cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7700458
title: OntoLAMA: LAnguage Model Analysis for Ontology Subsumption Inference

description: About

OntoLAMA is a set of language model (LM) probing datasets for ontology subsumption inference. The work follows the "LMs-as-KBs" literature but focuses on conceptualised knowledge extracted from formalised KBs such as the OWL ontologies. Specifically, the subsumption inference (SI) task is introduced and formulated in the Natural Language Inference (NLI) style, where the sub-concept and the super-concept involved in a subsumption axiom are verbalised and fitted into a template to form the premise and hypothesis, respectively. The sampled axioms are verified through ontology reasoning. The SI task is further divided into Atomic SI and Complex SI where the former involves only atomic named concepts and the latter involves both atomic and complex concepts. Real-world ontologies of different scales and domains are used for constructing OntoLAMA and in total there are four Atomic SI datasets and two Complex SI datasets.

 




Dataset Source
#Concepts
#EquivAxioms
#Datasets(Train/Dev/Test)




Schema.org
894
N/A


Atomic SI: 808/404/2, 830



DOID
11,157
N/A


Atomic SI: 90,500/11,312/11,314



FoodOn
30,995
2,383


Atomic SI: 768,486/96,060/96,062

Complex SI: 3,754/1,850/13,080



GO
43,303
11,456


Atomic SI: 772,870/96,608/96,610

Complex SI: 72,318/9,040/9,040



MNLI
N/A
N/A


biMNLI: 235,622/26,180/12,906





 

