cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14534088
title: Datasets: AFsample2 predicts multiple conformations and ensembles with AlphaFold2

description: Directory Overview

An overview of the directory structure, along with a description of each folder and its contents. Extract as follows.



tar --use-compress-program=unzstd -xvf analysis_results.tar.zst

tar --use-compress-program=unzstd -xvf input_datasets.tar.zst

tar --use-compress-program=unzstd -xvf generated_models.tar.zst


1. analysis_results



Contains results (.csv) of ensemble analysis

Files required to generate images for the manuscript with included summarize.ipynb notebook (updated notebook available at https://github.com/iamysk/AFsample2/blob/main/notebooks/summarize.ipynb)




tar --use-compress-program=unzstd -xvf analysis_results.tar.zst

└── analysis_results   ├── general   ├── oc23   │   ├── afsample2   │   ├── SPEACH_AF   │   ├── ...   └── tp16       ├── afsample2       ├── SPEACH_AF       ├── ...


2. generated_models



This directory stores models generated during the project.

It is organized by dataset names (e.g., oc23, tp16).


Inside generated_models:

oc23 and tp16: Subdirectories corresponding to models corresponding to various methods (AFcluster, AFsample, AFsample2, MSA subsampling, SPEACH_AF) employed in the study. All methods except AFcluster have been implemented in AFsample2 code.



tar --use-compress-program=unzstd -xvf input_datasets.tar.zst

└── input_datasets    ├── oc23    │   ├── fastas    │   ├── filtered_dict.pickle    # pdbids and stats for states    │   ├── msas                               # in .pkl format    │   └── pdbs                               # All reference pdbs used in the study    └── tp16        ├── fastas        ├── msas        └── pdbs


3. input_datasets



Contains raw input datasets used for analysis and model generation.

Organized by dataset names (e.g., oc23, tp16).


Inside input_datasets (oc23 and tp16):







fastas: Directory containing FASTA sequence files.

filtered_dict.pickle (in oc23 only): A Python pickle file with preprocessed or filtered data.

msas: Multiple Sequence Alignments (MSAs) in .pkl format used as input for modeling.

pdbs: PDB structure files related to the datasets.






tar --use-compress-program=unzstd -xvf generated_models.tar.zst

└── generated_models   ├── oc23   │   ├── afsample2   │   ├── SPEACH_AF   │   ├── ...   └── tp16       ├── afsample2       ├── SPEACH_AF       ├── ...


Citation

If you use this dataset, please cite the associated publications.
DOI: 10.15468/dl.wkcqdn
title: Occurrence Download

description: A dataset containing 5166 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (iNaturalist Research-grade Observations, Observation.org, Nature data from around the World, Waarnemingen.be - Hymenoptera occurrences in Flanders and the Brussels Capital Region, Belgium)",
 "MediaType is Image",
 "Sex is Male",
 "TaxonKey is Formicidae"
 ]
}

 The dataset includes 5166 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003313-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57967/hf/4687
title: AIME_1983_2024
DOI: 10.5281/zenodo.10715216
title: Variance representations and convergence rates for data-driven approximations of Koopman operators

description: Data and codes to re-create the numerical examples in submitted manuscript

Variance representations and convergence rates for data-driven approximations of Koopman operators

See README for detailed instructions.
DOI: 10.5281/zenodo.10715217
title: Extended Dynamic Mode Decomposition: Sharp bounds on the sample efficiency

description: Data and codes to re-create the numerical examples in arxiv preprint

Extended Dynamic Mode Decomposition: Sharp bounds on the sample efficiency,  arXiv:2402.02494

See README for detailed instructions.
DOI: 10.5281/zenodo.13236922
title: Variance representations and convergence rates for data-driven approximations of Koopman operators

description: Data and codes to re-create the numerical examples in submitted manuscript

Variance representations and convergence rates for data-driven approximations of Koopman operators

See README for detailed instructions.
DOI: 10.15468/dl.2599fn
title: Occurrence Download

description: A dataset containing 110 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Bombina fortinuptialis Liu & Tian, 1978"
 ]
}

 The dataset includes 110 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003366-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bvuekv
title: Occurrence Download

description: A dataset containing 193 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euphorbia jolkinii Boiss.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is Japan"
 ]
}

 The dataset includes 193 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003367-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q2gjdp
title: Occurrence Download

description: A dataset containing 998444 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Salmo salar Linnaeus, 1758"
 ]
}

