cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17100059
title: Ecological drivers of viral diversity and cross-species transmission in marine mammals (supporting data)

description: Supporting data and code for the paper entitled "Ecological drivers of viral diversity and cross-species transmission in marine mammals".

Data



Contigs resulting from pipeline (as described in Materials and Methods):



final_min_length_0vertebrate_viral_hits.csv: vertebrate viral contigs

final_min_length_0non_vertebrate_viral_hits.csv: non-vertebrate viral contigs

final_min_length_0all_viral_hits.csv: all contigs combined








Metadata:



final_min_length_0all_viral_hits.csv: details of samples and additional variables for each sequencing pool



vOTUs:



cluster_by_genus_len{150/250/400}.csv: vOTUs derived by clustering at all ID thresholds (see Materials and Methods) for three different contig length cutoffs





 

Code





Demographics_CommunityComposition_models.Rmd: Code to run GLM of demographic and taxonomic variables against viral richness, PERMANOVA of viral community composition and Mantel test of community composition versus host phylogenetic distance

Sharing.Rmd: Code to derive vOTUs from raw contigs, build unipartite virus-host network and run GLMs of network node degree against demographic and taxonomic variables
DOI: 10.18434/mds2-3901
title: Trojan Detection Software Challenge - object-detection-aug2022-test
DOI: 10.15468/dl.tvzcfv
title: Occurrence Download

description: A dataset containing 892 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dontostemon integrifolius"
 ]
}

 The dataset includes 892 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053515-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8bdeab
title: Occurrence Download

description: A dataset containing 697 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tecoma stans"
 ]
}

 The dataset includes 697 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053514-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4vy88k
title: Occurrence Download

description: A dataset containing 118 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Madagascar",
 "TaxonKey is Aframomum angustifolium"
 ]
}

 The dataset includes 118 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053516-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sd6ud6
title: Occurrence Download

description: A dataset containing 3563 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Living Specimen, Specimen, Fossil, Material citation, Material sample, Machine Observation)"
 ]
 }
 },
 "TaxonKey is Vicia faba",
 "Year is greater than or equal to 1981",
 "Year is less than or equal to 2010"
 ]
}

 The dataset includes 3563 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053513-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/24484
title: Chandra X-ray Observatory ObsId 24484

description: UNVEILING THE INTRA-CLUSTER MEDIUM PROPERTIES OF THE MOST MASSIVE GALAXY CLUSTERS AT z &gt; 0.9
DOI: 10.15468/dl.5rv4sg
title: Occurrence Download

description: A dataset containing 10368978 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "OccurrenceStatus is Present",
 "Year 2020-2020"
 ]
}

 The dataset includes 10368978 records from 5239 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053471-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mkpap3
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Thailand",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Aquilaria crassna Pierre",
 "Year 2000-2024"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013766-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.acbjvy
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "GadmGid is CHN.19_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Stachys chinensis Bunge ex Benth."
 ]
}

 The dataset includes 23 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013767-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9ke696
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "GadmGid is CHN.19_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Agropyron desertorum (Fisch. ex Link) Schult."
 ]
}

 The dataset includes 40 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013768-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8mw487
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Thlaspi sintenisii Bornm."
 ]
}

 The dataset includes 25 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013769-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hwsmg8
title: Occurrence Download

description: A dataset containing 1018498 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Juncus effusus L."
 ]
}

 The dataset includes 1018498 records from 3241 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013763-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13145/bacdive14171.20240510.9
title: Sphingobium xenophagum (Stolz et al. 2000) Pal et al. 2006

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14172.20240510.9
title: Sphingobium xenophagum (Stolz et al. 2000) Pal et al. 2006

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14173.20240510.9
title: Sphingobium chlorophenolicum (Nohynek et al. 1996) Takeuchi et al. 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14174.20240916.9.1
title: Sphingobium chlorophenolicum (Nohynek et al. 1996) Takeuchi et al. 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15468/dl.tqcabq
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Human Observation, Observation, Specimen)"
 ]
 }
 },
 "TaxonKey is Padda oryzivora (Linnaeus, 1758)"
 ]
}

