cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29828864
title: Gene annotation of<i> </i><i>Babesia ovis</i> (Israeli strain)

description: This dataset contains gene annotation information for a laboratory strain of <i>Babesia ovis</i> (Israeli strain).File Descriptionbovis_annotation_public.gff<br>This file contains the gene models predicted for <i>Babesia ovis</i>Gene annotation methodsRepeat MaskingPrior to structural annotation we created a species-specific repeat library using the RepeatModeler2 v2.0.2a package. From this repeat library, identification and masking of repeat sequences present in the genome was performed using RepeatMasker v4.1.5 (available at https://www.repeatmasker.org/). With this approach, approximately 16% of the genome was masked, roughly matching the predicted repetitive fraction from k-mer frequency analysis (Figure 1).Structural annotationStructural annotation was performed on the repeat-masked genome with Braker v3.0.3 incorporating external evidence in the form of all alveolata proteins from OrthoDB v11 (https://bioinf.uni-greifswald.de/bioinf/partitioned_odb11). Redundant gene models from GeneMark.hmm3 were removed.Functional annotationThe predicted genes were functionally annotated using the NBIS functional_annotation nextflow pipeline v2.0.0 (https://github.com/NBISweden/pipelines-nextflow). Briefly, this pipeline performs similarity searches between the annotated proteins and the UniProtKB/Swiss-Prot database (downloaded on 2022-12; 568,363 proteins) using BLAST. Then it uses InterProScan to query the proteins against InterPro v59-91 databases, and merges results using AGAT v1.2.0.tRNAs and rRNAsTransfer RNAs (tRNAs) were annotated using tRNAscan-SE v2.0.12. This analysis identified 46 tRNA genes. Ribosomal RNAs (rRNAs) were annotated using barrnap v0.9 (available at https://github.com/tseemann/barrnap). This analysis identified 13 rRNA genes including 3 copies of 18S, 5.8S, and 28S rRNAs, and 4 copies of 5S.Annotation integrationThe functionally annotated gene models were combined with organelle gene predictions and tRNA and rRNA predictions into the "bovis_annotation_public.gff" file available here.The genome assembly for <i>Babesia ovis</i> is not included in this dataset, as it is publicly available in the National Center for Biotechnology Information (NCBI) under accession GCA_051529585.1.<br>
DOI: 10.6084/m9.figshare.29828864.v1
title: Gene annotation of<i> </i><i>Babesia ovis</i> (Israeli strain)

description: This dataset contains gene annotation information for a laboratory strain of <i>Babesia ovis</i> (Israeli strain).File Descriptionbovis_annotation_public.gff<br>This file contains the gene models predicted for <i>Babesia ovis</i>Gene annotation methodsRepeat MaskingPrior to structural annotation we created a species-specific repeat library using the RepeatModeler2 v2.0.2a package. From this repeat library, identification and masking of repeat sequences present in the genome was performed using RepeatMasker v4.1.5 (available at https://www.repeatmasker.org/). With this approach, approximately 16% of the genome was masked, roughly matching the predicted repetitive fraction from k-mer frequency analysis (Figure 1).Structural annotationStructural annotation was performed on the repeat-masked genome with Braker v3.0.3 incorporating external evidence in the form of all alveolata proteins from OrthoDB v11 (https://bioinf.uni-greifswald.de/bioinf/partitioned_odb11). Redundant gene models from GeneMark.hmm3 were removed.Functional annotationThe predicted genes were functionally annotated using the NBIS functional_annotation nextflow pipeline v2.0.0 (https://github.com/NBISweden/pipelines-nextflow). Briefly, this pipeline performs similarity searches between the annotated proteins and the UniProtKB/Swiss-Prot database (downloaded on 2022-12; 568,363 proteins) using BLAST. Then it uses InterProScan to query the proteins against InterPro v59-91 databases, and merges results using AGAT v1.2.0.tRNAs and rRNAsTransfer RNAs (tRNAs) were annotated using tRNAscan-SE v2.0.12. This analysis identified 46 tRNA genes. Ribosomal RNAs (rRNAs) were annotated using barrnap v0.9 (available at https://github.com/tseemann/barrnap). This analysis identified 13 rRNA genes including 3 copies of 18S, 5.8S, and 28S rRNAs, and 4 copies of 5S.Annotation integrationThe functionally annotated gene models were combined with organelle gene predictions and tRNA and rRNA predictions into the "bovis_annotation_public.gff" file available here.The genome assembly for <i>Babesia ovis</i> is not included in this dataset, as it is publicly available in the National Center for Biotechnology Information (NCBI) under accession GCA_051529585.1.<br>
DOI: 10.15468/dl.8ntdjz
title: Occurrence Download

