
title: Occurrence Download

description: A dataset containing 741 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Melursus ursinus (Shaw, 1791)"
 ]
}

 The dataset includes 741 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022469-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nk17ny
title: Occurrence Download

description: A dataset containing 120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "Year 2000-2019",
 "Geometry POLYGON((-80.63965 43.19717,-71.93848 43.19717,-71.93848 47.93107,-80.63965 47.93107,-80.63965 43.19717))",
 "TaxonKey is Esox lucius Linnaeus, 1758",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 120 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016975-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xngx99
title: Occurrence Download

description: A dataset containing 5648 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-9.29375 38.83864,-9.28413 38.69516,-9.07402 38.70695,-9.07265 38.84506,-9.29375 38.83864))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Serinus serinus (Linnaeus, 1766)"
 ]
}

 The dataset includes 5648 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0230310-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x94bw7
title: Occurrence Download

description: A dataset containing 364 species occurrences available in GBIF matching the query:
{
 "or" : [
 "TaxonKey is Diplazium roemerianum (Kunze) C.Presl",
 "TaxonKey is Asplenium roemerianum Kunze"
 ]
}

 The dataset includes 364 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0230323-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hd7rr9
title: Occurrence Download

description: A dataset containing 10109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Circaea ×intermedia Ehrh.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 10109 records from 209 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079065-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hdauir
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Cribroheros bussingi (Loiselle, 1997)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 10 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016973-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u7cypu
title: Occurrence Download

description: A dataset containing 3251 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1000000.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Mangifera L."
 ]
}

 The dataset includes 3251 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0230345-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8z9sqr
title: Occurrence Download

description: A dataset containing 590 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cirsium glabrum DC.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 590 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079120-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hyq38j
title: Occurrence Download

description: A dataset containing 5982 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Caracterización de flora para la formulación y actualización de Planes de Manejo Ambiental en la jurisdicción de Corpoguavio"
 ]
}

 The dataset includes 5982 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016978-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fu748d
title: Occurrence Download

description: A dataset containing 11786 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trapa natans L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 11786 records from 275 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079141-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uwcp3g
title: Occurrence Download

description: A dataset containing 101 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Crepis pannonica (Jacq.) K.Koch"
 ]
}

 The dataset includes 101 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0239611-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hvrqhn
title: Occurrence Download

description: A dataset containing 1202 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lycalopex culpaeus (Molina, 1782)"
 ]
}

 The dataset includes 1202 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016980-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n79gc8
title: Occurrence Download

description: A dataset containing 8850980 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((61.69474 35.32744,61.11429 34.06422,60.64406 32.47352,60.56096 30.26861,62.17551 29.11566,65.01112 29.35547,66.77376 30.98625,70.54622 31.92036,74.10376 31.3221,76.18691 30.88373,78.18937 28.83349,82.00903 25.63068,88.17254 21.71834,90.46804 19.45199,94.08631 14.99971,98.90334 16.10651,100.6566 17.41356,99.83794 24.23352,99.9098 28.11002,99.38169 29.98141,99.96576 35.98857,82.71452 37.90384,70.00574 37.37081,61.69474 35.32744))"
 ]
}

 The dataset includes 8850980 records from 1846 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059869-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/tr9-7m6-lfs
title: Potentilla anserina L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/xzk-pv4-2c9
title: Potentilla argentea L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/y7q-wk2-6q7
title: Atriplex patula L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.5517/ccq9xvr
title: CCDC 664945: Experimental Crystal Structure Determination

description: Related Article: J.Vignolle, H.Gornitzka, B.Donnadieu, D.Bourissou, G.Bertrand|2008|Angew.Chem.,Int.Ed.|47|2271|doi:10.1002/anie.200704927
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccqd1pt
title: CCDC 666986: Experimental Crystal Structure Determination

description: Related Article: D.M.Khramov, E.L.Rosen, V.M.Lynch, C.W.Bielawski|2008|Angew.Chem.,Int.Ed.|47|2267|doi:10.1002/anie.200704978
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/b5d-vjz-pm9
title: Hieracium pilosella L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/qcl-p1k-fam
title: Bassia scoparia (L.) Voss

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/w64-5sm-pgv
title: Potentilla anserina L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.5517/ccq9xws
title: CCDC 664946: Experimental Crystal Structure Determination

description: Related Article: J.Vignolle, H.Gornitzka, B.Donnadieu, D.Bourissou, G.Bertrand|2008|Angew.Chem.,Int.Ed.|47|2271|doi:10.1002/anie.200704927
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/kab-ywm-84p
title: Potentilla argentea L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/mag-sx2-2zg
title: Potentilla argentea L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/s5k-22w-r7b
title: Atriplex rosea L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.5517/ccq9xxt
title: CCDC 664947: Experimental Crystal Structure Determination

description: Related Article: J.Vignolle, H.Gornitzka, B.Donnadieu, D.Bourissou, G.Bertrand|2008|Angew.Chem.,Int.Ed.|47|2271|doi:10.1002/anie.200704927
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccq9xyv
title: CCDC 664948: Experimental Crystal Structure Determination

description: Related Article: J.Vignolle, H.Gornitzka, B.Donnadieu, D.Bourissou, G.Bertrand|2008|Angew.Chem.,Int.Ed.|47|2271|doi:10.1002/anie.200704927
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/enh-q3s-azy
title: Potentilla argentea L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/nqx-6yj-79m
title: Potentilla anserina L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/pvq-624-znz
title: Potentilla alba L.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.5517/ccqhvmn
title: CCDC 670642: Experimental Crystal Structure Determination

description: Related Article: Xiang-Jian Kong, Yan-Ping Ren, Wen-Xian Chen, La-Sheng Long, Zhiping Zheng, Rong-Bin Huang, Lan-Sun Zheng|2008|Angew.Chem.,Int.Ed.|47|2398|doi:10.1002/anie.200705731
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccqq4n6
title: CCDC 676688: Experimental Crystal Structure Determination

description: Related Article: R.B.Lettan II, C.C.Woodward, K.A.Scheidt|2008|Angew.Chem.,Int.Ed.|47|2294|doi:10.1002/anie.200705229
description: Related Article: R.B.Lettan II, C.V.Galliford, C.C.Woodward, K.A.Scheidt|2009|J.Am.Chem.Soc.|131|8805|doi:10.1021/ja808811u
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/2jb-jbj-l3h
title: Potentilla argentea L.

description: Digital Specimen for the physical specimen hosted at University of Graz.