 The dataset includes 8 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059831-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13145/bacdive14175.20240510.9
title: Sphingobium chlorophenolicum (Nohynek et al. 1996) Takeuchi et al. 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14176.20240510.9
title: Sphingobium herbicidovorans (Zipper et al. 1997) Takeuchi et al. 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14177.20240916.9.1
title: Sphingobium yanoikuyae (Yabuuchi et al. 1990) Takeuchi et al. 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14178.20240510.9
title: Sphingobium yanoikuyae (Yabuuchi et al. 1990) Takeuchi et al. 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14179.20240510.9
title: Sphingobium yanoikuyae (Yabuuchi et al. 1990) Takeuchi et al. 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14180.20240916.9.1
title: Sphingobium yanoikuyae (Yabuuchi et al. 1990) Takeuchi et al. 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14181.20240916.9.1
title: Sphingobium cloacae (Fujii et al. 2001) Prakash and Lal 2006

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14182.20240916.9.1
title: Sphingobium amiense Ushiba et al. 2003

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14183.20240510.9
title: Sphingobium chungbukense (Kim et al. 2000) Pal et al. 2005

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14184.20240510.9
title: Sphingobium indicum Pal et al. 2005

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14185.20240510.9
title: Sphingobium indicum Pal et al. 2005

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14186.20240916.9.1
title: Sphingobium fuliginis Prakash and Lal 2006

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14187.20240510.9
title: Sphingobium aromaticiconvertens Wittich et al. 2007

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14188.20240510.9
title: Sphingobium olei Young et al. 2007

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14189.20240510.9
title: Sphingobium rhizovicinum Young et al. 2008

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15468/dl.8wu3rk
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Methanobacterium alcaliphilum Worakit et al., 1986"
 ]
}

 The dataset includes 13 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059833-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13145/bacdive14191.20240916.9.1
title: Sphingobium abikonense Kumari et al. 2009

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14193.20240916.9.1
title: Sphingobium vermicomposti Vaz-Moreira et al. 2009

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14194.20240916.9.1
title: Sphingobium scionense Liang and Lloyd-Jones 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14195.20240916.9.1
title: Sphingobium quisquiliarum Bala et al. 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14196.20240916.9.1
title: Sphingobium faniae Guo et al. 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15468/dl.f4ecqc
title: Occurrence Download

description: A dataset containing 215 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Namibia",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Crassula aurusbergensis G.Will., Crassula ausensis subsp. giessii (Friedrich) Toelken, Crassula ausensis subsp. ausensis, Crassula ausensis subsp. titanopsis Pavelka, Crassula elegans subsp. namibensis (Friedrich) Toelken, Crassula luederitzii Friedrich, Crassula numaisensis Friedrich, Crinum giessii Lehmiller, Crinum parvibulbosum Dinter ex Overkott, Cromidon pusillum (Roessler) Hilliard, Crotalaria aurea Dinter ex Baker f., Crotalaria colorata subsp. colorata, Crotalaria giessii M.M.le Roux & B.-E.van Wyk, Crotalaria kolbergii M.M.le Roux & B.-E.van Wyk, Crotalaria kurtii Schinz, Cryophytum longipapillosum (Dinter) Gerbaulet, Cucumis clavipetiolatus (J.H.Kirkbr.) Ghebret. & Thulin, Cyperus rehmii Merxm., Cyphostemma bainesii (Hook.fil.) Desc.)"
 ]
}

 The dataset includes 215 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059832-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13145/bacdive14197.20240510.9
title: Sphingobium qiguonii Yan et al. 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14198.20240916.9.1
title: Sphingobium wenxiniae Wang et al. 2011

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14199.20240510.9
title: Sphingobium mellinum Francis et al. 2014

