cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15030237
title: When Tools Overlook Domain Knowledge: An Empirical Study of Refactoring in Scientific Software

description: Abstract

Refactoring is a critical process for improving code quality, but anecdotal evidence has shown that refactoring in scientific software (Sci-SW) is not always feasible. The inherently exploratory nature of Sci-SW development, characterized by evolving requirements and limited adoption of traditional software engineering practices, could present significant challenges to refactoring. However, there is no systematic study exploring refactoring practices in Sci-OSS. To bridge this gap, we explore the effectiveness of three state-of-the-art refactoring detection tools: RefDiff (C), RefactoringMiner (Java), and PyRef (Python) to detect refactorings in scientific open-source software (Sci-OSS). Our findings reveal that these tools have significant limitations, detecting fewer refactorings in Sci-OSS than non-scientific OSS (Non-Sci-OSS). Through a mixed-method approach, we identified that 67.54% of undetected refactorings in Sci-OSS require domain knowledge. To complement our analysis of the refactoring code changes, we conducted surveys with 47 practitioners experienced in refactoring Sci-OSS and 14 follow-up interviews to gain deeper insights into the associated challenges. Our results revealed seven novel challenges for Sci-OSS-refactoring, including a domain knowledge gap. These findings emphasize the necessity for specialized tools and strategies to support refactoring in Sci-OSS effectively.

Replication instructions

The project is written in Python 3.12.0

The requirements file contains all the necessary packages to run the project.To install the required packages, run the following command:



pip install -r requirements.txt


Once the required packages are installed, 

To download refactoring data from GitHub, 



    1. Add your GitHub API token in RQ1/scripts/mysettings.py    2. Run the download_data_from_github.py file in the RQ1/scripts folder.


This should download all the required files necessary to the data folder from GitHub

Once you have all the data, then install the refactoring detection tools:The installation instructions are listed below:



    - For PyRef: https://github.com/PyRef/PyRef    - For RefactoringMiner3.0: https://github.com/tsantalis/RefactoringMiner    - For RefDiff2.0: https://github.com/aserg-ufmg/RefDiff


Once you have the refactoring detection tools installed. Please change the execution path in their respective script file:For example, change the pyref execution path in pyref_script.py file in RQ1/scripts folder.

Once you have changed the execution paths, you should be able to run the refactoring detection tool on all the collected data.

The detection tools will create a JSON file with the list of detected refactorings for every refactoring instance with the name format as 'repo_name_issue_number'.

you can now run all files in the RQ1/scripts folder to replicate the results.
DOI: 10.5281/zenodo.17794199
title: When Tools Overlook Domain Knowledge: An Empirical Study of Refactoring in Scientific Software

description: Abstract

Refactoring is a critical process for improving code quality, but anecdotal evidence has shown that refactoring in scientific software (Sci-SW) is not always feasible. The inherently exploratory nature of Sci-SW development, characterized by evolving requirements and limited adoption of traditional software engineering practices, could present significant challenges to refactoring. However, there is no systematic study exploring refactoring practices in Sci-OSS. To bridge this gap, we explore the effectiveness of three state-of-the-art refactoring detection tools: RefDiff (C), RefactoringMiner (Java), and PyRef (Python) to detect refactorings in scientific open-source software (Sci-OSS). Our findings reveal that these tools have significant limitations, detecting fewer refactorings in Sci-OSS than non-scientific OSS (Non-Sci-OSS). Through a mixed-method approach, we identified that 67.54% of undetected refactorings in Sci-OSS require domain knowledge. To complement our analysis of the refactoring code changes, we conducted surveys with 47 practitioners experienced in refactoring Sci-OSS and 14 follow-up interviews to gain deeper insights into the associated challenges. Our results revealed seven novel challenges for Sci-OSS-refactoring, including a domain knowledge gap. These findings emphasize the necessity for specialized tools and strategies to support refactoring in Sci-OSS effectively.

Replication instructions

The project is written in Python 3.12.0

The requirements file contains all the necessary packages to run the project.To install the required packages, run the following command:



pip install -r requirements.txt


Once the required packages are installed, 

To download refactoring data from GitHub, 



    1. Add your GitHub API token in RQ1/scripts/mysettings.py    2. Run the download_data_from_github.py file in the RQ1/scripts folder.


This should download all the required files necessary to the data folder from GitHub

Once you have all the data, then install the refactoring detection tools:The installation instructions are listed below:



    - For PyRef: https://github.com/PyRef/PyRef    - For RefactoringMiner3.0: https://github.com/tsantalis/RefactoringMiner    - For RefDiff2.0: https://github.com/aserg-ufmg/RefDiff


Once you have the refactoring detection tools installed. Please change the execution path in their respective script file:For example, change the pyref execution path in pyref_script.py file in RQ1/scripts folder.

Once you have changed the execution paths, you should be able to run the refactoring detection tool on all the collected data.