 The dataset includes 998444 records from 278 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003312-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28522598
title: Different _Expression_Genes.xlsx

description: This file contains DEGs of FGR vs Con, VT (villous lineage) vs EVT, and LAB (labyrinth lineage) vs Others.
DOI: 10.15468/dl.wd2sc7
title: Occurrence Download

description: A dataset containing 1937306 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Europe",
 "Geometry POLYGON((9.5803 53.61708,17.32932 55.08531,21.32617 58.42962,20.79015 63.09254,26.64626 66.15936,31.52224 66.58648,31.3591 72.62255,-5.91368 66.29991,6.68866 54.72825,9.5803 53.61708))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (CR, EN, VU)",
 "OccurrenceStatus is Present",
 "Year 2000-2025"
 ]
}

 The dataset includes 1937306 records from 174 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003363-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28522610
title: Comparing the efficacy of two camera trapping techniques for assessing the occupancy, detection and activity patterns of small Mustelids in Britain

description: Summary of detections for three mustelid species
DOI: 10.5281/zenodo.14958866
title: raw data - Development and Validation of a Model for Predicting Short-term Mortality in Elderly Patients with Sepsis: A Retrospective Cohort Study
DOI: 10.5281/zenodo.14958867
title: raw data - Development and Validation of a Model for Predicting Short-term Mortality in Elderly Patients with Sepsis: A Retrospective Cohort Study
DOI: 10.15468/dl.n22bkp
title: Occurrence Download

description: A dataset containing 421537 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "GadmGid is IND.17.13_1",
 "TaxonKey is Passeriformes",
 "Year 1994-2023"
 ]
}

 The dataset includes 421537 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003365-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25624917
title: OphthalVQA Dataset

description: A supplement to "<b>Unveiling the Clinical Incapabilities: A Benchmarking Study of GPT-4V(ision) for Ophthalmic Multimodal Image Analysis</b>".*Cite this paper: Xu, P., Chen, X., Zhao, Z., & Shi, D. (2024). Unveiling the clinical incapabilities: a benchmarking study of GPT-4V(ision) for ophthalmic multimodal image analysis. <i>The British journal of ophthalmology</i>, bjo-2023-325054. Advance online publication. https://doi.org/10.1136/bjo-2023-325054<br>
DOI: 10.15468/dl.pmwp4e
title: Occurrence Download

description: A dataset containing 27415 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Belgium",
 "TaxonKey is Salmo salar Linnaeus, 1758"
 ]
}

 The dataset includes 27415 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003314-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ptpwkc
title: Occurrence Download

description: A dataset containing 398 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Hageniella micans (Mitt.) B.C.Tan & Y.Jia",
 "Year 1970-2025"
 ]
}

 The dataset includes 398 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003368-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25592/uhhfdm.10649
title: An Interview About The History of Woyi And Kaabu, Abdu Njayi And Kelefaa Saane (NCAC_RDD_TAPE_0533B)

description: Woyi: Abdu Njayi
 Kelefaa Saane
 Kaabu 
 Civil war


<em><sup>Alternative names: Abdou, Diaye, Ndiaye, N'Diaye, Njie, Njai, Kelefa Sanneh, Kebba, Sidibeh, </sup></em> <em><sup>Bakary, Bakari, Bakery,</sup></em>
description: Published by NCAC - National Digital Archive of The Gambia, initiated by University of Hamburg, Asia-Africa-Institute, Germany, funded by Gerda Henkel Foundation, Germany
DOI: 10.25592/uhhfdm.10648
title: An Interview About The History of Woyi And Kaabu, Abdu Njayi And Kelefaa Saane (NCAC_RDD_TAPE_0533B)

description: Woyi: Abdu Njayi
 Kelefaa Saane
 Kaabu 
 Civil war


<em><sup>Alternative names: Abdou, Diaye, Ndiaye, N'Diaye, Njie, Njai, Kelefa Sanneh, Kebba, Sidibeh, </sup></em> <em><sup>Bakary, Bakari, Bakery,</sup></em>
description: Published by NCAC - National Digital Archive of The Gambia, initiated by University of Hamburg, Asia-Africa-Institute, Germany, funded by Gerda Henkel Foundation, Germany
DOI: 10.15468/dl.vrp9zv
title: Occurrence Download

description: A dataset containing 998444 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Salmo salar Linnaeus, 1758"
 ]
}

