cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.cmq33x
title: Occurrence Download

description: A dataset containing 1908 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hylotelephium spectabile (Boreau) H.Ohba",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1908 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016425-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4u5gv4
title: Occurrence Download

description: A dataset containing 144 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Atlapetes blancae Donegan, 2007"
 ]
}

 The dataset includes 144 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0209048-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wfhto5
title: Occurrence Download

description: A dataset containing 2028 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Elevation 1500.0-2210.0m",
 {
 "or" : [
 "Geometry POLYGON((-82.96875 -16.088042220148807,-73.12500000000001 -16.088042220148807,-73.12500000000001 1.8014609294680355,-82.96875 1.8014609294680355,-82.96875 -16.088042220148807))",
 "Geometry POLYGON((-82.96875 -16.088042220148793,-73.12500000000001 -16.088042220148793,-73.12500000000001 1.8014609294680355,-82.96875 1.8014609294680355,-82.96875 -16.088042220148793))",
 "Geometry POLYGON((-84.111328125 -16.362309510240834,-72.333984375 -16.362309510240834,-72.333984375 5.725311447610153,-84.111328125 5.725311447610153,-84.111328125 -16.362309510240834))"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Arecaceae",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2028 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022445-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bayn7q
title: Occurrence Download

description: A dataset containing 893 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cypripedium guttatum Sw."
 ]
}

 The dataset includes 893 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022445-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6zkbpf
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Guioa misimaensis Welzen"
 ]
}

 The dataset includes 13 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016423-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rhx82b
title: Occurrence Download

description: A dataset containing 6145 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is University of Michigan Museum of Paleontology - Vertebrates",
 "TaxonKey is Primates"
 ]
}

 The dataset includes 6145 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0210723-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v33yei
title: Occurrence Download

description: A dataset containing 893 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cypripedium guttatum Sw."
 ]
}

 The dataset includes 893 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022446-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mqdzpf
title: Occurrence Download

description: A dataset containing 11141779 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hirundo rustica Linnaeus, 1758",
 "HasCoordinate is true"
 ]
}

 The dataset includes 11141779 records from 1883 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0195103-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g84qry
title: Occurrence Download

description: A dataset containing 232 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Cuphea balsamona (Vand.) Cham. & Schltdl.)"
 ]
}

 The dataset includes 232 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027949-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bhq38t
title: Occurrence Download

description: A dataset containing 688 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Polyalthia suberosa (Roxb.) Thwaites)"
 ]
}

 The dataset includes 688 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027947-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dw6sb2
title: Occurrence Download

description: A dataset containing 5015 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Toxicodendron succedaneum (L.) Kuntze)"
 ]
}

 The dataset includes 5015 records from 195 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027948-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5n2uwn
title: Occurrence Download

description: A dataset containing 12279 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Scilla forbesii (Baker) Speta)"
 ]
}

 The dataset includes 12279 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027951-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vydkje
title: Occurrence Download

description: A dataset containing 1750 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Flaveria bidentis (L.) Kuntze)"
 ]
}

 The dataset includes 1750 records from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027950-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g76x8d
title: Occurrence Download

description: A dataset containing 12762 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Houttuynia cordata Thunb.)"
 ]
}

 The dataset includes 12762 records from 282 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027952-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gcbd2f
title: Occurrence Download

description: A dataset containing 269 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Brachiaria dictyoneura (Fig. & De Not.) Stapf)"
 ]
}

 The dataset includes 269 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027959-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mpmspj
title: Occurrence Download

description: A dataset containing 469 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Lonicera confusa (Sweet) DC.)"
 ]
}

 The dataset includes 469 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027960-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dkbeqp
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Niphona hookeri Gahan, 1900)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027953-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.64chdk
title: Occurrence Download

description: A dataset containing 3419 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Viburnum setigerum Hance)"
 ]
}

 The dataset includes 3419 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027958-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nm6hw8
title: Occurrence Download

description: A dataset containing 6990 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Setaria palmifolia (J.Koenig) Stapf)"
 ]
}

 The dataset includes 6990 records from 217 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027954-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.up234t
title: Occurrence Download

description: A dataset containing 3192 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Aniseia martinicensis (Jacq.) Choisy)"
 ]
}

