cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14633185
title: Pangenome Mutation-Annotated Networks

description: Pangenomics is an emerging field that uses a collection of genomes of a species instead of a single reference genome to overcome reference bias and study the within-species genetic diversity. Future pangenomics applications will require analyzing large and ever-growing collections of genomes. Therefore, the choice of data representation is a key determinant of the scope, as well as the computational and memory performance of pangenomic analyses. Current pangenome formats, while capable of storing genetic variations across multiple genomes, fail to capture the shared evolutionary and mutational histories among them, thereby limiting their applications. They are also inefficient for storage, and therefore face significant scaling challenges. In this manuscript, we propose PanMAN, a novel data structure that is information-wise richer than all existing pangenome formats – in addition to representing the alignment and genetic variation in a collection of genomes, PanMAN represents the shared mutational and evolutionary histories inferred between those genomes. By using “evolutionary compression”, PanMAN achieves 5.2 to 680-fold compression over other variation-preserving pangenomic formats. PanMAN's relative performance generally improves with larger datasets and it is compatible with any method for inferring phylogenies and ancestral nucleotide states. Using SARS-CoV-2 as a case study, we show that PanMAN offers a detailed and accurate portrayal of the pathogen's evolutionary and mutational history, facilitating the discovery of new biological insights. We also present panmanUtils, a software toolkit that supports common pangenomic analyses and makes PanMANs interoperable with existing tools and formats. PanMANs are poised to enhance the scale, speed, resolution, and overall scope of pangenomic analyses and data sharing.
DOI: 10.5281/zenodo.15059329
title: Pangenome Mutation-Annotated Networks

description: Pangenomics is an emerging field that uses a collection of genomes of a species instead of a single reference genome to overcome reference bias and study the within-species genetic diversity. Future pangenomics applications will require analyzing large and ever-growing collections of genomes. Therefore, the choice of data representation is a key determinant of the scope, as well as the computational and memory performance of pangenomic analyses. Current pangenome formats, while capable of storing genetic variations across multiple genomes, fail to capture the shared evolutionary and mutational histories among them, thereby limiting their applications. They are also inefficient for storage, and therefore face significant scaling challenges. In this manuscript, we propose PanMAN, a novel data structure that is information-wise richer than all existing pangenome formats – in addition to representing the alignment and genetic variation in a collection of genomes, PanMAN represents the shared mutational and evolutionary histories inferred between those genomes. By using “evolutionary compression”, PanMAN achieves 5.2 to 680-fold compression over other variation-preserving pangenomic formats. PanMAN's relative performance generally improves with larger datasets and it is compatible with any method for inferring phylogenies and ancestral nucleotide states. Using SARS-CoV-2 as a case study, we show that PanMAN offers a detailed and accurate portrayal of the pathogen's evolutionary and mutational history, facilitating the discovery of new biological insights. We also present panmanUtils, a software toolkit that supports common pangenomic analyses and makes PanMANs interoperable with existing tools and formats. PanMANs are poised to enhance the scale, speed, resolution, and overall scope of pangenomic analyses and data sharing.
DOI: 10.26030/9pxd-tj61
title: Microbial Observatory (ISS-MO): Draft Genome Sequence of two Aspergillus fumigatus Strains Isolated from the International Space Station

description: Aspergillus fumigatus is a saprophytic, filamentous fungus that is ubiquitous outdoors (soil, decaying vegetation) and indoors (hospitals, simulated closed habitats, etc.). A. fumigatus can adapt to various environmental conditions and form airborne conidia that are the inoculum for a variety of diseases (e.g. non- and invasive pulmonary infections, allergic bronchopulmonary aspergillosis, etc.) in immunocompromised hosts. In an on-going Microbial Observatory Experiments on the International Space Station (ISS) molecular phylogeny of several fungal isolates were characterized. Two strains, ISSF 21 and IF1SW-F4, were isolated from the HEPA filter and the surface of the Cupola of the ISS, respectively. Using primers targeting the internal transcribed spacers ITS1 and 2, both isolates were identified as A. fumigatus. The whole genome sequence analysis of ISSF 21 revealed increased number of single nucleotide polymorphisms (SNPs) when compared to the reference A. fumigatus 293. Knowing that A. fumigatus is an opportunistic pathogen and microgravity highly influences the antibiotic susceptibility and pathogenicity of microorganisms, we examined pathogenicity of both ISS isolates using the zebrafish larval model. The space station isolates (ISSF-021 and IF1SW-F4) were more virulent than two clinical strains (Af293 and CEA10) whose pathogenicity was highly characterized. Here the whole genome sequences of ISSF-021 strain are being deposited.
DOI: 10.15468/dl.8sua8u
title: Occurrence Download

