cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.leurgp
title: Occurrence Download

description: A dataset containing 446 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zornia pardina Mohlenbr."
 ]
}

 The dataset includes 446 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033329-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111304612
title: Church of St. Nicholas of the Roof, Ayios Nikolaos tis Stegis

description: [Text Description:] A domed church of the early eleventh century dedicated to St. Nicholas. ❧ [Medium:] Stone ❧ [Script Note:] Greek, Non-Text ❧ [Physical Object Description:] A domed church of the early eleventh century with a later steep-pitched room for protection against the snow. Located about 3 miles above Kakopetria, Cyprus in a wooded valley near a stream. ❧ [Physical Object Note:] The church is the sole remnant of an old monastery founded in the 11th century that flourished in the mid-Byzantine period and during Frankish rule but fell into decline in the 18th century, eventually dissolving. ❧ [Physical Object Note:] The church belongs to the domed cross-in square plan and gets its name from the second timber roof with flat tiles that were made in the Soleas district. The narthex, covered by a calotte and two traverse arches, was added at the beginning of the 12th century. At a later stage the church's original appearance was altered resulting in the destruction of important paintings. ❧
DOI: 10.15468/dl.jmrznx
title: Occurrence Download

description: A dataset containing 7046 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Occurrence evidence"
 ]
 },
 "Continent is Africa",
 {
 "or" : [
 "Country is Côte d’Ivoire",
 "Country is Togo",
 "Country is Benin",
 "Country is Cameroon",
 "Country is Ghana",
 "Country is Nigeria",
 "Country is Burkina Faso",
 "Country is Guinea-Bissau",
 "Country is Guinea",
 "Country is Senegal"
 ]
 },
 "TaxonKey is Pterocarpus erinaceus Poir."
 ]
}

 The dataset includes 7046 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0392071-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.axosib
title: Occurrence Download

description: A dataset containing 162 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sciurus pyrrhinus Thomas, 1898"
 ]
}

 The dataset includes 162 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005674-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xnqfon
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Spain",
 "TaxonKey is Exormotheca pustulosa Mitt."
 ]
}

 The dataset includes 43 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033562-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111304568
title: Church of St. Nicholas of the Roof, Ayios Nikolaos tis Stegis

description: [Text Description:] A domed church of the early eleventh century dedicated to St. Nicholas. ❧ [Medium:] Stone ❧ [Script Note:] Greek, Non-Text ❧ [Physical Object Description:] A domed church of the early eleventh century with a later steep-pitched room for protection against the snow. Located about 3 miles above Kakopetria, Cyprus in a wooded valley near a stream. ❧ [Physical Object Note:] The church is the sole remnant of an old monastery founded in the 11th century that flourished in the mid-Byzantine period and during Frankish rule but fell into decline in the 18th century, eventually dissolving. ❧ [Physical Object Note:] The church belongs to the domed cross-in square plan and gets its name from the second timber roof with flat tiles that were made in the Soleas district. The narthex, covered by a calotte and two traverse arches, was added at the beginning of the 12th century. At a later stage the church's original appearance was altered resulting in the destruction of important paintings. ❧
DOI: 10.25549/inscriptifact-ouc111132861
title: Vision of Gabriel

description: [Text Description:] Apocalyptic text written by someone named Gabriel ❧ [Medium:] Stone ❧ [Script Note:] Jewish ❧ [Physical Object Description:] Sandstone inscription, 96 x 37 cm. The stone is broken into serveral pieces: one large piece, making up 2/3 of the stone; a smaller piece, making up approximately 1/3 of the stone, with several smaller pieces in between. ❧ [Physical Object Note:] The text consists of 87 lines in two columns. The lines are ruled, and the columns double-ruled. ❧ [Physical Object Note:] Several areas show evidence of erasure and redrawn lines; on the left of the stone some of the rule lines seem to have been redrawn without a straight edge.
DOI: 10.15468/dl.8cnb2d
title: Occurrence Download

description: A dataset containing 132 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heterocentron mexicanum Hook. & Arn."
 ]
}

 The dataset includes 132 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0241975-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rqctre
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sturnira mistratensis Vega & Cadena, 2000"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005683-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x2ij5i
title: Occurrence Download

description: A dataset containing 33676 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oncorhynchus nerka (Walbaum, 1792)"
 ]
}