Citation

The relevant paper has been accepted at Findings of ACL 2023: https://aclanthology.org/2023.findings-acl.213/.

```@inproceedings{he2023language,
  title={Language Model Analysis for Ontology Subsumption Inference},
  author={He, Yuan and Chen, Jiaoyan and Jimenez-Ruiz, Ernesto and Dong, Hang and Horrocks, Ian},
  booktitle={Findings of the Association for Computational Linguistics: ACL 2023},
  pages={3439--3453},
  year={2023}
}```

Links



See instructions at: https://krr-oxford.github.io/DeepOnto/ontolama/

We have made available a convenient access of these datasets through Huggingface: https://huggingface.co/datasets/krr-oxford/OntoLAMA

The arxiv version is available at: https://arxiv.org/abs/2302.06761


Contact

Yuan He (yuan.he(at)cs.ox.ac.uk)
DOI: 10.15468/dl.cr348b
title: Occurrence Download

description: A dataset containing 593 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bulbostylis laniceps C.B.Clarke ex T.Durand & Schinz",
 "Continent is Africa"
 ]
}

 The dataset includes 593 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001252-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pb599p
title: Occurrence Download

description: A dataset containing 202 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ambrosia polystachya",
 "Country is Brazil",
 "HasCoordinate is true"
 ]
}

 The dataset includes 202 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018704-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.66jzbc
title: Occurrence Download

description: A dataset containing 19315 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 one of (Chelone glabra)"
 ]
}

 The dataset includes 19315 records from 125 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018705-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v9r9t8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ambrosia polystachya",
 "Country is Colombia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018706-250920141307145/datasets/export for details.
DOI: 10.5517/ccdc.csd.cc2mycgf
title: CCDC 2441295: Experimental Crystal Structure Determination

description: Related Article: Mukaila A. Ibrahim, René T. Boeré, Kathryn E. Preuss|2025|RSC Advances|15|32299|doi:10.1039/d5ra03587b
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2mycjh
title: CCDC 2441297: Experimental Crystal Structure Determination

description: Related Article: Mukaila A. Ibrahim, René T. Boeré, Kathryn E. Preuss|2025|RSC Advances|15|32299|doi:10.1039/d5ra03587b
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2hb9rx
title: CCDC 2303819: Experimental Crystal Structure Determination

description: Related Article: Saravanan Raju, Sanhati Sharangi, Harkesh B. Singh, R. S. Prabhuraj, Rohit Srivastava, Ray J. Butcher, Sangit Kumar|2025|Dalton Trans.|54|13235|doi:10.1039/d5dt00916b
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2nd0z2
title: CCDC 2454424: Experimental Crystal Structure Determination

description: Related Article: Guoqing Yang, Song Liu, Hanmin Huang|2025|Org.Lett.|27|10301|doi:10.1021/acs.orglett.5c03008
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p1597
title: CCDC 2473778: Experimental Crystal Structure Determination

description: Related Article: Nutan R. Darandale, Morgan E. John, Stephen A. Moggach, Dinesh N. Sawant, George A. Koutsantonis, Reto Dorta, Scott G. Stewart|2025|Org.Lett.|27|10526|doi:10.1021/acs.orglett.5c03230
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p49jp
title: CCDC 2476792: Experimental Crystal Structure Determination

description: Related Article: Priyanshu Gupta, Palash Roy, Akkattu T. Biju|2025|Org.Lett.|27|10477|doi:10.1021/acs.orglett.5c03346
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.ewaqf8
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parasesarma tripectinis",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018708-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2pbjsc
title: CCDC 2482783: Experimental Crystal Structure Determination

description: Related Article: Wei Qian, Fangyuan Hu, Qianxi Feng, Jiahui Ren, Qiaohong Huang, Shiling Liu, Fei Ling, Chunlin Wen, Yu Feng, Weihui Zhong|2025|Org.Process Res.Dev.|29|2400|doi:10.1021/acs.oprd.5c00255
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.2nsef4
title: Occurrence Download

description: A dataset containing 131 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Specimen)",
 "Month is one of (January, February, March, May, April, June, July, August, September, October, November, December)",
 "TaxonKey is Artibeus intermedius",
 "Year 2018-2025"
 ]
}

 The dataset includes 131 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018710-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x4keu9
title: Occurrence Download

description: A dataset containing 131 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material sample, Specimen)",
 "Month is one of (December, November, July, June, May, April, March, January)",
 "TaxonKey is Artibeus intermedius",
 "Year 2018-2025"
 ]
}

 The dataset includes 131 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018711-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g2rgyd
title: Occurrence Download

description: A dataset containing 1746 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 one of (Chelone lyonii)"
 ]
}

 The dataset includes 1746 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018712-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.262ak6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ambrosia polystachya",
 "Country is Germany",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018714-250920141307145/datasets/export for details.
DOI: 10.15468/dl.vayhy3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ambrosia polystachya",
 "Country is Estonia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018713-250920141307145/datasets/export for details.
DOI: 10.15468/dl.4fe4wx
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ambrosia polystachya",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018715-250920141307145/datasets/export for details.
DOI: 10.15468/dl.52ptqw
title: Occurrence Download

description: A dataset containing 162 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scandarma lintou",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 162 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018716-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17132433
title: pop-cosmos: COSMOS-like mock galaxy catalogs

description: This record contains data products associated with the paper "pop-cosmos: Insights from generative modeling of a deep, infrared-selected galaxy population" by Thorp et al. (2025). The mock galaxy catalogs are generated from the pop-cosmos model presented therein, with all plots in the paper being based on the catalogs included here. It also includes additional data products described in the paper "pop-cosmos: Star formation over 12 Gyr from generative modelling of a deep infrared-selected galaxy catalogue" by Deger et al. (2025).

Related software, including a demo notebook for working with the data in this record, can be found on GitHub. 

Galaxy-level parameter inferences for the COSMOS2020 galaxies are included in a seperate listing on Zenodo.

The current release includes the following files:



README_v1_1_0.txt: Detailed information about how to read the other files in the record.

mock_catalog_r_25.h5: Mock catalog of 2 million galaxies with $r<25$ in HDF5 format.

mock_catalog_Ch1_26.h5: Mock catalog of 2 million galaxies with $\textit{Ch.1}<26$ in HDF5 format.