 The dataset includes 3192 records from 242 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027961-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/ns6cxk
title: INC PAS The Atlas of Mammals of Poland

description: The dataset contains records of mammals amphibian species recorded in Poland, made after 1980. The data comes both from literature and from direct records in the field. Contributors include professional experts and amateur nature lovers.
DOI: 10.15468/dl.vjaq3r
title: Occurrence Download

description: A dataset containing 2484 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Corynephorus fasciculatus Boiss. & Reut.)"
 ]
}

 The dataset includes 2484 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027956-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qucnt8
title: Occurrence Download

description: A dataset containing 6994 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Solanum laciniatum Aiton)"
 ]
}

 The dataset includes 6994 records from 155 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027962-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/s5g-zc9-jfl
title: Colias tyche (Böber, 1812)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/gbv-71h-smd
title: Ochlodes Scudder, 1872

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/xm9-yar-add
title: Hipparchia semele Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dka-cfh-0hf
title: Arctia plantaginis (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/eal-yzg-rn4
title: Leucodonta bicoloria ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/yjv-esw-8y8
title: Coranarta cordigera Thunberg, 1788

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/4b2-b9y-eae
title: Colias tyche (Böber, 1812)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/byw-r1z-lql
title: Colias tyche (Böber, 1812)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/qmy-097-6zz
title: Cosmia (Calymnia) trapezina (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/vk9-c94-p63
title: Caradrina (Caradrina) morpheus (Hufnagel, 1766)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/2em-nly-l42
title: Charanyca (Charanyca) trigrammica (Hufnagel, 1766)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/he0-57t-yyf
title: Agriphila tristellus [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/8e9-jnm-b1f
title: Hipparchia semele Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/clq-q7p-lrk
title: Nymphalis antiopa (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/nwa-zxj-088
title: Leucoma salicis (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.5281/zenodo.17805430
title: A catalog of genes and species of the human skin microbiota

description: Dataset overviewThis dataset provides:a non-redundant high-quality catalog of 2.9 million genes392 Metagenomic Species Pangenomes (MSPs)This dataset can be used to analyze shotgun sequencing data of the human skin microbiota.
How to use this datasetCreate a gene abundance table by aligning reads from each sample against the catalog. For this purpose, you can use Meteor or NGLess. Then, normalize raw counts by gene length.Taxonomic profiling: the abundance of each species can be estimated as the average abundance of its 100 first core genes. To reduce the false positive rate, only consider that a species is present if at least 10/100 marker genes are detected.
Methods
Data sourcesThis dataset was built using the following data sources:118 isolate-derived genomes from the HMRGD246 isolate-derived genomes from the Skin Microbial Genome Collection (SMGC)1,407 skin metagenome assemblies from the Skin Microbial Genome Collection (SMGC)
Non-redundant gene catalogAfter filtering out short contigs (<1500 bp), genes were predicted with Prodigal on genomes (mode: single) and metagenome assemblies (mode: meta). Complete genes (partial=00) were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
Functional annotationKOs assignments were obtained with KofamScan using the KEGG 107 database.
MSPs recoveryReads from the 1,120 skin metagenomes available in the bioproject PRJNA46333 were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (2.9M genes quantified in 1,120samples). Then, co-abundant genes were binned in 392 Metagenomic Species Pan-genomes (MSPs, i.e. clusters of co-abundant genes that likely belong to the same microbial species) using MSPminer.
MSPs taxonomic annotationTaxonomic annotation was performed by alignment of all core and accessory genes against representative genomes of the GTDB database (release r214) using blastn (version 2.7.1, task = megablast, word_size = 16). A species-level assignment was given if > 50% of the genes matched the representative genome of a given species, with a mean nucleotide identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MSPs were assigned to a higher taxonomic level (genus to superkingdom), if more than 50% of their genes had the same annotation.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the MSPs (or the corresponding genome if available) with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJNA46333 (cohort used in catalogue assembly) and PRJEB80549 (independent cohort not used in assembly).
DOI: 10.3535/w2h-9ma-24a
title: Pleurota bicostella (Clerck, 1761)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/wvy-ry0-j7b
title: Leucoma salicis (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.5281/zenodo.10679308
title: A catalog of genes and species of the human skin microbiota