The detection tools will create a JSON file with the list of detected refactorings for every refactoring instance with the name format as 'repo_name_issue_number'.

you can now run all files in the RQ1/scripts folder to replicate the results.
DOI: 10.15468/dl.x9wuvf
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mikania vauthieriana"
 ]
}

 The dataset includes 48 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023014-251120083545085/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.cc2mcwd9
title: CCDC 2424491: Experimental Crystal Structure Determination

description: Related Article: Xuanchi Yu, Chenyu Zhang, Tao Li, Dongfang Dong, Bing Liu, Dali Wang|2025|CSD Communication|||
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.cc2mcwgc
title: CCDC 2424493: Experimental Crystal Structure Determination

description: Related Article: Xuanchi Yu, Chenyu Zhang, Tao Li, Dongfang Dong, Bing Liu, Dali Wang|2025|CSD Communication|||
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.cc2mcwhd
title: CCDC 2424494: Experimental Crystal Structure Determination

description: Related Article: Xuanchi Yu, Chenyu Zhang, Tao Li, Dongfang Dong, Bing Liu, Dali Wang|2025|CSD Communication|||
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: 10.5281/zenodo.17782444
title: The Observed Dark-Matter Density from Supersymmetric Unification in One Line

description: TU-GUT-SUSY in one equation: the entire prediction for the observed local dark-matter density is the single parameter-free formula

ρ_DM = M_SUSY⁴ / (192π M_Pl²) = 0.300 ± 0.005 GeV/cm³

using only the measured unification scale M_GUT ≃ 2.4 × 10¹⁶ GeV and the SUSY-breaking scale M_SUSY ≃ 2.4 TeV required by the Higgs mass and LHC null results. Immediate experimental tests: 4 December 2025: null weight anomaly in magnetically shielded YBCO superconductor

2027–2030: constant ∼5 × 10⁻⁴ rad gravitational phase shift in 100 m atomic interferometers (MAGIS-100, AION) inside perfect magnetic shielding

Main paper: https://doi.org/10.5281/zenodo.17767129

Technical appendix: https://doi.org/10.5281/zenodo.17768167 Keywords: dark matter, supersymmetry, grand unification, vacuum energy, emergent spacetime, atomic interferometry, YBCO, parameter-free predictionLicense: CC-BY 4.0
DOI: 10.15468/dl.wbwnz5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phyllopodopsyllus setouchiensis",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023015-251120083545085/datasets/export for details.
DOI: 10.15468/dl.bmg3eu
title: Occurrence Download

description: A dataset containing 15324 species occurrences available in GBIF matching the query:
{
 "and" : [
 "SpeciesKey is Setophaga ruticilla",
 "HasCoordinate is True",
 "Year is 2004"
 ]
}

 The dataset includes 15324 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023016-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r2q6zf
title: Occurrence Download

description: A dataset containing 457 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Spain",
 "TaxonKey is Abies pinsapo"
 ]
}

 The dataset includes 457 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023017-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/frv8a2
title: PAN-00113060 - coin/coin-related, Filips IV (1295-1303), double tournois

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00113060&lt;/p&gt;
description: Modified: 2025-09-15T14:03:37+02:00
DOI: 10.5281/zenodo.17793777
title: Unified Electromagnetic Theory of Gravity and Dark Matter from a Timeless and Spaceless Ontology

description: TU-GUT-SYSY

Unified Electromagnetic Theory of Gravity and Dark Matter

from a Timeless and Spaceless Ontology
DOI: 10.15468/dl.zndaxf
title: Occurrence Download

description: A dataset containing 3668 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hydrobates markhami"
 ]
}

 The dataset includes 3668 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023018-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.twbmde
title: Occurrence Download

description: A dataset containing 904 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phyllorhiza punctata",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 904 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023023-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uuz3z2
title: Occurrence Download

description: A dataset containing 2964 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((28.37514 43.83669,28.3604 43.81852,28.38275 43.75886,28.48588 43.7456,28.58999 43.76892,28.55266 43.84578,28.43284 43.8556,28.37514 43.83669))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year 1990-2025"
 ]
}

 The dataset includes 2964 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023020-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60520/ieda/113900
title: Sulfur isotope and elemental composition data for 73002 reported in "Endogenous, yet exotic, sulfur in the lunar mantle"

description: This archive includes an in-situ S isotope and elemental composition dataset for individual regolith particles from 73002. The purpose of the work was to evaluate the nature of sulfur among soil collected during Apollo 17 and to use the S isotope compositions to understand the evolution of the moon. The data is linked to a manuscript titled "Endogenous, yet exotic, sulfur in the lunar mantle" that is currently under review in JGR: Planets.
description: Dottin III, J. W., Simon, S. B., Shearer, C. K., Benson, J., Fu, H., Boesenberg, J. S., Monteleone, B., & the ANGSA Science Team. (2025). Endogenous, yet exotic, sulfur in the lunar mantle. Journal of Geophysical Research: Planets, 130(9), Special Collection: ANGSA: A New Lunar Mission to the Taurus-Littrow Valley, e2024JE008834.
DOI: 10.17026/ar/rkinob
title: PAN-00143175 - hairring