description: A dataset containing 342 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "TaxonKey is Ceroxylon Bonpl. ex DC."
 ]
}

 The dataset includes 342 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019257-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jhszxz
title: Occurrence Download

description: A dataset containing 676 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Falagria caesa Erichson, 1837",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 676 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019256-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15002560
title: Dataset of Leaf Phenology and Physiological Status: Chlorophyll Content and Spectral Vegetation Indices for Multiple Plant Species

description: This dataset, named “Seguimiento_fenologico”, contains data from a phenological study focused on monitoring several plant species' leaf development and physiological state. The study uses non-destructive methods, combining chlorophyll content measurements with a wide range of spectral indices of vegetation derived from leaf reflectance.

The columns included in the dataset are:

Plant species: the plant species from which the leaf sample was taken (e.g., Coffea arabica, Manihot esculenta, Persea americana, Musa paradisiaca, Saccharum officinarum, Solanum lycopersicum, Solanum tuberosum, Zea mays).

Leaf: Descriptor indicating leaf number.Chlorophyll A: Measure of chlorophyll A content in the leaf. Chlorophyll B: Measure of chlorophyll B content in the leaf. NDVI: Widely used vegetation index sensitive to green biomass.GNDVI: Similar to NDVI but using the green and near-infrared bands, often more sensitive to chlorophyll content.NDRE: Uses the red-edge band, which is especially sensitive to chlorophyll content and plant stress.OSAVI: Index designed to minimize the effects of soil background on vegetation indices.CVI: Index related explicitly to chlorophyll content.CCCI: Index designed to estimate canopy chlorophyll content.EVI: Enhanced vegetation index that minimizes canopy background and atmospheric influences.ARVI: Index designed to be less sensitive to atmospheric effects.ARVI2: A variation of ARVI.GLI: A simple index based on a green band, often related to greenness.ATSAVI: Another soil-adjusted vegetation index.RBNDVI: NDVI was calculated using the red and blue bands.NGRDI: The color index is based on the green and red bands.IVC: A simple vegetation index calculated as the difference between near-infrared and red reflectance.GARI: Green-focused atmospheric resistance index.RDVI: A variation of DVI.NLI: Nonlinear vegetation index.MNLI: A modified version of NLI.MSAVI2: An enhanced soil-adjusted vegetation index.TDVI: A transformed version of DVI.GEMI: Nonlinear vegetation index less sensitive to atmospheric effects.CIGreen: Chlorophyll index based on the green band.SR: Simple ratio vegetation index, often NIR/Red.IPVI: Percentage of infrared reflectance.GRNDVI: Another variation of NDVI uses green and red bands.GBNDVI: Variation of NDVI using green and blue bands.BNDVI: NDVI variation using blue and red bands.CIrededge: Chlorophyll index using the red-edge band.NDWI: Index sensitive to water content in vegetation.RENDVI: Another variation of NDVI using the red-edge band.RENDVI2: A variation of RENDVI.MTCI: The Chlorophyll index was explicitly designed for MERIS data but applies to other data sets.Leaf stage: Phenological stage of the leaf (e.g., Ripening, Senescence, Wilting).
DOI: 10.5281/zenodo.15002561
title: Dataset of Leaf Phenology and Physiological Status: Chlorophyll Content and Spectral Vegetation Indices for Multiple Plant Species

description: This dataset, named “Seguimiento_fenologico”, contains data from a phenological study focused on monitoring several plant species' leaf development and physiological state. The study uses non-destructive methods, combining chlorophyll content measurements with a wide range of spectral indices of vegetation derived from leaf reflectance.