 The dataset includes 998444 records from 278 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003360-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14168153
title: Supplementary Data and Scripts

description: Supplementary sata and scripts for assessing the impact of aircraft emissions on urban air quality
DOI: 10.5281/zenodo.14168154
title: Scripts

description: Scripts  for assessing the impact of aircraft emissions on urban air quality
DOI: 10.5281/zenodo.14958846
title: Supplementary Data and Scripts

description: Supplementary sata and scripts for assessing the impact of aircraft emissions on urban air quality
DOI: 10.15468/dl.q69492
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Jackiopsis ornata (Wall.) Ridsdale"
 ]
}

 The dataset includes 32 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003371-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qht34h
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Bombina lichuanensis Ye & Fei, 1993"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003370-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57967/hf/4688
title: orderly_qa
DOI: 10.15468/dl.2eyyv4
title: Occurrence Download

description: A dataset containing 1203 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Bombina maxima (Boulenger, 1905)"
 ]
}

 The dataset includes 1203 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003316-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4fz44j
title: Occurrence Download

description: A dataset containing 378 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is India",
 "Geometry POLYGON((442.86964 24.12156,443.50457 24.12156,443.50457 24.71819,442.86964 24.71819,442.86964 24.12156))"
 ]
}

 The dataset includes 378 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003372-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rs7z77
title: Occurrence Download

description: A dataset containing 4837 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is SWE.13.19_1",
 "Month is February",
 "Year 2022-2022"
 ]
}

 The dataset includes 4837 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003317-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25592/uhhfdm.11893
title: An Interview About The History of Kaabu (NCAC_RDD_TAPE_0538B)

description: SE1: Continuation of TAPE_0538A




SE2: Kaabu


 Origin of Kaabu
 Origin of state names
 Nyanci
 Mankotobaa Saane
 Janke Waali
 Wars of Futa
 Manna rulers and fortified places
 Clans and social groups of Manna
 Naming of Sarafa Nyaaleng Jeenung and his career
 Great jalang
 Pajadinka
 Settlement of Kafinrang/Manna
 Origin of Mandinka clan names
 Pajadi clan names


<em><sup>Alternative names: Mankotoba, Sanneh, Wali, Wally, Nyaleng, Jenung, Alhagi, Alhagie, Alhajie, Foday, Seedy, Seedi, Sidibeh, </sup></em> <em><sup>Bakary, Bakari, Bakery, Kebba</sup></em>
description: Published by NCAC - National Digital Archive of The Gambia, initiated by University of Hamburg, Asia-Africa-Institute, Germany, funded by Gerda Henkel Foundation, Germany
DOI: 10.25592/uhhfdm.11892
title: An Interview About The History of Kaabu (NCAC_RDD_TAPE_0538B)

description: SE1: Continuation of TAPE_0538A




SE2: Kaabu


 Origin of Kaabu
 Origin of state names
 Nyanci
 Mankotobaa Saane
 Janke Waali
 Wars of Futa
 Manna rulers and fortified places
 Clans and social groups of Manna
 Naming of Sarafa Nyaaleng Jeenung and his career
 Great jalang
 Pajadinka
 Settlement of Kafinrang/Manna
 Origin of Mandinka clan names
 Pajadi clan names


<em><sup>Alternative names: Mankotoba, Sanneh, Wali, Wally, Nyaleng, Jenung, Alhagi, Alhagie, Alhajie, Foday, Seedy, Seedi, Sidibeh, </sup></em> <em><sup>Bakary, Bakari, Bakery, Kebba</sup></em>
description: Published by NCAC - National Digital Archive of The Gambia, initiated by University of Hamburg, Asia-Africa-Institute, Germany, funded by Gerda Henkel Foundation, Germany
DOI: 10.15468/dl.6p626k
title: Occurrence Download

description: A dataset listing the 135 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is India",
 "Geometry POLYGON((442.86964 24.12156,443.50457 24.12156,443.50457 24.71819,442.86964 24.71819,442.86964 24.12156))"
 ]
}

 The dataset's 135 records were derived from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003369-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.stbrem
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((89.90511 -8.93795,117.09489 -8.93795,117.09489 1.93795,89.90511 1.93795,89.90511 -8.93795))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Dipterocarpus cinereus Slooten"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003373-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48320/284f30c3-2057-4d5d-ba36-74a48a2a3dcc
title: Health Index. Ukraine: Wave 3, 2018
DOI: 10.15125/bath-01501
title: Dataset for "Filament Type Recognition for Additive Manufacturing Using a Spectroscopy Sensor and Machine Learning"

description: The file contains data collected from three sensors: AS72651, AS72652, and AS72653. Each of these sensor-specific files includes three folders representing different measurement distances: 12mm, 16mm, and 20mm. These folders contain data collected from 12 different filaments. Additionally, there is data recorded without a filament, labeled as "no_object." The following example of organizational structure is consistent across all filament data.