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14200.20240916.9.1
title: Sphingomonas echinoides (Heumann 1962) Denner et al. 1999

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14201.20240916.9.1
title: Sphingomonas paucimobilis (Holmes et al. 1977) Yabuuchi et al. 1990

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14202.20240916.9.1
title: Sphingomonas paucimobilis (Holmes et al. 1977) Yabuuchi et al. 1990

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14203.20240510.9
title: Sphingomonas sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14204.20240510.9
title: Sphingobium yanoikuyae (Yabuuchi et al. 1990) Takeuchi et al. 2001

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14205.20240510.9
title: Sphingomonas sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14206.20240510.9
title: Sphingomonas sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14207.20240510.9
title: Sphingobium quisquiliarum Bala et al. 2010

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14208.20240510.9
title: Sphingomonas sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive14209.20240510.9
title: Sphingobium xenophagum (Stolz et al. 2000) Pal et al. 2006

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15468/dl.tyb2wh
title: Occurrence Download

description: A dataset containing 32225 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is one of (Burkina Faso, South Africa, Tanzania, United Republic of, Madagascar)",
 "TaxonKey is Combretaceae"
 ]
}

 The dataset includes 32225 records from 103 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001838-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6btdnd
title: Occurrence Download

description: A dataset containing 636 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Hydromantes platycephalus (Camp, 1916))"
 ]
}

 The dataset includes 636 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001839-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/ifao.archives.113633
title: MONASTÈRES COPTES_nb_1973_06501

description: Référence : nb_1973_06501<br />Site : Esna<br />Secteur : Deir el-Chohada; Église primitive<br />Type : photographie<br />
DOI: 10.15468/dl.25wc5f
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bulbostylis gardneriana (Steud.) Beetle"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107882-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.csw7jd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chloropicophyceae",
 "HasCoordinate is true",
 "Country is one of (Romania)",
 "HasGeospatialIssue is false",
 "Year is greater than 2009"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0233401-210914110416597/datasets/export for details.
DOI: 10.15468/dl.94du3z
title: Occurrence Download

description: A dataset containing 429 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Suivi des oiseaux de passage : programme ACT - Programme ACT : Répartition Caille des blés 2002 - 2006 Coordonnées GPS Lambert 93"
 ]
}

 The dataset includes 429 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025728-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/ifao.archives.113632
title: MONASTÈRES COPTES_nb_1973_06221

description: Référence : nb_1973_06221<br />Site : Sohag<br />Secteur : Deir el-Abiad; Hurus<br />Type : photographie<br />
DOI: 10.15468/dl.ae263z
title: Occurrence Download

description: A dataset containing 2327 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "Continent is Europe",
 "Year is greater than 1978",
 "Year is less than 2014",
 "HasGeospatialIssue is false",
 "TaxonKey is Rubia agostinhoi Dans. & P.Silva"
 ]
}

 The dataset includes 2327 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107791-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/ifao.archives.113631
title: MONASTÈRES COPTES_nb_1973_06220

description: Référence : nb_1973_06220<br />Site : Sohag<br />Secteur : Deir el-Abiad<br />Type : photographie<br />
DOI: 10.15468/dl.mgra3y
title: Occurrence Download

description: A dataset containing 2436 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Liliopsida",
 "HasCoordinate is true",
 "Country is one of (Romania)",
 "HasGeospatialIssue is false",
 "Year is greater than 2009"
 ]
}

 The dataset includes 2436 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0233458-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/ifao.archives.113630
title: MONASTÈRES COPTES_nb_1973_06219

description: Référence : nb_1973_06219<br />Site : Sohag<br />Secteur : Deir el-Abiad<br />Type : photographie<br />
DOI: 10.34816/ifao.archives.113629
title: MONASTÈRES COPTES_nb_1973_06218

description: Référence : nb_1973_06218<br />Site : Sohag<br />Secteur : Deir el-Abiad<br />Type : photographie<br />