description: A dataset containing 2436 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Myrmotherula cherriei)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 2436 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015196-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bmg7t8
title: Occurrence Download

description: A dataset containing 28135 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dama dama",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 28135 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015195-250802193616735/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.29828666
title: Aligned supermatrix of Campylotropis

description: The shrub genus <i>Campylotropis </i>(Fabaceae, trib. Desmodieae, subtrib. Lespedezinae), encompasses approximately 40 species, predominantly distributed across temperate and subtropical East Asia, with its diversity centered in the Hengduan Mountains and southern China. Historical constraints in sampling and methodological approaches have long obscured its evolutionary history and species relationships. This study provides the most comprehensive phylogenomic analysis of <i>Campylotropis</i> to date, incorporating 91 samples representing 40 taxa. Leveraging sequence data from 77 plastid genes and 1,233 single-copy nuclear genes (SCGs), we reconstructed the genus’s phylogenomic framework, estimated divergence times, inferred ancestral area distributions, and traced the evolution of key morphological traits. Our results robustly confirm the monophyly of <i>Campylotropis</i>, distinguishing it from allied genera. We delineated six well-supported clades within the genus and resolved previously unresolved relationships. We found that global climate change and tectonic activities since the late Miocene likely shaped lineage diversification, with Quaternary climate oscillations potentially triggering rapid radiation within the genus. Ancestral area reconstruction suggests that <i>Campylotropis</i> originated in the Hengduan Mountains and southern China before dispersing swiftly across adjacent East Asian regions. By integrating extensive sampling with nuclear genomic data, this study elucidates the evolutionary history of <i>Campylotropis</i> and enhances our understanding of diversification processes in biodiversity hotspots.
DOI: 10.6084/m9.figshare.29828666.v2
title: Aligned supermatrix of Campylotropis

description: The shrub genus <i>Campylotropis </i>(Fabaceae, trib. Desmodieae, subtrib. Lespedezinae), encompasses approximately 40 species, predominantly distributed across temperate and subtropical East Asia, with its diversity centered in the Hengduan Mountains and southern China. Historical constraints in sampling and methodological approaches have long obscured its evolutionary history and species relationships. This study provides the most comprehensive phylogenomic analysis of <i>Campylotropis</i> to date, incorporating 91 samples representing 40 taxa. Leveraging sequence data from 77 plastid genes and 1,233 single-copy nuclear genes (SCGs), we reconstructed the genus’s phylogenomic framework, estimated divergence times, inferred ancestral area distributions, and traced the evolution of key morphological traits. Our results robustly confirm the monophyly of <i>Campylotropis</i>, distinguishing it from allied genera. We delineated six well-supported clades within the genus and resolved previously unresolved relationships. We found that global climate change and tectonic activities since the late Miocene likely shaped lineage diversification, with Quaternary climate oscillations potentially triggering rapid radiation within the genus. Ancestral area reconstruction suggests that <i>Campylotropis</i> originated in the Hengduan Mountains and southern China before dispersing swiftly across adjacent East Asian regions. By integrating extensive sampling with nuclear genomic data, this study elucidates the evolutionary history of <i>Campylotropis</i> and enhances our understanding of diversification processes in biodiversity hotspots.
DOI: 10.6084/m9.figshare.29828666.v1
title: 齐上Campylotropis 的

description: 灌木属 <i>Campylotropis</i>（豆科，trib.Desmodieae，亚类。Lespedezinae）包括大约 40 个物种，主要分布在温带和亚热带东亚，其多样性集中在横断山脉和中国南部。长期以来，抽样和方法论方法的历史限制掩盖了其进化历史和物种关系。这项研究提供了<i>Campylotropis</i>的 91 个样本0。利用77个质体基因和1,233单拷贝核基因（SCG），重建了该属的系统发育框架，估计了发散时间，推断了祖先面积分布，并追踪了关键形态性状的演变。我们的结果有力地证实<i>Campylotropis</i>，将其与相关属区分开来。我们划定了该属内六个得到充分支持的进化枝，并解决了以前未解决的关系。我们发现全球气候变化和自中新世晚期以来可能塑造了谱系多样化，第四纪气候振荡可能会引发该属内的快速辐射。祖先区域重建表明，<i>寒门</i>起源于横断山脉和中国南部，然后迅速扩散到邻近的东亚地区。通过将广泛的采样与核基因组数据相结合，本研究阐明<i>坎幽门虫</i>，并增强了我们对生物多样性热点地区多样化过程的理解。
DOI: 10.15472/2b7erz
title: Diversidad de bacterias en el suelo del Páramo de Chingaza

