cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.13145/bacdive114723.20230509.8.1
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/bacdive114724.20230509.8.1
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/bacdive114725.20230509.8.1
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/bacdive114726.20230509.8.1
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/bacdive114727.20230509.8.1
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/bacdive114728.20230509.8.1
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/bacdive114729.20230509.8.1
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/bacdive114730.20230509.8.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.5281/zenodo.14610062
title: Spatioselective Deposition of Passivating and Electrocatalytic Layers on Silicon Nanowire Arrays

description: Datasets referring the manuscript "Spatioselective Deposition of Passivating and Electrocatalytic Layers on Silicon Nanowire Arrays" published in ACS Applied Materials and Interfaces

https://pubs.acs.org/doi/full/10.1021/acsami.0c14013

Please read the .txt file for more information concerning the datasets
DOI: 10.5281/zenodo.14610063
title: Spatioselective Deposition of Passivating and Electrocatalytic Layers on Silicon Nanowire Arrays

description: Datasets referring the manuscript "Spatioselective Deposition of Passivating and Electrocatalytic Layers on Silicon Nanowire Arrays" published in ACS Applied Materials and Interfaces

https://pubs.acs.org/doi/full/10.1021/acsami.0c14013

Please read the .txt file for more information concerning the datasets
DOI: 10.13145/bacdive114731.20230509.8.1
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/bacdive114732.20230509.8.1
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/bacdive114733.20230509.8.1
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/bacdive114734.20230509.8.1
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/bacdive114735.20230509.8.1
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/bacdive114736.20230509.8.1
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/bacdive114737.20230509.8.1
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/bacdive114738.20230509.8.1
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/bacdive114739.20230509.8.1
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/bacdive114740.20230509.8.1
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/bacdive114741.20230509.8.1
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/bacdive114742.20230509.8.1
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/bacdive114743.20230509.8.1
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/bacdive114744.20230509.8.1
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/bacdive114745.20230509.8.1
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/bacdive114746.20230509.8.1
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/bacdive114747.20230509.8.1
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/bacdive114748.20230509.8.1
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/bacdive114749.20230509.8.1
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/bacdive114750.20230509.8.1
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/bacdive114751.20230509.8.1
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/bacdive114752.20230509.8.1
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15468/dl.fwbcb7
title: Occurrence Download

description: A dataset listing the 46 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-39.76892 -19.01546,-42.65537 -18.21934,-43.32313 -18.2398,-43.66778 -18.83207,-43.64624 -19.19865,-43.40929 -19.54411,-43.517 -19.90908,-43.45238 -20.51551,-43.49546 -20.83796,-43.56008 -21.26013,-43.08618 -21.38052,-42.18148 -21.03914,-41.49217 -20.69697,-41.10444 -20.33383,-40.65209 -19.96983,-40.30744 -19.82805,-39.96279 -19.84831,-39.7043 -19.66586,-39.53197 -19.32066,-39.76892 -19.01546))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ephemeroptera"
 ]
}

 The dataset's 46 records were derived from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014289-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eada7j
title: Occurrence Download

description: A dataset containing 399847 species occurrences available in GBIF matching the query:
{
 "and" : [
 "SpeciesKey is one of (Cerastium holosteoides Fr.)",
 "BasisOfRecord is one of (Human Observation, Observation, Occurrence evidence)",
 "Year is greater than or equal to 1901",
 "Year is less than or equal to 2019",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 399847 records from 856 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014286-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r46gy7
title: Occurrence Download

description: A dataset containing 547 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Taxidea taxus (Schreber, 1777)"
 ]
}

 The dataset includes 547 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014309-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z6qeze
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Rhynchostele candidula (Rchb.f.) Soto Arenas & Salazar"
 ]
}

 The dataset includes 48 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014310-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13932136
title: Theoretical calculations for 10.1126/sciadv.adl4481

description: This dataset contains the data for the density fuctional theory calculations in the paper 10.1126/sciadv.adl4481

This includes: input files for quantum espresso, input files for bands up, plot scripts. All details required to reproduce the calculations are also detailed in the paper.
DOI: 10.5281/zenodo.13932137
title: Theoretical calculations for 10.1126/sciadv.adl4481

description: This dataset contains the data for the density fuctional theory calculations in the paper 10.1126/sciadv.adl4481

