cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15117900
title: Dataset of bond dissociation energies

description:  

This directory consists of the data files needed to train BonDNet. Note, further processing might be needed to extract the necessary information, since this is not formatted the same as what BonDNet expects. See the below link for what BonDNet expects: https://github.com/mjwen/bondnet/tree/master/bondnet/scripts/examples/train

Files





molecules.sdf All molecules in the dataset are stored in this file. The file is in SDF format, which can be read by RdKit, Open Babel or other cheminformatics tools.




molecule_attributes.yaml This consists of additional attributes for each molecule in the dataset. Note, they are not used in the BonDNet paper.




reactions.yaml This file consists of all the bond dissociation reactions, a reaction may look like this:



- atom_mapping:
    - 0: 0
      1: 2
      2: 1
    - 0: 3
  bond_mapping:
    - 0: 2
      1: 0
      2: 3
    - {}
  id: 5f07dfcc578f819b3d12721e_broken_bond-0-3_species-C-H
  index: 1
  products:
    - 8251
    - 97
  reactants:
    - 7943
  value: 4.331072762383323


 

Here are the key fields:



reactants: ID of the reactant molecules (in the molecules.sdf file)

products: ID of the product molecules (in the molecules.sdf file)

value: The bond dissociation energy of the reaction in eV

atom_mapping: The mapping of atoms in the reactants and products. The first index is the reactant index, the second index is the product index.

bond_mapping: The mapping of bonds in the reactants and products. The first index is the reactant index, the second index is the product index.


Reference



Wen, Mingjian, Samuel M. Blau, Evan Walter Clark Spotte-Smith, Shyam Dwaraknath, and Kristin A. Persson. "BonDNet: a graph neural network for the prediction of bond dissociation energies for charged molecules." Chemical science 12, no. 5 (2021): 1858-1868.
DOI: 10.5281/zenodo.15117901
title: Dataset of bond dissociation energies

description:  

This directory consists of the data files needed to train BonDNet. Note, further processing might be needed to extract the necessary information, since this is not formatted the same as what BonDNet expects. See the below link for what BonDNet expects: https://github.com/mjwen/bondnet/tree/master/bondnet/scripts/examples/train

Files





molecules.sdf All molecules in the dataset are stored in this file. The file is in SDF format, which can be read by RdKit, Open Babel or other cheminformatics tools.




molecule_attributes.yaml This consists of additional attributes for each molecule in the dataset. Note, they are not used in the BonDNet paper.




reactions.yaml This file consists of all the bond dissociation reactions, a reaction may look like this:



- atom_mapping:
    - 0: 0
      1: 2
      2: 1
    - 0: 3
  bond_mapping:
    - 0: 2
      1: 0
      2: 3
    - {}
  id: 5f07dfcc578f819b3d12721e_broken_bond-0-3_species-C-H
  index: 1
  products:
    - 8251
    - 97
  reactants:
    - 7943
  value: 4.331072762383323


 

Here are the key fields:



reactants: ID of the reactant molecules (in the molecules.sdf file)

products: ID of the product molecules (in the molecules.sdf file)

value: The bond dissociation energy of the reaction in eV

atom_mapping: The mapping of atoms in the reactants and products. The first index is the reactant index, the second index is the product index.

bond_mapping: The mapping of bonds in the reactants and products. The first index is the reactant index, the second index is the product index.


Reference



Wen, Mingjian, Samuel M. Blau, Evan Walter Clark Spotte-Smith, Shyam Dwaraknath, and Kristin A. Persson. "BonDNet: a graph neural network for the prediction of bond dissociation energies for charged molecules." Chemical science 12, no. 5 (2021): 1858-1868.
DOI: 10.6084/m9.figshare.21571602.v4
title: data.zip

description: Ground reaction force，Muscle force, joint force，Joint torque，Skeletal model
DOI: 10.3535/nt9-7vk-p2k
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/y5y-hbj-808
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.15121602.v1
title: FlamingoComplete2.25.21.csv

description: <b>Wading through water: effects of water depth and speed on the drag and kinematics of walking Chilean flamingos, <i>Phoenicopterus chilensis</i></b>
DOI: 10.25573/data.28230089.v1
title: 787.3 Raw Data

description: This data contains the demultiplexed sequencing reads for all of the larvae as well as the male paternal parent for 787.3. Data is paired end.
DOI: 10.3535/0aj-jql-slr
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wnn-ghc-306
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/138-pc6-9l8
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/x84-qzd-hk2
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/q1v-yje-6t9
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/sn4-f6y-x44
title: Minerals