description: En este trabajo muestra la diversidad de bacterias en el suelo del Páramo de Chingaza y en la materia orgánica semi-descompuesta de la turbera ubicada en laguna seca.
DOI: 10.15468/dl.264v5r
title: Occurrence Download

description: A dataset containing 9106 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CAN",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Monochamus"
 ]
}

 The dataset includes 9106 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015197-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5mgkjh
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dama dama",
 "Country is North Macedonia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015198-250802193616735/datasets/export for details.
DOI: 10.5066/f7765ch1
title: Exposure potential of salt marsh units in Edwin B. Forsythe National Wildlife Refuge to environmental health stressors

description: Natural and anthropogenic contaminants, pathogens, and viruses are found in soils and sediments throughout the United States. Enhanced dispersion and concentration of these environmental health stressors in coastal regions can result from sea level rise and storm-derived disturbances. The combination of existing environmental health stressors and those mobilized by natural or anthropogenic disasters could adversely impact the health and resilience of coastal communities and ecosystems. This dataset displays the exposure potential to environmental health stressors in the Edwin B. Forsythe National Wildlife Refuge (EBFNWR), which spans over Great Bay, Little Egg Harbor, and Barnegat Bay in New Jersey, USA. Exposure potential is calculated with the Sediment-bound Contaminant Resiliency and Response (SCoRR) ranking system (Reilly and others, 2015) designed to define baseline and post-event sediment-bound environmental health stressors. Facilities obtained from the Environmental Protection Agencys (EPA) Toxic Release Inventory (TRI) and Facility Registry Service (FRS) databases were ranked based on their potential contaminant hazard. Ranks were based in part on previous work by Olsen and others (2013), literature reviews, and an expert review panel. A 2000 meter search radius was used to identify nearby ranked facility locations. As part of the Hurricane Sandy Science Plan, the U.S. Geological Survey has started a Wetland Synthesis Project to expand National Assessment of Coastal Change Hazards and forecast products to coastal wetlands. The intent is to provide federal, state, and local managers with tools to estimate their vulnerability and ecosystem service potential. For this purpose, the response and resilience of coastal wetlands to physical factors need to be assessed in terms of the ensuing change to their vulnerability and ecosystem services. EBFNWR was selected as a pilot study area.
DOI: 10.6084/m9.figshare.29828870
title: Data - Borrowing Discouragement and SMEs.xlsx

description: This dataset is extracted from the World Bank Enterprise Surveys and represents borrower discouragement data for numerous countries and is limited to SMEs with less than 250 full-time employees and Sales of less than $500 million.
DOI: 10.6084/m9.figshare.29828870.v1
title: Data - Borrowing Discouragement and SMEs.xlsx

description: This dataset is extracted from the World Bank Enterprise Surveys and represents borrower discouragement data for numerous countries and is limited to SMEs with less than 250 full-time employees and Sales of less than $500 million.
DOI: 10.15468/dl.ycvunw
title: Occurrence Download

description: A dataset containing 111 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dama dama",
 "Country is Norway",
 "HasCoordinate is true"
 ]
}

 The dataset includes 111 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015201-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7ksyyh
title: Occurrence Download

description: A dataset containing 10791 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Epibulus insidiator"
 ]
}

 The dataset includes 10791 records from 143 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015202-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wep54b
title: Occurrence Download

description: A dataset containing 7984 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Myrmotherula ignota)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 7984 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015200-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xf724x
title: Occurrence Download

description: A dataset containing 105 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Myrmotherula grisea)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 105 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015203-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16316012
title: Shifu-inspired fungal paper yarns
DOI: 10.5281/zenodo.16608835
title: Shifu-inspired fungal paper yarns
DOI: 10.25824/redu/up7gan
title: Dataset generated during the study of violacein production parameters by Janthinobacterium sp. in cultures conducted in shaken flasks

description: This dataset contains UV-Vis spectrophotometric data collected during the study of pigment (violacein) production parameters and cell growth throughout the cultivation of Janthinobacterium sp. in shaken flasks, conducted using an experimental design approach.
DOI: 10.15468/dl.cenbe4
title: Occurrence Download