 The dataset includes 33676 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033345-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc111304507
title: The Church of the Holy Cross, Timios Stavros, Pelendria

description: [Text Description:] A complex church in Pelendri dedicated to the Holy Cross, 12th c. ❧ [Medium:] Stone ❧ [Script Note:] Greek, Non-Text ❧ [Physical Object Description:] Located in Pelendri. Originally a single-aisled domed building with arched recesses in the side walls. ❧ [Physical Object Note:] In the 14th c. it was extended to the north. A similar aisle was added to the south probably in 16th c. ❧ [Physical Object Note:] Built and painted in the 12th c., and repainted in the 14th-15th centuries. ❧
DOI: 10.25549/inscriptifact-ouc111133286
title: Daniel (Premier Exemplaire), 1Q71 Daniel a:Alternate Text Title,1Q Daniel a:Alternate Text Title,

description: [Text Description:] Parts of Daniel 1:10-17 and 2:2-6 ❧ [Text or Publication Number Note:] 1Q71 Dan a ❧ [Excavation Description:] Found in Qumran Cave 1 by George Isha'ya in 1949 and delivered to Mar Athanasius Samuel, Metropolitan of St. Mark's Monastery in Jerusalem. ❧ [Medium:] Parchment ❧ [Script Note:] Jewish ❧ [Physical Object Description:] Two parchment fragments, some blackening. The fragment containing Col. I has part of 1Q72 adhering to the back.
DOI: 10.15468/dl.wsphwx
title: Occurrence Download

description: A dataset containing 1472 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Teius teyou (Daudin, 1802)"
 ]
}

 The dataset includes 1472 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0241984-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14967784
title: 20-Year Time-Series of Summertime CTD, LADCP and Finescale Observations Across Drake Passage from the SR1b Repeat-Hydrography Section

description: This data base contains three sets of oceanographic profiles with data from Conductivity-Temperature-Depth (CTD), Lowered Acoustic Doppler Current Profiler (LADCP), as well as several derived parameters of internal-wave (finescale) properties from the 19 repeat summertime occupations of the UK SR1b section across the ACC carried out between 2002 and 2019. 

Reference: Thurnherr, A. M., Y. L. Firing, T. K. Chereskin, and S. Waterman (2025). Summertime internal-wave properties along the SR1b section across Drake Passage. J. Phys. Oceanogr. (in press).
DOI: 10.5281/zenodo.14967785
title: 20-Year Time-Series of Summertime CTD, LADCP and Finescale Observations Across Drake Passage from the SR1b Repeat-Hydrography Section

description: This data base contains three sets of oceanographic profiles with data from Conductivity-Temperature-Depth (CTD), Lowered Acoustic Doppler Current Profiler (LADCP), as well as several derived parameters of internal-wave (finescale) properties from the 19 repeat summertime occupations of the UK SR1b section across the ACC carried out between 2002 and 2019. 

Reference: Thurnherr, A. M., Y. L. Firing, T. K. Chereskin, and S. Waterman (2025). Summertime internal-wave properties along the SR1b section across Drake Passage. J. Phys. Oceanogr. (in press).
DOI: 10.15468/dl.4rd346
title: Occurrence Download

description: A dataset containing 105 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Pleocarphus revolutus D.Don"
 ]
}

 The dataset includes 105 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025278-250310093411724/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.28167065
title: <b>When Code Smells Meet ML: On the Lifecycle of ML-specific Code Smells in ML-enabled Systems </b>- Replication Package

description: Replication Package of the article: <b>When Code Smells Meet ML: On the Lifecycle of ML-specific Code Smells in ML-enabled Systems</b>In this package you can find our online technical report with more details for each Machine Learning-Specific Code Smell and our replication package with data, script and our tool: CodeSmile. More details in the included README.md <br><br><br>Abstract:<br><br>The adoption of Machine Learning (ML)--enabled systems is steadily increasing.Nevertheless, there is a shortage of ML-specific quality assurance approaches, possibly because of the limited knowledge of how quality-related concerns emerge and evolve in ML-enabled systems.In this paper, we aim to investigate the emergence and evolution of specific types of quality-related concerns known as ML-specific code smells, \ie sub-optimal implementation solutions applied on ML pipelines that may significantly decrease the quality and maintainability of ML-enabled systems. More specifically, it presents a study of ML-specific code smells by empirically analyzing (i) their prevalence in real ML-enabled systems, (ii) how they are introduced and removed, and (iii) their survivability.Therefore, we provide an exploratory study, mining a large dataset of ML-enabled systems and analyzing over 400k commits about \numProjectsSampling projects. We tracked and inspected the introduction and evolution of ML smells through \CodeSmile, a novel ML smell detector that we built to enable our investigation and to detect ML-specific code smells.<br>Our results reveal that: 1) \CodeSmile can detect ML-CSs with 0.87\% and 0.78\% of precision and recall, respectively. 2) ML-CSs are often introduced during the file modification during new feature tasks. 3) Smells are typically removed due to new features, enhancement, or refactoring tasks. And, lastly, the majority of ML-CSs are resolved within the first 10\% of commits.
DOI: 10.6084/m9.figshare.28167065.v2
title: <b>When Code Smells Meet ML: On the Lifecycle of ML-specific Code Smells in ML-enabled Systems </b>- Replication Package