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bk7-tzk-0a3
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/l28-ll7-vjv
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/7j3-bye-gs8
title: †Holopea J. Hall, 1847

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/pz1-0vy-ll1
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/apb-eax-4y5
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ghd-ryc-cs7
title: Minerals

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.7516277.v1
title: Physical and Mechanical Characterization of Eucalyptus camaldulensis Young Wood for Rural Architecture Uses

description: ABSTRACT This study aimed to analyze the quality of Eucalyptus camaldulensis young wood of planted trees in Rio Tinto, Paraíba, Brazil, for use in rural architecture. Physico-mechanical tests were carried out through simplified characterization. The physical tests obtained were moisture content, basic and apparent specific gravity and shrinkage of the wood, in addition to the anisotropy coefficient. To obtain the compression parallel to fibers results, linear variable differential transformers (LVDTs) bound to the sample and the data acquisition system for the determination of the resistance and stiffness values of wood were used. The values obtained showed that the young wood of E. camaldulensis fits in 20 C strength rating for hardwoods, determined by the Brazilian Standard, still not being recommended for structural purposes, but appropriate to be applied in secondary elements of rural architecture, as fences, playgrounds and for rustic furniture manufacture.
DOI: 10.3535/9ch-p94-sf4
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/mky-rxa-tb0
title: †Holopea J. Hall, 1847

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/cks-k0k-vfq
title: †Subulites Emmons, 1842

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/n6e-02v-1cg
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/z7x-8am-psm
title: †Subulites Emmons, 1842

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zgp-906-xfl
title: Calcite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.13237940.v1
title: Pore-scale Modeling of Spontaneous Imbibition in Porous Media Using the Lattice Boltzmann Method

description: These data is uesd in the paper "Pore-scale Modeling of Spontaneous Imbibition in Porous Media Using the Lattice Boltzmann Method".
DOI: 10.6084/m9.figshare.24489868.v1
title: Data associated with the manuscript "Optical, electronic, and structural properties of ScAlMgO4" by T. Stefaniuk et al., Physical Review B 107, 085205 (2023).

description: Data associated with the manuscript "Optical, electronic, and structural properties of ScAlMgO4" by T. Stefaniuk et al., Physical Review B 107, 085205 (2023).
DOI: 10.3535/175-aaq-mh5
title: †Subulites Emmons, 1842

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/169-lap-v8p
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/e7p-vfe-v4n
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.19735525.v1
title: Cognitive energy budgets

description: <strong>Cognitive energy budgets</strong> <br> Explore cognitive overload in computational and screen time work balanced with the remainder of 'life'.
DOI: 10.3535/1dj-kgx-aka
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/eyh-vws-tjl
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/atp-dje-3zx
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/msl-h7w-n1v
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.1142735.v1
title: Expanding on the 1st example of the train scenario

description: Expanding on the 1st example of the train scenario
DOI: 10.3535/acv-db7-q9g
title: †Dalmanella Hall & Clarke, 1892

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/w08-c1k-ync
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/550-nwa-4qa
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/btd-k1h-qnb
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.25922182.v3
title: Data associated with Fusarium asiaticum vivivirus 1