description: A dataset containing 22221 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Geometry POLYGON((-115.1647 37.65684,-115.378 37.67373,-115.4271 37.50599,-115.4504 37.61634,-115.6779 37.54731,-115.5296 37.24377,-115.7473 37.02409,-116.0185 37.27166,-115.928 36.99763,-115.9906 36.93546,-116.6995 36.9972,-116.8065 37.28315,-116.9092 37.19524,-117.0246 37.43963,-117.1808 37.52838,-117.879 37.40723,-117.9617 37.28309,-117.8731 37.28723,-117.7944 37.07732,-117.9544 37.00084,-117.9515 36.88746,-117.8227 36.66252,-117.5905 36.53221,-117.702 36.54888,-117.7001 36.33985,-117.8002 36.52408,-117.9937 36.60588,-118.0845 36.84138,-118.2462 36.70385,-118.0401 36.46577,-117.8747 35.6612,-118.1077 35.52994,-118.0064 35.30001,-118.067 35.21965,-118.7917 34.78093,-118.4387 34.71956,-117.4643 34.26589,-117.1769 34.41801,-116.4889 34.32896,-116.5167 34.16457,-116.3997 34.13626,-116.4803 34.10575,-116.3148 34.09686,-115.9023 33.67817,-115.4918 33.71225,-115.3721 33.95609,-115.2841 33.87187,-115.5649 34.39096,-115.3579 34.50802,-115.2336 34.50913,-115.1734 34.281,-115.0287 34.49015,-114.9045 34.48742,-114.8483 34.31828,-114.0637 34.52534,-113.7549 34.46349,-113.6928 34.6298,-113.9285 34.76649,-114.0439 35.11463,-113.8177 35.22367,-113.8187 35.40141,-113.7145 35.4153,-113.8815 35.71407,-114.0844 35.81357,-113.816 36.22755,-113.7161 36.52703,-113.7669 36.72443,-113.3502 36.84576,-113.2794 37.29557,-113.8386 37.20913,-113.9632 37.38364,-114.3332 37.26329,-114.575 37.38097,-114.8029 37.22457,-114.8184 37.32927,-114.9423 37.28012,-115.1626 37.47778,-115.1647 37.65684))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pipilo maculatus"
 ]
}

 The dataset includes 22221 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015204-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5066/f7w37tgk
title: Continuous and optimized 3-arcsecond elevation model for United States east and west coasts

description: Investigations of coastal change and coastal resources often require continuous elevation profiles from the seafloor to coastal terrestrial landscapes. Differences in elevation data collection in the terrestrial and marine environments result in separate elevation products that may not share a vertical datum. This data release contains the compilation of multiple elevation products into a continuous digital elevation model at a resolution of 3-arcseconds (approximately 90 meters) from the terrestrial landscape to the seafloor for the contiguous U.S. and portions of Mexico and Canada, focused on the coastal interface. All datasets were converted to a consistent horizontal datum, the North American Datum of 1983, but the native vertical datum for each dataset was not adjusted. Artifacts in the source elevation products were identified visually and replaced with other available elevation products when possible, corrected using various spatial tools, or otherwise marked for future correction.
DOI: 10.15468/dl.82ha3z
title: Occurrence Download

description: A dataset containing 21128 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Eichhornia crassipes"
 ]
}

 The dataset includes 21128 records from 641 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015206-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/8t3-cwb-63r
title: †Lytoceras sutile (Oppel, 1863)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yf0-3hq-ne0
title: Kayserops

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7rc-3lg-nea
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5qd-1fv-vx1
title: Phacops

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c1g-4ns-35w
title: Equus (Equus) caballus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vkh-9bx-acq
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z0h-l8f-694
title: Myodes Pallas, 1811

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3kl-sl3-l34
title: †Protetragonites quadrisulcatus (d'Orbigny, 1841)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xb5-8mf-shn
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/t8a-5q8-qza
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1rz-4qr-a5k
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8rr-p3t-8b4
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h2x-mhq-6d4
title: Kayserops

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wsp-g0g-8my
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bjc-jse-j13
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wqa-ygh-mhm
title: Equus (Equus) caballus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/drs-n6k-glz
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6s9-1en-bxc
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wfm-ryy-p8p
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m5w-e9q-tjf
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pfz-qh1-nrk
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s3h-wla-cq7
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/01s-bwx-m9t
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c5q-vdv-0pl
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/78q-d1c-tnl
title: Branchiopoda

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kn1-myv-56f
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.