description: Replication Package of the article: <b>When Code Smells Meet ML: On the Lifecycle of ML-specific Code Smells in ML-enabled Systems</b>In this package you can find our online technical report with more details for each Machine Learning-Specific Code Smell and our replication package with data, script and our tool: CodeSmile. More details in the included README.md <br><br><br>Abstract:<br><br>The adoption of Machine Learning (ML)--enabled systems is steadily increasing.Nevertheless, there is a shortage of ML-specific quality assurance approaches, possibly because of the limited knowledge of how quality-related concerns emerge and evolve in ML-enabled systems.In this paper, we aim to investigate the emergence and evolution of specific types of quality-related concerns known as ML-specific code smells, \ie sub-optimal implementation solutions applied on ML pipelines that may significantly decrease the quality and maintainability of ML-enabled systems. More specifically, it presents a study of ML-specific code smells by empirically analyzing (i) their prevalence in real ML-enabled systems, (ii) how they are introduced and removed, and (iii) their survivability.Therefore, we provide an exploratory study, mining a large dataset of ML-enabled systems and analyzing over 400k commits about \numProjectsSampling projects. We tracked and inspected the introduction and evolution of ML smells through \CodeSmile, a novel ML smell detector that we built to enable our investigation and to detect ML-specific code smells.<br>Our results reveal that: 1) \CodeSmile can detect ML-CSs with 0.87\% and 0.78\% of precision and recall, respectively. 2) ML-CSs are often introduced during the file modification during new feature tasks. 3) Smells are typically removed due to new features, enhancement, or refactoring tasks. And, lastly, the majority of ML-CSs are resolved within the first 10\% of commits.
DOI: 10.15468/dl.hwguk9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Meles meles (Linnaeus, 1758)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is Switzerland",
 "Year is greater than or equal to 2010",
 "Year is less than or equal to 2020"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025281-250310093411724/datasets/export for details.
DOI: 10.25574/30158
title: Chandra X-ray Observatory ObsId 30158

description: A TREASURY SURVEY PROBING THE BARYON & ENERGY CYCLE AND X-RAY BINARY EVOLUTION IN GALAXIES AT HIGH ANGULAR RESOLUTION
DOI: 10.60656/8248be3414a94b15
title: Custom collection of ice effective radius data from Granada on 9 Feb 2025
DOI: 10.15468/dl.cf6jn7
title: Occurrence Download

description: A dataset containing 5173 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material sample, Specimen)",
 "TaxonKey is Cerdocyon thous (Linnaeus, 1766)",
 "Year 1970-2025"
 ]
}

 The dataset includes 5173 records from 268 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025280-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zw68jy
title: Occurrence Download

description: A dataset containing 3924 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stevia serrata Cav."
 ]
}

 The dataset includes 3924 records from 150 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025279-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hdezuh
title: Occurrence Download

description: A dataset containing 4089 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Calliandra eriophylla Benth.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4089 records from 114 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025282-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cwurzt
title: Occurrence Download

description: A dataset containing 4148 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (EN, CR)",
 "StateProvince is NOrth Carolina"
 ]
}

 The dataset includes 4148 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025283-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bv2gay
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Gentianella columnae (Ten.) Holub",
 "Year 1960-2025"
 ]
}

 The dataset includes 73 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025284-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4e6mwa
title: Occurrence Download

description: A dataset listing the 4032962 species recorded in GBIF matching the query:
{
 "OccurrenceStatus" : [
 "is Present"
 ]
}

 The dataset's 4032962 records were derived from 71907 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025257-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14983480
title: Large-scale discovery, analysis, and design of protein energy landscapes

description: *** IMPORTANT! Please Register to use of these data so that we can continue to release new useful datasets! This will take 10 seconds!! ***This repository contains datasets generated for our study on protein energy landscapes using our multiplex hydrogen-deuterium exchange (mHDX) analysis. The datasets include raw and processed HDX data, NMR results, curated subsets, and machine learning splits with interpretable and deep learning-derived features. These resources support various analyses, including protein stability assessment, EX1 kinetics evaluation, and predictive modeling.

Available Datasets:



Dataset_0_InitialOrder: Initial DNA sequences from all libraries (15,715 unique sequences).