description: The discovery of diverse segmented RNA viruses through metatranscriptomics has enabled researchers to trace the evolutionary trajectories of these viruses. However, this effort has been hindered by the limited availability of complete genome sequences and the low similarity of novel viral segments. In this study, we characterized Fusarium asiaticum vivivirus 1 (FaVvV1), a +ssRNA mycovirus with 10 RNA segments (S1 to S10, encoding VP1 to VP10), in phytopathogenic fungus Fusarium asiaticum. VP1 and VP2 exhibit homology to replication proteins of martellivirals, while VP3 and VP5 share similarities with nuclear inclusion protein a and cylindrical inclusion helicase of potyvirids, respectively. FaVvV1 forms rod-shaped virions, with VP8 functions as a structural protein resembling the helical capsid of potyvirids and closterovirids. To explore the conservation and evolution of viviviruses, we mined 23 published SRA datasets, identifying 29 vivivirus-related viruses (vivivirids) comprising a total of 186 viral segments. VP1–VP3, VP5, and VP8 were identified as conserved hallmark proteins of viviviruses. Phylogenetic and structural analyses suggest multiple genome segmentations and gene/domain duplications involved in the evolution of vivivirids. VP3, VP5 and VP8 probably share a common ancestor with potyvirids. These findings highlight the intricate evolutionary mechanisms underlying segmented virus diversity and adaptation.
DOI: 10.3535/dvb-wdb-d7t
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.1612249.v1
title: Primeros Auxilios

description: Conceptos Básicos de primeros Auxilios , para los trabajadores de las empresas
DOI: 10.3535/395-7ak-kld
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/76m-f1d-z7y
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/l0d-r9d-kch
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/lhv-1n3-10m
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.4737835.v1
title: Oblique wedge extrusion of UHP/HP complexes in the Late Triassic: structural analysis and zircon ages of the Atbashi Complex, South Tianshan, Kyrgyzstan

description: The exhumation and tectonic emplacement of eclogites and blueschists takes place in forearc accretionary complexes by either forearc- or backarc-directed extrusion, but few examples have been well analysed in detail. Here we present an example of oblique wedge extrusion of UHP/HP rocks in the Atbashi accretionary complex of the Kyrgyz South Tianshan. Our field mapping and structural analysis demonstrate that the Atbashi Eclogite–Blueschist Complex is situated in a complicated duplex formed by a northerly dextral transpression system and a southerly sinistral transtension system. The two major shear systems suggest that the Atbashi Complex was extruded obliquely southwestwards during eastward penetration of the southern tip of the Yili–Central Tianshan Arc of the Kazakhstan Orocline during the Late Triassic. Also, we report new zircon U–Pb metamorphic ages of four eclogites and one garnet-bearing quartz-schist from the Atbashi complex of 217–221 Ma and 223.9 Ma, respectively, suggesting that the main extrusion was later than previously proposed and that the final orogenesis was not completed until the Late Triassic. The HP/UHP rocks have an oblique plunge to the NE and extrusion took place southwestwards during escape tectonics along the South Tianshan accretionary wedge in the Late Triassic. Our work shows that the movement of HP/UHP rocks had a 3D style with an arc-parallel structure, and sheds light on earlier 2D models with either forearc- or backarc-directed extrusions, which indicates that more systematic structural and geochronological work is needed to characterize the accretionary tectonics of many orogens around the world. Our data on the timing of extrusion and emplacement of the Atbashi Eclogite–Blueschist Complex also help to resolve the long-standing controversy about the time of terminal orogeny of the Central Asian Orogenic Belt.
DOI: 10.3535/c3v-nvx-4rv
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/qk1-hrv-ang
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.17632/wsbvtbg9bj
title: Psychiatric comorbidities in conduct disorders and neurobiological bases

description: Conduct disorder is rarely isolated, and the international literature shows a high and very diverse comorbidity. This article presents in particular the psychiatric comorbidity of conduct disorder with other externalized disorders such as attention deficit hyperactivity disorder (ADHD), oppositional defiant disorder (ODD), and internalized disorders such as mood disorder (depressive and bipolar disorder), anxiety disorders, including post-traumatic stress disorder and substance use disorders (abuse/dependence). These disorders seem to have a neurobiological substrate which implicates brain and hormonal changes, neurotransmitters alterations and environmental influences.
DOI: 10.3535/ebs-t1a-b23
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/yme-sqv-p4r
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1cr-l5w-5ad
title: †Holopea J. Hall, 1847