The columns included in the dataset are:

Plant species: the plant species from which the leaf sample was taken (e.g., Coffea arabica, Manihot esculenta, Persea americana, Musa paradisiaca, Saccharum officinarum, Solanum lycopersicum, Solanum tuberosum, Zea mays).

Leaf: Descriptor indicating leaf number.Chlorophyll A: Measure of chlorophyll A content in the leaf. Chlorophyll B: Measure of chlorophyll B content in the leaf. NDVI: Widely used vegetation index sensitive to green biomass.GNDVI: Similar to NDVI but using the green and near-infrared bands, often more sensitive to chlorophyll content.NDRE: Uses the red-edge band, which is especially sensitive to chlorophyll content and plant stress.OSAVI: Index designed to minimize the effects of soil background on vegetation indices.CVI: Index related explicitly to chlorophyll content.CCCI: Index designed to estimate canopy chlorophyll content.EVI: Enhanced vegetation index that minimizes canopy background and atmospheric influences.ARVI: Index designed to be less sensitive to atmospheric effects.ARVI2: A variation of ARVI.GLI: A simple index based on a green band, often related to greenness.ATSAVI: Another soil-adjusted vegetation index.RBNDVI: NDVI was calculated using the red and blue bands.NGRDI: The color index is based on the green and red bands.IVC: A simple vegetation index calculated as the difference between near-infrared and red reflectance.GARI: Green-focused atmospheric resistance index.RDVI: A variation of DVI.NLI: Nonlinear vegetation index.MNLI: A modified version of NLI.MSAVI2: An enhanced soil-adjusted vegetation index.TDVI: A transformed version of DVI.GEMI: Nonlinear vegetation index less sensitive to atmospheric effects.CIGreen: Chlorophyll index based on the green band.SR: Simple ratio vegetation index, often NIR/Red.IPVI: Percentage of infrared reflectance.GRNDVI: Another variation of NDVI uses green and red bands.GBNDVI: Variation of NDVI using green and blue bands.BNDVI: NDVI variation using blue and red bands.CIrededge: Chlorophyll index using the red-edge band.NDWI: Index sensitive to water content in vegetation.RENDVI: Another variation of NDVI using the red-edge band.RENDVI2: A variation of RENDVI.MTCI: The Chlorophyll index was explicitly designed for MERIS data but applies to other data sets.Leaf stage: Phenological stage of the leaf (e.g., Ripening, Senescence, Wilting).
DOI: 10.15468/dl.82gvzg
title: Occurrence Download

description: A dataset listing the 4 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-89.25335 48.42582,-89.27103 48.42092,-89.27099 48.41107,-89.26435 48.41098,-89.26135 48.41173,-89.25858 48.41193,-89.2582 48.41801,-89.25739 48.41868,-89.25577 48.4194,-89.2537 48.42001,-89.25304 48.42102,-89.25289 48.42415,-89.25291 48.42544,-89.25335 48.42582))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (EN, VU, NT, CR)",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 4 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019253-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.564fp8
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-18.84747 29.4288,-14.27952 29.4288,-14.27952 33.3908,-18.84747 33.3908,-18.84747 29.4288))",
 "OccurrenceStatus is Present",
 "TaxonKey is Lobularia canariensis subsp. rosula-venti (Svent.) L.Borgen"
 ]
}

 The dataset includes 38 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019258-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m65cvm
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Egretta eulophotes (Swinhoe, 1860)",
 "Year 2024-2025"
 ]
}

 The dataset's 1 records were derived from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019251-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.5794319
title: Grammar [IO Bijapur 14] الكافية فى النحو

description: Grammar.

This manuscript is now IO Bijapur 14 in the India Office collections.

[metadata: Otto Loth, A Catalogue of the Arabic Manuscripts in the Library of the India Office, (volume 1), no. 901 here with notations and hyperlinks].


901

B 14. Size 91/2 in. by 51/2 in.; foll. 227. Three lines in a page.

IBN ḤÂJIB'S (Jamâl al-dîn Abu ‘Amr ‘Othmân b. ‘Omar, d. A.H. 646) الكافية فى النحو . See Ḥ. Kh. v. 6 ; Cat. St. Petersb. 154; Flügel [d. 1870], Hdss. Wien, i. 162; etc.

