cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24435/materialscloud:2018.0003/v2
title: In Silico Design of 2D and 3D Covalent Organic Frameworks for Methane Storage Applications

description: Here we present 69,840 covalent organic frameworks (COFs) assembled in silico from a set of 666 distinct organic linkers into 2D-layered and 3D configurations. We investigate the feasibility of using these frameworks for methane storage by using grand-canonical Monte Carlo (GCMC) simulations to calculate their deliverable capacities (DCs). From these calculations, we predict that the best structure in the database is linker91_C_linker91_C_tbd, a structure composed of carbon-carbon bonded triazine linkers in the tbd topology. This structure has a predicted 65-bar DC of 216 v STP/v, greater than that of the best current methane storage material. We also predict other top performing materials, with 305 structures having DCs of over 190 v STP/v, and 34 of these having DCs of over 200 v STP/v. This archive entry contains the database of assembled COF structures (in CIF file format) together with all of their properties. Among the calculated properties for each structure are the framework density, the methane heats of desorption at the storage and depletion pressures, the methane uptakes at the storage and deplation pressures, the supercell volume, and the geometric surface area. Structures are also labeled according to their bond types (amide, amine, imine, carbon-carbon, or mixed) and their dimensionalities (2D or 3D).
DOI: 10.24435/materialscloud:2018.0003/v3
title: In Silico Design of 2D and 3D Covalent Organic Frameworks for Methane Storage Applications

description: Here we present 69,840 covalent organic frameworks (COFs) assembled in silico from a set of 666 distinct organic linkers into 2D-layered and 3D configurations. We investigate the feasibility of using these frameworks for methane storage by using grand-canonical Monte Carlo (GCMC) simulations to calculate their deliverable capacities (DCs). From these calculations, we predict that the best structure in the database is linker91_C_linker91_C_tbd, a structure composed of carbon-carbon bonded triazine linkers in the tbd topology. This structure has a predicted 65-bar DC of 216 v STP/v, greater than that of the best current methane storage material. We also predict other top performing materials, with 305 structures having DCs of over 190 v STP/v, and 34 of these having DCs of over 200 v STP/v. 
This archive entry contains the database of assembled COF structures (in CIF file format) together with all of their properties, which can be explored using interactive figures. Among the calculated properties for each structure are the framework density, the methane heats of desorption at the storage and depletion pressures, the methane uptakes at the storage and deplation pressures, the supercell volume, and the geometric surface area. Structures are also labeled according to their bond types (amide, amine, imine, carbon-carbon, or mixed) and their dimensionalities (2D or 3D).
DOI: 10.24435/materialscloud:2018.0012/v1
title: The geometric blueprint of perovskites

description: Perovskite minerals form an essential component of the Earth's mantle, and synthetic crystals are ubiquitous in electronics, photonics, and energy technology. The extraordinary chemical diversity of these crystals raises the question of how many and which perovskites are yet to be discovered. Here we show that the "no-rattling" principle postulated by Goldschmidt in 1926, describing the geometric conditions under which a perovskite can form, is much more effective than previously thought and allows us to predict perovskites with a fidelity of 80%. By supplementing this principle with inferential statistics and internet data mining we establish that currently known perovskites are only the tip of the iceberg, and we enumerate 90,000 hitherto-unknown compounds awaiting to be studied. Our results suggest that geometric blueprints may enable the systematic screening of millions of compounds and offer untapped opportunities in structure prediction and materials design.
DOI: 10.24435/materialscloud:7v-n3
title: In Silico Design of 2D and 3D Covalent Organic Frameworks for Methane Storage Applications

description: Here we present 69,840 covalent organic frameworks (COFs) assembled in silico from a set of 666 distinct organic linkers into 2D-layered and 3D configurations. We investigate the feasibility of using these frameworks for methane storage by using grand-canonical Monte Carlo (GCMC) simulations to calculate their deliverable capacities (DCs). From these calculations, we predict that the best structure in the database is linker91_C_linker91_C_tbd, a structure composed of carbon-carbon bonded triazine linkers in the tbd topology. This structure has a predicted 65-bar DC of 216 v STP/v, greater than that of the best current methane storage material. We also predict other top performing materials, with 305 structures having DCs of over 190 v STP/v, and 34 of these having DCs of over 200 v STP/v. 
This archive entry contains the database of assembled COF structures (in CIF file format) together with all of their properties, which can be explored using interactive figures. Among the calculated properties for each structure are the framework density, the methane heats of desorption at the storage and depletion pressures, the methane uptakes at the storage and deplation pressures, the supercell volume, and the geometric surface area. Structures are also labeled according to their bond types (amide, amine, imine, carbon-carbon, or mixed) and their dimensionalities (2D or 3D).
DOI: 10.24435/materialscloud:aa-f0
title: The geometric blueprint of perovskites