If you use any of the products from this record, please cite Alsing et al. (2024) and Thorp et al. (2025). If you use the rest-frame NUVrJ photometry, please additionally cite Deger et al. (2025).

If you spot any issues or have any requests, please contact the corresponding author (Stephen Thorp) using the details in the README.

References:



Alsing et al. (2024). ApJS 274, 12. [arXiv:2402.00935][doi]

Thorp et al. (2025). ApJ, accepted. [arXiv:2506.12122]

Deger et al. (2025). MNRAS, submitted. [arXiv:2509.20430]
DOI: 10.15468/dl.5gkmqa
title: Occurrence Download

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Specimen)",
 "Continent is North America",
 "Country is Belize",
 "Month is one of (January, February, March, April, May, June, July, August, September, October, November, December)",
 "TaxonKey is Artibeus intermedius",
 "Year 2017-2025"
 ]
}

 The dataset includes 81 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018718-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17206510
title: D1.2 Improved global point source emissions dataset

description: This dataset consists on an updated and improved version of the global bottom-up point source dataset that was constructed in the framework of the CoCO2 HE project, and that provides emissions of CO2 and co-emitted species (NOx, CO, SO2, CH4) for power plants by fuel type (coal, natural gas, oil, biomass and waste), cement plants and iron and steel plants at their exact geographical location for the year 2021, as well as associated temporal (i.e., monthly, weekly, hourly) and vertical distribution profiles to support modelling efforts.

This data accompanies the CORSO project Deliverable D1.2 Improved global point source emissions dataset available at:

https://www.corso-project.eu/deliverables
DOI: 10.5281/zenodo.17206511
title: D1.2 Improved global point source emissions dataset

description: This dataset consists on an updated and improved version of the global bottom-up point source dataset that was constructed in the framework of the CoCO2 HE project, and that provides emissions of CO2 and co-emitted species (NOx, CO, SO2, CH4) for power plants by fuel type (coal, natural gas, oil, biomass and waste), cement plants and iron and steel plants at their exact geographical location for the year 2021, as well as associated temporal (i.e., monthly, weekly, hourly) and vertical distribution profiles to support modelling efforts.

This data accompanies the CORSO project Deliverable D1.2 Improved global point source emissions dataset available at:

https://www.corso-project.eu/deliverables
DOI: 10.15468/dl.7mmvde
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ambrosia polystachya",
 "Country is Jamaica",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018719-250920141307145/datasets/export for details.
DOI: 10.15468/dl.8x4x78
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ambrosia polystachya",
 "Country is Kazakhstan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018720-250920141307145/datasets/export for details.
DOI: 10.15468/dl.qtxgrd
title: Occurrence Download

description: A dataset containing 519 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 one of (Chelone obliqua)"
 ]
}

 The dataset includes 519 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018717-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17206549
title: Magnetic and elemental data of a ferromanganes nodule from the Magellan Seamounts

description: The western Pacific serves as a crucial archive of past oceanic and climatic variability, offering key insights into deep-sea redox dynamics and their linkage to global climate change. In this study, we utilize paleomagnetic stratigraphy and metal distribution data from a ferromanganese nodule in the Magellan Seamounts to reconstruct redox conditions during the Plio-Pleistocene epochs and to evaluate their links with global climate changes. Our key findings include: (1) 18 magnetozones are identified in the nodule and preliminarily correlated to the geomagnetic polarity timescale from chrons C1n to C3r. This correlation suggests nodule growth rates of 2.7–5.8 mm/Myr over the past 5.4 Myr. (2) Arborization-like growth structures are observed within the nodule, along with evidence for a hydrogenetic genesis, allowing for a regional redox reconstruction. By integrating the Mn/Fe ratio and Co content of the nodule, we reveal a sustained decline in redox conditions since ~3.2 Ma, and identify a synchronized anti-phase relationship with multiple intervals of better ventilation in the Magellan Seamounts comparing other sites in the North Pacific. The complex interplay between bathymetric features and regional circulation likely contributed to spatial heterogeneity in redox states. Our findings highlight the role of unique topography and geomorphology in modulating bottom-water circulation and redox dynamics during past climate transitions.
DOI: 10.5281/zenodo.17206550
title: Magnetic and elemental data of a ferromanganes nodule from the Magellan Seamounts

description: The western Pacific serves as a crucial archive of past oceanic and climatic variability, offering key insights into deep-sea redox dynamics and their linkage to global climate change. In this study, we utilize paleomagnetic stratigraphy and metal distribution data from a ferromanganese nodule in the Magellan Seamounts to reconstruct redox conditions during the Plio-Pleistocene epochs and to evaluate their links with global climate changes. Our key findings include: (1) 18 magnetozones are identified in the nodule and preliminarily correlated to the geomagnetic polarity timescale from chrons C1n to C3r. This correlation suggests nodule growth rates of 2.7–5.8 mm/Myr over the past 5.4 Myr. (2) Arborization-like growth structures are observed within the nodule, along with evidence for a hydrogenetic genesis, allowing for a regional redox reconstruction. By integrating the Mn/Fe ratio and Co content of the nodule, we reveal a sustained decline in redox conditions since ~3.2 Ma, and identify a synchronized anti-phase relationship with multiple intervals of better ventilation in the Magellan Seamounts comparing other sites in the North Pacific. The complex interplay between bathymetric features and regional circulation likely contributed to spatial heterogeneity in redox states. Our findings highlight the role of unique topography and geomorphology in modulating bottom-water circulation and redox dynamics during past climate transitions.
DOI: 10.5281/zenodo.16839073
title: Multiscale simulations reveal dynamics interfacial network and membrane remodeling of the ankyrin-1 complex

description: This dataset contains representative molecular dynamics (MD) trajectory segments and their corresponding topology files from the study. All files have been preprocessed to remove solvent molecules (and lipids for all-atom data), enabling efficient visualization and analysis.

The dataset consists of three parts:

All-atom simulations – (1) one unbiased 2 μs production trajectory, (2) four independent 2 ns trajectories used for binding free energy calculations, (3) one em.gro and (4) one rmsd_ref.gro.

Coarse-grained simulations – four 2-μs production trajectories: (1) full ankyrin-1 complex, (2) membrane-only control, (3) full complex including the ankyrin-1 subunit, and (4) truncated complex excluding the ankyrin-1 subunit.

Topology files – complete topology files required to reproduce and analyze the simulations.

These subsets capture the key interfacial interactions and membrane remodeling patterns described in the study, while significantly reducing file size for convenient download. The full trajectories are available from the corresponding author upon reasonable request.