This includes: input files for quantum espresso, input files for bands up, plot scripts. All details required to reproduce the calculations are also detailed in the paper.
DOI: 10.15468/dl.qhbdeg
title: Occurrence Download

description: A dataset containing 8881 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-98.35 19.4,-97.5 19.4,-97.5 20.9,-98.35 20.9,-98.35 19.4))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 8881 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014311-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10841353
title: ORION Examples

description: Example configuration and input data for the Operational Forecasting of Induced Seismicity (ORION) code, based on the Illinois Basin Decatur Project (IBDP). Additional datasets are also included. More information about ORION can be found on EDX.
DOI: 10.34945/f57s3t
title: Functional Forelimb Recovery and Corticospinal Tract Changes after Chondroitinase Treatment in Male Primates after Cervical C7 Spinal Hemisection

description: STUDY PURPOSE: The purpose of the study was to evaluate the behavioral and neurobiological effects of intraparenchymal treatment with the enzyme chondroitinase (Chase) in rhesus monkeys that had undergone cervical (C7) spinal cord hemisection, targeting spinal cord circuits that control hand function. DATA COLLECTED: Fourteen (14) male Rhesus macaques, aged 6-10 years were assessed. Hand function was assessed using measures of open-field scoring of object manipulation, as well as the Brinkman board task to assess digital manipulation and fine motor skills. Five different boards of increasing difficulty were presented sequentially in each testing session. Difficulty was increased by: (1) increasing the depth of wells from which monkeys needed to extract the food reward; (2) altering the angle of the well relative to the monkey’s position; and (3) increasing the number of reward wells. Subjects were scored on the number of rewards obtained from each board, the time they took to clear the board and whether they used a pincer grasp. Tracing with biotin dextran amine and anterograde tracer dextran-conjugated AlexaFluor 440 was perfromed in order to measure corticospinal axon growth, and the number of synapses formed by corticospinal terminals in gray matter caudal to the lesion was also assessed (colocalization of BDA and synaptophysin). DATA USAGE NOTES:
DOI: 10.15468/dl.shwmjd
title: Occurrence Download

description: A dataset containing 2145 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Acacia notabilis F.Muell."
 ]
}

 The dataset includes 2145 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014312-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.868ep4
title: Occurrence Download

description: A dataset containing 242627 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-52.4132 -7.64733,-49.35478 -7.64733,-47.9542 -5.43212,-52.07891 -4.64781,-52.4132 -7.64733))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 242627 records from 346 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014303-241007104925546/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13932124
title: Datasets for COSMOS

description: COSMOS is a computational tool crafted to overcome the challenges associated with integrating spatially resolved multi-omics data. This software harnesses a graph neural network algorithm to deliver cutting-edge solutions for analyzing biological data that encompasses various omics types within a spatial framework. Key features of COSMOS include domain segmentation, effective visualization, and the creation of spatiotemporal maps. These capabilities empower researchers to gain a deeper understanding of the spatial and temporal dynamics within biological samples, distinguishing COSMOS from other tools that may only support single omics types or lack comprehensive spatial integration. The proven superior performance of COSMOS underscores its value as an essential resource in the realm of spatial omics.

Paper: Cooperative Integration of Spatially Resolved Multi-Omics Data with COSMOS, Zhou Y., X. Xiao, L. Dong, C. Tang, G. Xiao*, and L Xu*, 2024.
DOI: 10.5281/zenodo.13932125
title: Datasets for COSMOS

description: COSMOS is a computational tool crafted to overcome the challenges associated with integrating spatially resolved multi-omics data. This software harnesses a graph neural network algorithm to deliver cutting-edge solutions for analyzing biological data that encompasses various omics types within a spatial framework. Key features of COSMOS include domain segmentation, effective visualization, and the creation of spatiotemporal maps. These capabilities empower researchers to gain a deeper understanding of the spatial and temporal dynamics within biological samples, distinguishing COSMOS from other tools that may only support single omics types or lack comprehensive spatial integration. The proven superior performance of COSMOS underscores its value as an essential resource in the realm of spatial omics.

Paper: Cooperative Integration of Spatially Resolved Multi-Omics Data with COSMOS, Zhou Y., X. Xiao, L. Dong, C. Tang, G. Xiao*, and L Xu*, 2024.
DOI: 10.5281/zenodo.13932144
title: Datasets for COSMOS

description: COSMOS is a computational tool crafted to overcome the challenges associated with integrating spatially resolved multi-omics data. This software harnesses a graph neural network algorithm to deliver cutting-edge solutions for analyzing biological data that encompasses various omics types within a spatial framework. Key features of COSMOS include domain segmentation, effective visualization, and the creation of spatiotemporal maps. These capabilities empower researchers to gain a deeper understanding of the spatial and temporal dynamics within biological samples, distinguishing COSMOS from other tools that may only support single omics types or lack comprehensive spatial integration. The proven superior performance of COSMOS underscores its value as an essential resource in the realm of spatial omics.

Paper: Cooperative Integration of Spatially Resolved Multi-Omics Data with COSMOS, Zhou Y., X. Xiao, L. Dong, C. Tang, G. Xiao*, and L Xu*, 2024.
DOI: 10.5281/zenodo.10257838
title: Generative AI for designing and validating easily synthesizable and structurally novel antibiotics: Data and Models

description: This repository contains data and models used in the following paper.

Swanson, K., Liu, G., Catacutan, D., Zou, J. & Stokes, J. Generative AI for designing and validating easily synthesizable and structurally novel antibiotics. Nature Machine Intelligence, 2024.

The data and models are meant to be used with the SyntheMol code. More details about how to use the data and models with the code are available here.

The Data.zip file has the following structure. Note that the numbers for the Data subdirectories correspond to the supplementary data numbers in the paper (e.g., 1_training_data corresponds to Supplementary Data 1).