description: Perovskite minerals form an essential component of the Earth's mantle, and synthetic crystals are ubiquitous in electronics, photonics, and energy technology. The extraordinary chemical diversity of these crystals raises the question of how many and which perovskites are yet to be discovered. Here we show that the "no-rattling" principle postulated by Goldschmidt in 1926, describing the geometric conditions under which a perovskite can form, is much more effective than previously thought and allows us to predict perovskites with a fidelity of 80%. By supplementing this principle with inferential statistics and internet data mining we establish that currently known perovskites are only the tip of the iceberg, and we enumerate 90,000 hitherto-unknown compounds awaiting to be studied. Our results suggest that geometric blueprints may enable the systematic screening of millions of compounds and offer untapped opportunities in structure prediction and materials design.
DOI: 10.5281/zenodo.15350947
title: Data from: De novo genome assembly of Ansell's mole-rat (Fukomys anselli)

description: This repository contains genome assembly, gene structure annotation, and repeat annotation files for the Ansell’s mole-rat genome assembly, DKFZ_Fans_1.0 (GenBank: JBPETH000000000).

Genome assembly

The genome was de novo assembled and polished using Flye v2.9.5 from ONT long reads basecalled by Dorado v0.9.0. Base errors were corrected with Illumina short reads using NextPolish v1.4.1. Haplotigs and overlaps were removed with purge_dups v1.2.6. Contamination was screened with BLAST+ v2.16.0 and BlobToolkit v4.4.0. Cleaned contigs were scaffolded with YaHS v1.2.2 using Hi-C data processed via a modified Arima Genomics mapping pipeline. The assembly was manually curated using Juicebox with Assembly Tools v2.17.0.



DKFZ_Fans_1.0.fa.gz: Final curated assembly (FASTA).

DKFZ_Fans_1.0.agp: Final curated assembly scaffold structure (AGP).


Annotation of gene structures

Gene structures were predicted with BRAKER v3.0.8 using Ansell’s mole-rat RNA-seq data from nine tissues, OrthoDB v12 vertebrate proteins, and NCBI RefSeq-annotated proteins from 41 rodent species. Genes predicted by AUGUSTUS and GeneMark-ETP that were combined and filtered by TSEBRA, guided by glires_odb10 via compleasm to enhance BUSCO completeness.



DKFZ_Fans_1.0.braker.{gtf,gff3}.gz: Final gene set (GTF/GFF3).

DKFZ_Fans_1.0.braker.codingseq.gz: Final gene set coding sequences (FASTA).

DKFZ_Fans_1.0.braker.aa.gz: Final gene set protein sequences (FASTA).


Annotation of repetitive elements

Repeats and transposable elements were identified using Earl Grey v5.1.1 based on a de novo repeat library and known Fukomys damarensis repeats from the Dfam v3.7.



DKFZ_Fans_1.0.filteredRepeats.{gff,bed}.gz: Repeat and transposable element annotations (GFF3/BED).
DOI: 10.24435/materialscloud:2018.0011/v2
title: Capturing chemical intuition in synthesis of metal-organic frameworks

description: We report a methodology using machine learning to capture chemical intuition from a set of (partially) failed attempts to synthesize a metal organic framework. We define chemical intuition as the collection of unwritten guidelines used by synthetic chemists to find the right synthesis conditions. As (partially) failed experiments usually remain unreported, we have reconstructed a typical track of failed experiments in a successful search for finding the optimal synthesis conditions that yields HKUST-1 with the highest surface area reported to date. We illustrate the importance of quantifying this chemical intuition for the synthesis of novel materials.
DOI: 10.24435/materialscloud:76-52
title: Capturing chemical intuition in synthesis of metal-organic frameworks

description: We report a methodology using machine learning to capture chemical intuition from a set of (partially) failed attempts to synthesize a metal organic framework. We define chemical intuition as the collection of unwritten guidelines used by synthetic chemists to find the right synthesis conditions. As (partially) failed experiments usually remain unreported, we have reconstructed a typical track of failed experiments in a successful search for finding the optimal synthesis conditions that yields HKUST-1 with the highest surface area reported to date. We illustrate the importance of quantifying this chemical intuition for the synthesis of novel materials.
DOI: 10.24435/materialscloud:2019.0014/v1
title: Approximation of Collective Variables by anncolvar

description: Biomolecular simulations are computationally expensive. This limits their application in drug or protein design and related fields. Several methods have been developed to address this problem. These methods often use an artificial force or potential acting on selected degrees of freedom known as collective variables. This requires explicit calculation of a collective variable (and its derivatives) from molecular structure. For collective variables that cannot be calculated explicitly or such calculations is slow we developed anncolvar package (https://github.com/spiwokv/anncolvar). This package approximates collective variables using artificial neural networks. It was tested on Isomap low dimensional representation of cyclooctane derivative or solvent-accessible surface area of Trp-cage miniprotein.
DOI: 10.15468/dl.2gs67x
title: Occurrence Download

description: A dataset containing 103 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anguis cephallonica Werner, 1894"
 ]
}