Folder : AS72651 ->12mm->first measurement: abs_carbonfiber1.csv
                                               ->second measurement: abs_carbonfiber2.csv
                                               ->third measurement: abs_carbonfiber3.csv
                                               ->three measurements together: abs_carbonfiber.csv

Each collected dataset is stored in CSV format. The data can be utilized for filament recognition using machine learning models, enabling the identification of different filament types based on sensor measurements.
description: The methodology is described in the associated paper.
DOI: 10.6084/m9.figshare.28522697
title: <b>Citation Proximity-Context Analysis for </b><b>Interdisciplinary Common Knowledge Discovery</b>

description: The academic barrier between disciplines can impede scientific communication and collaboration, resulting in the isolated development of common concepts and methodologies within independent fields. However, identifying and elucidating common knowledge across disciplines can enhance cross-field visibility, reduce redundant research efforts, as well as promote the diffusion and application of knowledge across domains. Therefore, this study proposes a methodology that leverages citation context to identify common knowledge among disciplines. By analyzing co-cited patterns in citation contexts drawn from existing cases of interdisciplinary common knowledge and extracting these patterns from a large-scale dataset, we designed evaluation metrics that consider commonality, interdisciplinarity, and novelty to identify valid, novel, potentially useful, and understandable interdisciplinary common knowledge. Eventually, 1,044 candidate pairs of interdisciplinary knowledge were identified. Among them, seven cases with remarkable interdisciplinary common novelty were analyzed. Each of these cases demonstrated the vital intersections in problem-solving approaches and fundamental methodologies, highlighting the potential for knowledge integration across different disciplines. The study underscores the challenges posed by disciplinary barriers in recognizing interdisciplinarity knowledge and contributes a systematic approach to fostering interdisciplinary communication of knowledge.
DOI: 10.15468/dl.2x2u7r
title: Occurrence Download

description: A dataset containing 1353 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pisonia grandis R.Br."
 ]
}

 The dataset includes 1353 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003374-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vmp9fz
title: Occurrence Download

description: A dataset containing 531 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "GadmGid is PAK.7.8_1",
 "TaxonKey is Passeriformes",
 "Year 1994-2023"
 ]
}

 The dataset includes 531 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003375-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qnz48g
title: Occurrence Download

description: A dataset containing 36626 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((24.85239 58.31495,25.14247 58.31495,25.14247 58.47093,24.85239 58.47093,24.85239 58.31495))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 36626 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003376-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.23729/fd-67e95e60-137b-34d4-8ad2-ba925cfc8a42
title: TLS point clouds of mature even-aged Norway spruces in South-Eastern Finland

description: 476 individual mature Norway spruce trees recorded with multi-scan TLS in 2020.
Accompanied by field references (dbh and h), as well as sawmill-measured total log volume, log-section length and top-end diameter, and log biomass.
DOI: 10.15468/dl.pecag9
title: Occurrence Download

description: A dataset containing 2926 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Blastus cochinchinensis Lour."
 ]
}

 The dataset includes 2926 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003318-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14958478
title: Dataset of global terrestrial gross primary productivity from 2000 to 2020

description: This dataset comprises global gross primary productivity (GPP) data spanning from 2000 to 2020. The data in this dataset are of float type, with units of g C m-2 year-1. The temporal resolution is one year, the spatial resolution is 1 km, and the fill value is 0.
DOI: 10.5281/zenodo.14958479
title: Dataset of global terrestrial gross primary productivity from 2000 to 2020

description: This dataset comprises global gross primary productivity (GPP) data spanning from 2000 to 2020. The data in this dataset are of float type, with units of g C m-2 year-1. The temporal resolution is one year, the spatial resolution is 1 km, and the fill value is 0.