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wp5-vlf-3rz
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.14839614.v1
title: Coloc. with Markers Data and Analysis

description: This is the Data and associated output used for demonstrating SynapseJ use to find synapses on marked cells.
DOI: 10.6084/m9.figshare.22795817.v1
title: Alignments and tree files

description: Sequence alignments and tree files for Figures 2–4.
DOI: 10.6084/m9.figshare.27083041.v1
title: <b>Causal Links Between Gut Microbiota, Plasma Metabolites, and Iron Deficiency Anaemia: A Mendelian Randomization Analysis</b>

description: Table S1: Instrumental variables of gut microbiota after clumping and exclusion of week IVs; Table S2: Instrumental variables of plasma metabolites after clumping and exclusion of week IVs; Table S3: Causal effects of gut microbiota on IDA (Forward MR analysis); Table S4: Causal effects of hemorrhoids on identified gut microbiota (Reverse MR analysis); Table S5: Genetic correlation between identified gut microbiota and IDA (LDSC analysis); Table S6: Causal associations between plasma metabolites and IDA (Associations only with PIVW less than 0.05 and consistent with all sensitivity analysis were listed); Table S7: Causal associations between identified gut microbiota and 65 plasma metabolites; Table S8: Mediation analysis between gut microbiota, plasma metabolites, and IDA.
DOI: 10.6084/m9.figshare.878253_d54
title: substrate_temperature_degC_rock_25_shade.zip

description: Substrate temperature (deg C) at depths of 0, 2.5, 5, 10, 15, 20, 30, 50 and 100 cm under ground assuming a rock substrate and 25% shade from vegetation. Each netCDF file contains 24 layers of global extent, one for each hour of the day (starting at 0:00 hrs) for a given month of the year, at ~15km resolution.
 
 
 
Fileset Description:
The microclim dataset provides microclimate estimates of conditions above and below ground for each hour of the day for the middle day of each month based on a long-term average climatology. Details of this dataset are presented in [Kearney et al. 2014].
The dataset comprises a set of NetCDF files with one file per variable per month, each file comprising 24 layers (one for each hour of the day from 0:00 hrs to 23:00 hrs, so layer 13 is 12:00 midday) for the globe (852 rows, 2159 columns, latitudinal extents -58.57 to 83.43 degrees, longitudinal extents -180.00 to 180.00 degrees). For the naming convention, mon is month of the year (1 to 12, where 1 = Jan, 12 = Dec), shd is shade level in % (0, 25, 50, 75, 90, 100), and sub is substrate (soil, rock, sand).
To facilitate downloading the data, the NetCDF files are grouped into compressed (zipped) files, one per variable per shade and substrate type, each comprising all monthly values and, for the substrate temperatures, all depths. Note that not all variables are shade or substrate specific, specifically zenith angle, wind speeds, solar radiation, and 120 cm air temperature and relative humidity.
DOI: 10.3535/19m-y1a-75c
title: †Holopea J. Hall, 1847

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zt8-nmy-x2r
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/g27-h8z-27p
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/qew-pjx-hsj
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.15468/dl.h9uce3
title: Occurrence Download

description: A dataset containing 3217170 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Coronella austriaca Laurenti, 1768, Barbastella barbastellus (Schreber, 1774), Saxicola rubetra (Linnaeus, 1758), Anas crecca Linnaeus, 1758, Lanius excubitor Linnaeus, 1758, Plecotus auritus (Linnaeus, 1758), Caprimulgus europaeus Linnaeus, 1758, Crex crex (Linnaeus, 1758), Lucanus cervus (Linnaeus, 1758), Lyrurus tetrix (Linnaeus, 1758), Gallinago gallinago (Linnaeus, 1758), Tetrao tetrix Linnaeus, 1758)",
 "Year is not null",
 "Year is one of (2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023)",
 "HasCoordinate is TRUE",
 "DecimalLatitude is greater than or equal to 44.95782311925129",
 "DecimalLatitude is less than or equal to 58.30331634439415",
 "DecimalLongitude is greater than or equal to -10.001896207643075",
 "DecimalLongitude is less than or equal to 30.31691447027875",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 3217170 records from 3627 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009713-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1103898.10fu
title: SH1103898.10FU

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.