 The dataset includes 103 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050565-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qewvqj
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Decalobanthus mammosus (Lour.) A.R.Simões & Staples"
 ]
}

 The dataset includes 35 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023672-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lhssxq
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Espeletia azucarina Cuatrec."
 ]
}

 The dataset includes 17 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008840-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ecpkdp
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphorbia hajhirensis Radcl.-Sm."
 ]
}

 The dataset includes 10 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050564-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qmps6u
title: Occurrence Download

description: A dataset containing 5094 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is OSAC North American Pyraloidea -beta version"
 ]
}

 The dataset includes 5094 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023690-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bolehh
title: Occurrence Download

description: A dataset containing 634 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hybomitra illota (Osten Sacken, 1876)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 634 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008841-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ajnqvh
title: Occurrence Download

description: A dataset containing 493617 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "PublishingCountry is Ukraine"
 ]
}

 The dataset includes 493617 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028202-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qyp8vg
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euryops marlothii B.Nord."
 ]
}

 The dataset includes 38 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050604-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c3u6ms
title: Occurrence Download

description: A dataset containing 1715 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caulerpa prolifera (Forssk.) J.V.Lamour."
 ]
}

 The dataset includes 1715 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008841-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2k9pzz
title: Occurrence Download

description: A dataset containing 3685 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Sweden",
 "TaxonKey is Pollachius virens (Linnaeus, 1758)"
 ]
}

 The dataset includes 3685 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028204-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2y4qwt
title: Occurrence Download

description: A dataset containing 2629 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Vitex megapotamica (Spreng.) Moldenke, Psilogyne viticifolia DC., Vitex bignonioides Kunth, Vitex megapotamica var. multinervis (Cham.) Moldenke, Vitex montevidensis Cham., Vitex montevidensis var. multinervis Cham., Vitex multinervis (Cham.) Schauer, Vitex taruma Mart., Vitex viticifolia (DC.) B.L.Rob.)"
 ]
}

 The dataset includes 2629 records from 174 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040629-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sjzy1m
title: Occurrence Download

description: A dataset containing 6293 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hygrocybe reidii Kühner"
 ]
}

 The dataset includes 6293 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008841-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e86hkp
title: Occurrence Download

description: A dataset containing 131 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Impatiens rostellata Franch."
 ]
}

 The dataset includes 131 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028221-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5ka2qr
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bulbophyllum caecum J.J.Sm."
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072561-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.la4ci7
title: Occurrence Download

description: A dataset containing 1062 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fungi",
 "Geometry POLYGON((-23 20,-23 2,10 2,10 20,-23 20))"
 ]
}

 The dataset includes 1062 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008842-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mv48hq
title: Occurrence Download

description: A dataset containing 2236 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 Copsychus luzoniensis (Kittlitz, 1832)"
 ]
}

 The dataset includes 2236 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023677-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ui2xfc
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Geometry POLYGON((-79.797 37.446,-79.797 39.715,-77.114 39.715,-77.114 37.446,-79.797 37.446))",
 "HasCoordinate is true",
 "TaxonKey is Oplismenus undulatifolius (Ard.) Roem. & Schult.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008842-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sq5ty2
title: Occurrence Download

description: A dataset containing 5941 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 Cyanoramphus auriceps (Kuhl, 1820)"
 ]
}

 The dataset includes 5941 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023661-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ugutqc
title: Occurrence Download

description: A dataset containing 120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "TaxonKey is Sphagneticola trilobata (L.) Pruski"
 ]
}

 The dataset includes 120 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015091-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6a6haz
title: Occurrence Download

description: A dataset containing 156265 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Bat Banding"
 ]
}

 The dataset includes 156265 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008842-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7f5wqn
title: Occurrence Download

description: A dataset containing 5589 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 Anthreptes simplex (S.Muller, 1843)"
 ]
}

 The dataset includes 5589 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050566-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3zwc4d
title: Occurrence Download

description: A dataset containing 119 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 Alisterus amboinensis (Linnaeus, 1766)"
 ]
}

 The dataset includes 119 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023668-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uzxecq
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Jatropha martiusii (Pohl) Baill.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 28 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008843-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.