description: Dataset overviewThis dataset provides:a non-redundant high-quality catalog of 2.9 million genes392 Metagenomic Species Pangenomes (MSPs)This dataset can be used to analyze shotgun sequencing data of the human skin microbiota.
How to use this datasetCreate a gene abundance table by aligning reads from each sample against the catalog. For this purpose, you can use Meteor or NGLess. Then, normalize raw counts by gene length.Taxonomic profiling: the abundance of each species can be estimated as the average abundance of its 100 first core genes. To reduce the false positive rate, only consider that a species is present if at least 10/100 marker genes are detected.
Methods
Data sourcesThis dataset was built using the following data sources:118 isolate-derived genomes from the HMRGD246 isolate-derived genomes from the Skin Microbial Genome Collection (SMGC)1,407 skin metagenome assemblies from the Skin Microbial Genome Collection (SMGC)
Non-redundant gene catalogAfter filtering out short contigs (<1500 bp), genes were predicted with Prodigal on genomes (mode: single) and metagenome assemblies (mode: meta). Complete genes (partial=00) were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
Functional annotationKOs assignments were obtained with KofamScan using the KEGG 107 database.
MSPs recoveryReads from the 1,120 skin metagenomes available in the bioproject PRJNA46333 were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (2.9M genes quantified in 1,120samples). Then, co-abundant genes were binned in 392 Metagenomic Species Pan-genomes (MSPs, i.e. clusters of co-abundant genes that likely belong to the same microbial species) using MSPminer.
MSPs taxonomic annotationTaxonomic annotation was performed by alignment of all core and accessory genes against representative genomes of the GTDB database (release r214) using blastn (version 2.7.1, task = megablast, word_size = 16). A species-level assignment was given if > 50% of the genes matched the representative genome of a given species, with a mean nucleotide identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MSPs were assigned to a higher taxonomic level (genus to superkingdom), if more than 50% of their genes had the same annotation.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the MSPs (or the corresponding genome if available) with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJNA46333 (cohort used in catalogue assembly) and PRJEB80549 (independent cohort not used in assembly).
DOI: 10.3535/7r4-gee-pjw
title: Acrobasis repandana Fabricius, 1798

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/g9s-93x-d1q
title: Abrostola tripartita (Hufnagel, 1766)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/nv1-dnt-m80
title: Lacanobia (Dianobia) contigua [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.5281/zenodo.17823592
title: Data for submitted paper "Cross-Shelf Transport in the Northern South China Sea Shelf: Quantification and Mechanisms"

description: Software and Data for manuscript 'Cross-Shelf Transport in the Northern South China Sea Shelf: Quantification and Mechanisms'.

This repository contains three files

(1) A modified version of the ROMS source code used in the numerical experimentsand;

(2) Validation  data in the model.

Model forcing files (Boundary, Surface) exceeds the size limit, thus are not uploaded in this repo.
DOI: 10.5281/zenodo.17823593
title: Data for submitted paper "Cross-Shelf Transport in the Northern South China Sea Shelf: Quantification and Mechanisms"

description: Software and Data for manuscript 'Cross-Shelf Transport in the Northern South China Sea Shelf: Quantification and Mechanisms'.

This repository contains three files

(1) A modified version of the ROMS source code used in the numerical experimentsand;

(2) Validation  data in the model.

Model forcing files (Boundary, Surface) exceeds the size limit, thus are not uploaded in this repo.
DOI: 10.3535/d56-4nt-pgh
title: Hypena proboscidalis (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/t59-xlh-7ct
title: Agonopterix heracliana Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/vrr-fd7-b94
title: Cyclophora albipunctata (Hufnagel, 1767)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/4q2-8x8-rj4
title: Agriphila tristellus [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/e43-fse-ym8
title: Hypena proboscidalis (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/3d0-c2y-s8r
title: Agonopterix heracliana Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/h8d-acc-71e
title: Gluphisia crenata (Esper, 1785)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/58m-pq2-q0c
title: Chilo phragmitella Hübner, 1805

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.