cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17284940
title: Datasets for MulitModalSpectralTransformer project

description: Data Repository for "Advancing Structure Elucidation with a Flexible Multi-Spectral AI Model"

IMPORTANT NOTE: This is part of a multi-part data repository. Due to the large size of the files, the complete dataset, models, and experimental results are split across three separate Zenodo uploads. To fully reproduce the findings of our publication, you must download all files from all three of the following links:





Data Repository Part 1: https://doi.org/10.5281/zenodo.16076914




Data Repository Part 2: https://doi.org/10.5281/zenodo.16257786




Data Repository Part 3: https://doi.org/10.5281/zenodo.17284940



This repository contains the complete dataset, pre-trained models, and experimental results required to reproduce the findings presented in our publication, "Advancing Structure Elucidation with a Flexible Multi-Spectral AI Model." The source code is available separately on GitHub.

Contents

The downloaded files are split archives that, once combined and extracted, will create the following folders:





models/: Pre-trained model weights for MultiModalSpectralTransformer (MMST), SGNN, Mol2Mol, and ChemProp-IR networks.




data/: Complete training and validation datasets, including:





ZINC dataset (4M molecules with simulated spectra)




PubChem dataset (1.5M molecules with simulated spectra)




IBM Alberts dataset (650k molecules with simulated spectra)






past_experiments/: Complete experimental validation results, benchmarks, and reproducibility data.



Note: To reproduce the reviewer-requested global impact analysis, you must also download the Reviewer_Experiment_Global_Impact.zip file separately and extract its contents into the past_experiments/ChemXriv/ directory after completing the main setup.

Setup Instructions





Clone the GitHub repository:git clone https://github.com/mpriessner/MultiModalSpectralTransformer.git




Download all compressed files: Make sure to download every .partXX file from all three Zenodo links provided above. Place all of them together in the same directory.




Combine and Extract: Once all parts are downloaded, use a file archiver that supports split .tar.xz archives (like tar on Linux/macOS or 7-Zip on Windows) to extract the contents. You only need to run the extraction command on the first part of each archive (e.g., data.tar.xz.partaa); the tool will automatically find and combine the other parts.




Organize Folders: Move the extracted folders (models, data, and past_experiments) directly into the main repository directory you cloned in step 1.



After extraction, your repository structure should contain the necessary models/, data/, and past_experiments/ folders with all the files required for running the notebooks and reproducing the results.

For implementation details, usage instructions, and the complete source code, please refer to our Github Reporitory: https://github.com/mpriessner/MultiModalSpectralTransformer
DOI: 10.5281/zenodo.16378227
title: Supplementary data for "Revisiting the Oxygen Fugacity of Martian Meteorites: Implications for the Redox History of the Mantle of Mars"
DOI: 10.5281/zenodo.17285148
title: Supplementary data for "Revisiting the Oxygen Fugacity of Martian Meteorites: Implications for the Redox History of the Mantle of Mars"
DOI: 10.15468/dl.utgnew
title: Occurrence Download

description: A dataset containing 569845 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Corvus monedula)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 569845 records from 2577 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057476-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zyht35
title: Occurrence Download

description: A dataset containing 1472 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mustela lutreola (Linnaeus, 1761)"
 ]
}

 The dataset includes 1472 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0180263-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yyseyk
title: Occurrence Download

description: A dataset containing 9634639 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Pl@ntNet automatically identified occurrences"
 ]
}

 The dataset includes 9634639 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0343035-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h65vn7
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sideritis pumila (Christ) Mend.-Heuer"
 ]
}

 The dataset includes 72 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0128612-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ef9ruh
title: Occurrence Download

description: A dataset containing 166 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Calpodes ethlius (Stoll, 1782)"
 ]
}

 The dataset includes 166 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0180280-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tcpn7p
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Primula latisecta W.W.Sm."
 ]
}

 The dataset includes 23 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095019-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/6b48mm
title: PELD - MG | Comunidade Fitoplanctonica de duas bacias do Rio Doce - MG

description: Esse recurso contém dados de análises qualitativas da comunidade fitoplanctônica de amostras coletadas na sub-bacia do rio Piranga e na sub-bacia do rio Santo Antônio, ambas contidas na bacia do rio Doce. As amostras foram coletadas sazonalmente (seca e chuva) nos anos de 2018 e 2019.
DOI: 10.15468/dl.hq995k
title: Occurrence Download

description: A dataset containing 1266 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Numenius arquata (Linnaeus, 1758)",
 "Year 1970-2020"
 ]
}

 The dataset includes 1266 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002872-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ker93g
title: Occurrence Download

description: A dataset containing 590 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Distichodus fasciolatus Boulenger, 1898"
 ]
}

 The dataset includes 590 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0340510-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mp5vdg
title: Occurrence Download