Dataset_1_UnfilteredData: Minimally filtered HDX data based on confident identifications and PO score < 50 (8,293 unique sequences).

Dataset_2_SuccessfulHDX: Proteins passing quality control metrics, including EX1 kinetics (5,778 unique sequences).

Dataset_3_MeasurablyStable: Proteins reaching full deuteration with ΔGunfold > 2 kcal/mol and passing EX1 kinetics filter (3,590 unique sequences).

Dataset_4_HDXNMR: HDX-NMR results per condition, including average ΔGopen per position (16 unique sequences).

Dataset_5_MesophilicThermophilic: Subset of proteins from natural domains classified as mesophilic or thermophilic based on optimal growth temperature (>40°C) (1,637 unique sequences).

Dataset_6_splits_interpretable: Machine learning splits with interpretable features (3,193 unique sequences).

Dataset_6_splits_esm2: Machine learning splits with ESM2-derived features (3,465 unique sequences).

Dataset_6_splits_unirep: Machine learning splits with Unirep-derived features (3,465 unique sequences).

Dataset_6_splits_saprot: Machine learning splits with SaProt-derived features (3,465 unique sequences).

Dataset_7_mHDX_cDNA: Subset of Dataset_2 (best PO scored candidate, EX1 kinetics excluded) overlapping with cDNA proteolysis assay data from Tsuboyama et al. (2023) (4,464 unique sequences).

Dataset_8_PDFs: Comprehensive plots generated using the mhdx_pipeline and hdxrate_pipeline, visualizing time-dependent mass distributions and fits to exchange rates. A Jupyter notebook is included to facilitate navigation. (Note: This dataset is split into eight parts for uploading purposes — .zip_part_aa through .zip_part_ah. Please concatenate the parts before unzipping.)

Dataset_9_AlphaFoldModels: AlphaFold 2 models/Rosetta relaxed from Dataset_2_SucessfulHDX (5,778 unique sequences)
DOI: 10.5281/zenodo.14983481
title: Large-scale discovery, analysis, and design of protein energy landscapes

description: *** IMPORTANT! Please Register to use of these data so that we can continue to release new useful datasets! This will take 10 seconds!! ***This repository contains datasets generated for our study on protein energy landscapes using our multiplex hydrogen-deuterium exchange (mHDX) analysis. The datasets include raw and processed HDX data, NMR results, curated subsets, and machine learning splits with interpretable and deep learning-derived features. These resources support various analyses, including protein stability assessment, EX1 kinetics evaluation, and predictive modeling.

Available Datasets:



Dataset_0_InitialOrder: Initial DNA sequences from all libraries (15,715 unique sequences).

Dataset_1_UnfilteredData: Minimally filtered HDX data based on confident identifications and PO score < 50 (8,293 unique sequences).

Dataset_2_SuccessfulHDX: Proteins passing quality control metrics, including EX1 kinetics (5,778 unique sequences).

Dataset_3_MeasurablyStable: Proteins reaching full deuteration with ΔGunfold > 2 kcal/mol and passing EX1 kinetics filter (3,590 unique sequences).

Dataset_4_HDXNMR: HDX-NMR results per condition, including average ΔGopen per position (16 unique sequences).

Dataset_5_MesophilicThermophilic: Subset of proteins from natural domains classified as mesophilic or thermophilic based on optimal growth temperature (>40°C) (1,637 unique sequences).

Dataset_6_splits_interpretable: Machine learning splits with interpretable features (3,193 unique sequences).

Dataset_6_splits_esm2: Machine learning splits with ESM2-derived features (3,465 unique sequences).

Dataset_6_splits_unirep: Machine learning splits with Unirep-derived features (3,465 unique sequences).

Dataset_6_splits_saprot: Machine learning splits with SaProt-derived features (3,465 unique sequences).

Dataset_7_mHDX_cDNA: Subset of Dataset_2 (best PO scored candidate, EX1 kinetics excluded) overlapping with cDNA proteolysis assay data from Tsuboyama et al. (2023) (4,464 unique sequences).

Dataset_8_PDFs: Comprehensive plots generated using the mhdx_pipeline and hdxrate_pipeline, visualizing time-dependent mass distributions and fits to exchange rates. A Jupyter notebook is included to facilitate navigation. (Note: This dataset is split into eight parts for uploading purposes — .zip_part_aa through .zip_part_ah. Please concatenate the parts before unzipping.)

Dataset_9_AlphaFoldModels: AlphaFold 2 models/Rosetta relaxed from Dataset_2_SucessfulHDX (5,778 unique sequences)