Data

  1_training_data: The Acinetobacter baumannii inhibition data used to train antibiotic property prediction models.

  2_chembl: Known antibiotic and antibacterial molecules from ChEMBL, which are used to compute the novelty of generated antibiotic candidates.

  4_real_space: Data files and statistics for the Enamine REAL Space. The molecular building blocks file is version 2021 q3-4 while all other REAL Space details are computed from the full enumerated REAL space version 2022 q1-2 (downloaded on August 30, 2022).

  5_generations_clogp: Compounds generated by SyntheMol using Chemprop models trained to predict cLogP.

  6_generations_chemprop: Compounds generated by SyntheMol using Chemprop models trained to predict A. baumannii inhibition.

  7_generations_chemprop_rdkit: Compounds generated by SyntheMol using Chemprop-RDKit models trained to predict A. baumannii inhibition.

  8_generations_random_forest: Compounds generated by SyntheMol using random forest models trained to predict A. baumannii inhibition.

  9_synthesized: Information on the 58 SyntheMol-generated compounds that were successfully synthesized by Enamine.

The Models.zip file contains one folder for each model used in the paper. Note that each model is technically an ensemble of ten individual models, so each directory contains ten model files.
DOI: 10.5281/zenodo.10257839
title: Generative AI for designing and validating easily synthesizable and structurally novel antibiotics: Data and Models

description: This repository contains data and models used in the following paper.

Swanson, K., Liu, G., Catacutan, D., Zou, J. & Stokes, J. Generative AI for designing and validating easily synthesizable and structurally novel antibiotics. Nature Machine Intelligence, 2024.

The data and models are meant to be used with the SyntheMol code. More details about how to use the data and models with the code are available here.

The Data.zip file has the following structure. Note that the numbers for the Data subdirectories correspond to the supplementary data numbers in the paper (e.g., 1_training_data corresponds to Supplementary Data 1).

Data

  1_training_data: The Acinetobacter baumannii inhibition data used to train antibiotic property prediction models.

  2_chembl: Known antibiotic and antibacterial molecules from ChEMBL, which are used to compute the novelty of generated antibiotic candidates.

  4_real_space: Data files and statistics for the Enamine REAL Space. The molecular building blocks file is version 2021 q3-4 while all other REAL Space details are computed from the full enumerated REAL space version 2022 q1-2 (downloaded on August 30, 2022).

  5_generations_clogp: Compounds generated by SyntheMol using Chemprop models trained to predict cLogP.

  6_generations_chemprop: Compounds generated by SyntheMol using Chemprop models trained to predict A. baumannii inhibition.

  7_generations_chemprop_rdkit: Compounds generated by SyntheMol using Chemprop-RDKit models trained to predict A. baumannii inhibition.

  8_generations_random_forest: Compounds generated by SyntheMol using random forest models trained to predict A. baumannii inhibition.

  9_synthesized: Information on the 58 SyntheMol-generated compounds that were successfully synthesized by Enamine.

The Models.zip file contains one folder for each model used in the paper. Note that each model is technically an ensemble of ten individual models, so each directory contains ten model files.
DOI: 10.5281/zenodo.13932150
title: Generative AI for designing and validating easily synthesizable and structurally novel antibiotics: Data and Models

description: This repository contains data and models used in the following paper.

Swanson, K., Liu, G., Catacutan, D., Zou, J. & Stokes, J. Generative AI for designing and validating easily synthesizable and structurally novel antibiotics. Nature Machine Intelligence, 2024.

The data and models are meant to be used with the SyntheMol code. More details about how to use the data and models with the code are available here.

The Data.zip file has the following structure. Note that the numbers for the Data subdirectories correspond to the supplementary data numbers in the paper (e.g., 1_training_data corresponds to Supplementary Data 1).

Data

  1_training_data: The Acinetobacter baumannii inhibition data used to train antibiotic property prediction models.

  2_chembl: Known antibiotic and antibacterial molecules from ChEMBL, which are used to compute the novelty of generated antibiotic candidates.

  4_real_space: Data files and statistics for the Enamine REAL Space. The molecular building blocks file is version 2021 q3-4 while all other REAL Space details are computed from the full enumerated REAL space version 2022 q1-2 (downloaded on August 30, 2022).

  5_generations_clogp: Compounds generated by SyntheMol using Chemprop models trained to predict cLogP.

  6_generations_chemprop: Compounds generated by SyntheMol using Chemprop models trained to predict A. baumannii inhibition.

  7_generations_chemprop_rdkit: Compounds generated by SyntheMol using Chemprop-RDKit models trained to predict A. baumannii inhibition.

  8_generations_random_forest: Compounds generated by SyntheMol using random forest models trained to predict A. baumannii inhibition.

  9_synthesized: Information on the 58 SyntheMol-generated compounds that were successfully synthesized by Enamine.

The Models.zip file contains one folder for each model used in the paper. Note that each model is technically an ensemble of ten individual models, so each directory contains ten model files.