description: A dataset containing 1092 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((33.6731 46.21785,33.47534 46.01985,32.57446 45.68316,32.2229 45.46784,32.28882 45.1278,33.10181 44.45731,33.89282 44.25307,34.44214 44.31599,35.38696 44.48867,36.39771 44.73893,36.55151 44.97257,36.4856 45.22074,36.79321 45.29808,36.72729 45.59098,36.04614 45.63709,35.49683 45.60635,35.18921 45.69851,34.96948 45.91294,34.66187 45.95879,33.6731 46.21785))",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "TaxonKey is Centaurea ovina Pall. ex Willd.",
 "TaxonKey is Centaurea comperiana Steven",
 "TaxonKey is Centaurea arenaria M.Bieb. ex Willd.",
 "TaxonKey is Bellis sylvestris Cirillo",
 "TaxonKey is Artemisia dzevanovskyi Leonova",
 "TaxonKey is Anthemis sterilis Steven",
 "TaxonKey is Eremurus tauricus Steven",
 "TaxonKey is Asphodeline taurica (Pall. ex M.Bieb.) Endl.",
 "TaxonKey is Epipactis persica (Soó) Hausskn. ex Nannf.",
 "TaxonKey is Epipactis palustris (L.) Crantz",
 "TaxonKey is Epipactis muelleri Godfery",
 "TaxonKey is Epipactis microphylla (Ehrh.) Sw.",
 "TaxonKey is Epipactis leptochila (Godfery) Godfery",
 "TaxonKey is Epipactis krymmontana Kreutz, Fateryga & Efimov",
 "TaxonKey is Epipactis helleborine (L.) Crantz",
 "TaxonKey is Epipactis distans Arv.-Touv.",
 "TaxonKey is Dactylorhiza romana (Sebast.) Soó",
 "TaxonKey is Dactylorhiza iberica (M.Bieb. ex Willd.) Soó",
 "TaxonKey is Cypripedium calceolus L.",
 "TaxonKey is Comperia comperiana (Steven) Asch. & Graebn.",
 "TaxonKey is Coeloglossum viride (L.) Hartm.",
 "TaxonKey is Anacamptis laxiflora subsp. elegans (Heuff.) Kuropatkin & Efimov",
 "TaxonKey is Anacamptis coriophora (L.) R.M.Bateman, Pridgeon & M.W.Chase",
 "TaxonKey is Iris pseudacorus L.",
 "TaxonKey is Gladiolus italicus Mill.",
 "TaxonKey is Gladiolus imbricatus L.",
 "TaxonKey is Scilla siberica Haw.",
 "TaxonKey is Asparagus maritimus (L.) Mill.",
 "TaxonKey is Anthericum liliago L.",
 "TaxonKey is Sternbergia colchiciflora Waldst. & Kit.",
 "TaxonKey is Allium tarkhankuticum Seregin",
 "TaxonKey is Allium siculum subsp. dioscoridis (Sm.) K.Richt.",
 "TaxonKey is Allium pervestitum Klokov",
 "TaxonKey is Allium nathaliae Seregin",
 "TaxonKey is Seseli lehmannii Degen",
 "TaxonKey is Heracleum ligusticifolium M.Bieb.",
 "TaxonKey is Ferula euxina Pimenov",
 "TaxonKey is Bifora testiculata (L.) Spreng.",
 "TaxonKey is Gymnocarpium dryopteris (L.) Newman",
 "TaxonKey is Asplenium lepidum subsp. haussknechtii (Godet & Reut. ex Milde) Brownsey",
 "TaxonKey is Asplenium billotii F.W.Schultz",
 "TaxonKey is Asplenium adiantum-nigrum L.",
 "TaxonKey is Equisetum fluviatile L.",
 "TaxonKey is Botrychium lunaria (L.) Sw.",
 "TaxonKey is Ophioglossum vulgatum L."
 ]
 },
 "Year 1900-2022"
 ]
}

 The dataset includes 1092 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0180292-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h4zcka
title: Occurrence Download

description: A dataset containing 6645 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Primula latifolia Lapeyr."
 ]
}

 The dataset includes 6645 records from 126 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0095017-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gy7h8r
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Brycinus abeli (Fowler, 1936)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0329524-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ubqjh9
title: Occurrence Download

description: A dataset listing the 6 species recorded in GBIF matching the query:
{
 "and" : [
 "GadmGid is BRA.11_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Velloziaceae"
 ]
}

 The dataset's 6 records were derived from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0100291-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d96792
title: Occurrence Download

description: A dataset containing 13317 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation)",
 "Country is Portugal",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ranidae",
 "Year 1980-2024"
 ]
}

 The dataset includes 13317 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008978-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dr9pqk
title: Occurrence Download

description: A dataset containing 157 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Agalychnis moreletii (Duméril, 1853)",
 "Year 1960-2022"
 ]
}

 The dataset includes 157 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0376574-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.55kxa4
title: Occurrence Download

description: A dataset containing 455 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is Stactolaema whytii",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year 2011-2021",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen, Material citation, Material sample)"
 ]
 }
 }
 ]
}

 The dataset includes 455 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0085273-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vwypbs
title: Occurrence Download

description: A dataset listing the 12778 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Collections des Herbiers d’Afrique de l'Ouest et d'Afrique Centrale"
 ]
}

 The dataset's 12778 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008962-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j2t8h7
title: Occurrence Download

description: A dataset containing 138 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Primula kitaibeliana Schott"
 ]
}

 The dataset includes 138 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0094999-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yjtmxe
title: Occurrence Download

description: A dataset containing 725 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "TaxonKey is Hesperia nevada (Scudder, 1874)"
 ]
}

 The dataset includes 725 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0180345-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pd26u5
title: Occurrence Download

description: A dataset containing 6701 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-120.57464 17.18334,33.57464 17.18334,33.57464 78.81666,-120.57464 78.81666,-120.57464 17.18334))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Allium tricoccum Aiton"
 ]
}

 The dataset includes 6701 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0100317-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yasjax
title: Occurrence Download

description: A dataset containing 14130515 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Portugal",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Animalia, Sander lucioperca (Linnaeus, 1758))"
 ]
}

 The dataset includes 14130515 records from 1274 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008968-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh0214215.10fu
title: SH0214215.10FU

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: 10.15156/bio/sh0214216.10fu
title: SH0214216.10FU

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: 10.15156/bio/sh0214217.10fu
title: SH0214217.10FU

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: 10.15156/bio/sh0214218.10fu
title: SH0214218.10FU

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: 10.15156/bio/sh0214219.10fu
title: SH0214219.10FU

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: 10.15156/bio/sh0214220.10fu
title: SH0214220.10FU

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.