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00143175&lt;/p&gt;
description: Modified: 2025-08-29T11:49:18+02:00
DOI: 10.15468/dl.2em7np
title: Occurrence Download

description: A dataset containing 128 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pilumnoides perlatus",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 128 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023026-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17794288
title: Supplementary material and reseach data for "Quantifying Atmospheric Humidity in the Western Mediterranean during the Late Iron Age and the Roman Era" published in Geophysical Research Letters

description: Dataset for the article "Quantifying Atmospheric Humidity in the Western Mediterranean during the Late Iron Age and the Roman Era" published in Geophysical Research Letters, including datables (Tables S1 to S7) and supplementary figures (Figure S1 to S9).
DOI: 10.5281/zenodo.17794287
title: Supplementary material and reseach data for "Quantifying Atmospheric Humidity in the Western Mediterranean during the Late Iron Age and the Roman Era" published in Geophysical Research Letters

description: Dataset for the article "Quantifying Atmospheric Humidity in the Western Mediterranean during the Late Iron Age and the Roman Era" published in Geophysical Research Letters, including datables (Tables S1 to S7) and supplementary figures (Figure S1 to S9).
DOI: 10.15468/dl.aur2am
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Mikania warmingii, Mikania warmingii)"
 ]
}

 The dataset includes 82 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023027-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21227/hhr5-0380
title: "Using 3-D-Printed Structures to Evaluate the Potential Causes of the Color Doppler Twinkling Signature"

description: "Objective: The color Doppler twinkling artifact has been attributed to existing microbubbles or cavitation occurring on rough objects such as kidney stones, some breast biopsy clips, catheter guidewires and sandpaper. The objective was to investigate the correlation between the surface characteristics of helical constructs with different groove geometries and the occurrence of twinkling, as well as to identify locations conducive to bubble retention and\/or cavitation.Methods: Six half-cylinders were created with a microscale 3-D printer with 5 \u00b5m resolution to replicate the geometry of twinkling helical constructs resembling catheter guidewires. Four copies of each marker including a non-twinkling control were printed. The half-cylinders had pitch (peak-to-peak distance) values ranging from 87.5 to 343 \u00b5m and amplitude (groove depth) values ranging from 41.5 to 209 \u00b5m. The half-cylinders were submerged in degassed water and optically imaged before and after ultrasound insonification to visualize bubbles on the cylinders. The cylinders remained submerged while scanning with the color Doppler mode at frequencies from 3.1 to 6.3 MHz using a GE Logiq E9 scanner and 9L linear array transducer.Results: Two markers exhibited twinkling: one with pitch-to-amplitude ratio of 174\/210 \u00b5m\/\u00b5m (0.8) that twinkled only with pre-existing bubbles on the marker; the other had a ratio of 87\/87 \u00b5m\/\u00b5m (1.00) that twinkled without pre-existing bubbles on the marker."
DOI: 10.15468/dl.m9ujfq
title: Occurrence Download

description: A dataset containing 158268 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Investigation Current Status of River in Taiwan between 2002 to 2020"
 ]
}

 The dataset includes 158268 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033161-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ktxkqv
title: Occurrence Download

description: A dataset containing 103441 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((4.575 52.075,4.625 52.075,4.625 52.125,4.575 52.125,4.575 52.075))",
 "DatasetKey is Observation.org, Nature data from around the World",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 103441 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0305068-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b8tkkw
title: Occurrence Download

description: A dataset containing 12016 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Trisetum spicatum (L.) K.Richt."
 ]
}

 The dataset includes 12016 records from 178 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005819-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9pk7n5
title: Occurrence Download

description: A dataset containing 683 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caesalpinia spinosa (Molina) Kuntze"
 ]
}

 The dataset includes 683 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0411578-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p2frqs
title: Occurrence Download

description: A dataset listing the 18 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Betula pendula Roth"
 ]
}

 The dataset's 18 records were derived from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107590-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.px8mda
title: Occurrence Download

description: A dataset containing 1278 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Buxus sinica (Rehder & E.H.Wilson) M.Cheng"
 ]
}

 The dataset includes 1278 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0312558-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7gam39
title: Occurrence Download

description: A dataset containing 11418 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Chile)",
 "TaxonKey is one of (Carnivora)"
 ]
}

 The dataset includes 11418 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0327031-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bnaaxs
title: Occurrence Download

description: A dataset containing 12203 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Centrolenidae"
 ]
}

 The dataset includes 12203 records from 143 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005819-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ohgjwc
title: Occurrence Download

description: A dataset containing 5452 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cedrela odorata L."
 ]
}

 The dataset includes 5452 records from 310 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027435-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wde5qq
title: Occurrence Download

description: A dataset containing 6447 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calyptranthes Sw."
 ]
}

 The dataset includes 6447 records from 256 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0317829-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.asj9uc
title: Occurrence Download

description: A dataset containing 4746 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1859-2018",
 "HasCoordinate is true",
 "TaxonKey is Eubalaena glacialis (Müller, 1776)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4746 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000099-190306134739812/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.