Published at Rome, 1592. Edited by Baillie (Five Books on Arabic Grammar, vol. iii.), Calcutta, 1803.

Printed at Bûlâḳ, A.H. 1255, etc. Cf. [Hendrik Engelinus] Weijers [1805-44] in Orientalia, i. 349 sqq. 

Well written, with vowel-points. Copious marginal notes.

The seal of Muḥammad ‘Âdil Shâh [d. 1656 CE] is on the title-page, and that of Âḳâ Riḍwân ‘Âdilshâhî is at the end of the book. Library of ‘Âlamgîr, A.H. 1069.

Cat. 235, iii.

[Bijapur Collection]
DOI: 10.5281/zenodo.5794320
title: Grammar [IO Bijapur 14] الكافية فى النحو

description: Grammar.

This manuscript is now IO Bijapur 14 in the India Office collections.

[metadata: Otto Loth, A Catalogue of the Arabic Manuscripts in the Library of the India Office, (volume 1), no. 901 here with notations and hyperlinks].


901

B 14. Size 91/2 in. by 51/2 in.; foll. 227. Three lines in a page.

IBN ḤÂJIB'S (Jamâl al-dîn Abu ‘Amr ‘Othmân b. ‘Omar, d. A.H. 646) الكافية فى النحو . See Ḥ. Kh. v. 6 ; Cat. St. Petersb. 154; Flügel [d. 1870], Hdss. Wien, i. 162; etc.

Published at Rome, 1592. Edited by Baillie (Five Books on Arabic Grammar, vol. iii.), Calcutta, 1803.

Printed at Bûlâḳ, A.H. 1255, etc. Cf. [Hendrik Engelinus] Weijers [1805-44] in Orientalia, i. 349 sqq. 

Well written, with vowel-points. Copious marginal notes.

The seal of Muḥammad ‘Âdil Shâh [d. 1656 CE] is on the title-page, and that of Âḳâ Riḍwân ‘Âdilshâhî is at the end of the book. Library of ‘Âlamgîr, A.H. 1069.

Cat. 235, iii.

[Bijapur Collection]
DOI: 10.15468/dl.8aqr5c
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-74.2922 40.49768,-73.75094 40.57622,-73.78798 40.85649,-73.92397 40.89541,-74.07849 40.64777,-74.19087 40.6353,-74.2922 40.49768))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Dianthus armeria L."
 ]
}

 The dataset includes 16 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019259-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eabtt8
title: Occurrence Download

description: A dataset containing 527503 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Calystegia sepium (L.) R.Br."
 ]
}

 The dataset includes 527503 records from 2752 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019240-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13145/bacdive112246.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112246.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0103894.10fu
title: SH0103894.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5517/ccdc.csd.cc2pg52f
title: CCDC 2486264: Experimental Crystal Structure Determination

description: Related Article: Yu Liu, Lan Bao, Xiang Lyu, Zhonglin Wang, Zhengrun Chen, Jinhuan Dong, Xianxiu Xu, Zhongyan Hu|2025|Chin.Chem.Lett.|||doi:10.1016/j.cclet.2025.112201
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/ccdc.csd.cc2phg7x
title: CCDC 2487509: Experimental Crystal Structure Determination

description: Related Article: Alireza Najafipour, Rahman Bikas, Neda Heydari, Tadeusz Lis|2025|Inorg.Chem.Commun.|183||doi:10.1016/j.inoche.2025.115825
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: 10.13145/bacdive112247.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112247.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0103895.10fu
title: SH0103895.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5517/ccdc.csd.cc2phg8y
title: CCDC 2487510: Experimental Crystal Structure Determination

description: Related Article: Alireza Najafipour, Rahman Bikas, Neda Heydari, Tadeusz Lis|2025|Inorg.Chem.Commun.|183||doi:10.1016/j.inoche.2025.115825
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/ccdc.csd.cc2phg9z
title: CCDC 2487511: Experimental Crystal Structure Determination

description: Related Article: Alireza Najafipour, Rahman Bikas, Neda Heydari, Tadeusz Lis|2025|Inorg.Chem.Commun.|183||doi:10.1016/j.inoche.2025.115825
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: 10.13145/bacdive112248.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112248.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.