cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18615687
title: DOME Copilot - Data Files (V1)

description: Archive Content: DOME_Copilot_Data_Package.zip

The main data package is organised into the following directories and files:

1. Metadata Index





DOME_Copilot_Data_Package_Metadata.csv: A comprehensive index mapping every PMCID (PubMed Central ID) in the dataset to the directories where its data can be found. Use this to quickly locate resources.



2. Registry & Ground Truth





DOME_Registry_Human_Reviews_258_20260205.json: The core reference dataset containing expert human-reviewed metadata annotations for the DOME Registry papers. 258 entries.



3. Copilot Output (AI Generated)





Copilot_Processed_Datasets_JSON/:




Contains the structured JSON metadata generated by the DOME Copilot pipeline.




Includes processed versions for the Registry Cohort (222 papers) and the Experimental Cohort (1012 papers). 


Note: API reapired metadata files also available.


4. Supplementary Data Material This archive contains the raw supplementary material downloaded from PMC for the study cohorts, which serves as input data for the DOME analysis.





DOME_Registry_PMC_Supplementary/: Main PDF & upplementary files for the 222 articles in the DOME Registry (Source Truth).




Positive_PMC_Supplementary/: Main PDF & Supplementary files for the 1012 "Positive" articles (Machine Learning relevant - Experimental Cohort).




Negative_PMC_Supplementary/: Main PDF & Supplementary files for the 1012 "Negative" articles (Control set / Non-ML).



5. Evaluation Data





30_Evaluation_Source_JSONs_Human_and_Copilot_Including_PDFs/:




The specific source files used for the deep-dive comparative evaluation (Human vs. AI) on a diverse subset of 30 from 222 processed papers.




Contains the Copilot JSONs, Human JSONs, and original PDFs used in the evaluation interface.



Notes





Matching: The DOME_Copilot_Data_Package_Metadata.csv file is the key to linking entries across these folders. Not all papers have supplementary data.




Privacy: User-specific data (profiles, emails) has been excluded.
DOI: 10.5440/1334616
title: Mosaicked Historic Airborne Imagery from Seward Peninsula, Alaska, Starting in the 1950's

description: Historical airborne imagery for each Seward Peninsula NGEE Arctic site - Teller, Kougarok, Council - were obtained with multiple years for each site in order to identify landscape changes over time when compared to more recent imagery. This dataset includes mosaicked, geolocated and, where possible, orthorectified, historic airborne and recent satellite imagery. The older photos were sourced from the USGS Earth Explorer site and the newer, satellite imagery is from the Statewide Digital Mapping Initiative (SDMI) project managed by the Geographic Information Network of Alaska on behalf of the state of Alaska. Check with Jessica Cherry (jessica.cherry@alaska.edu), University of Alaska, and Lisa Wirth (lisa@gina.alaska.edu), Geographic Information Network of Alaska (GINA) and the Statewide Digital Mapping Initiative (SDMI), for citation information and redistribution restrictions of the imagery. Dataset includes the following types of files: *.tif, *.txt, *.pdf, *.jpg, *.xml. Please refer to metadata files included inside the data folders for detailed descriptions of the data products.
The use of historical aerial photographs in combination with more recent satellite imagery has proven effective at detecting and quantifying landscape changes.
The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).
DOI: 10.15468/dl.9bp625
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptodoras marki",
 "DecimalLatitude is not null",
 "DecimalLongitude is not null"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009845-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ah4wn3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Geesinkorchis alaticallosa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009847-260208012135463/datasets/export for details.
DOI: 10.15468/dl.h6ddd5
title: Occurrence Download

description: A dataset containing 2714 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anemopaegma carajasense",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 2714 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009846-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7303/9618239
title: The Religious Orders Study and Memory and Aging Project
DOI: 10.15468/dl.2p9nmb
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptodoras myersi",
 "DecimalLatitude is not null",
 "DecimalLongitude is not null"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009849-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vht6bh
title: Occurrence Download

description: A dataset containing 211 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Genoplesium fimbriatum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 211 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009848-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4g8agy
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Axonopus longispicus",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 70 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009850-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18615678
title: Validation of the HTS Altea-Garay Cryogenic Module: Monte Carlo Robustness Analysis and MTTR Stability Report.

description: This document presents the technical validation of the HTS Altea-Garay Cryogenic Module, a mobile and scalable infrastructure solution for the quantum computing market.

Key technical milestones included in this release:

Monte Carlo Robustness (n=300): Statistical proof of immunity against thermal (\tau) and electronic gain fluctuations, showing near-zero slopes (0.002399 and 0.000117 respectively).

Stability Metrics: Achievement of a final coherence (\gamma^2) of 0.0593 at 45Hz, confirming microKelvin (\mu K) stability.

Industrial Readiness: Validation of the Mean Time To Repair (MTTR) of 4 hours or less through modular MCI architecture.

The data confirms a 'Solid / Invincible' state, outperforming traditional laboratory dilution refrigerators by enabling true industrial mobility and active instability suppression (\nabla B > 0).
DOI: 10.5281/zenodo.18615677
title: Validation of the HTS Altea-Garay Cryogenic Module: Monte Carlo Robustness Analysis and MTTR Stability Report.

description: This document presents the technical validation of the HTS Altea-Garay Cryogenic Module, a mobile and scalable infrastructure solution for the quantum computing market.

Key technical milestones included in this release:

Monte Carlo Robustness (n=300): Statistical proof of immunity against thermal (\tau) and electronic gain fluctuations, showing near-zero slopes (0.002399 and 0.000117 respectively).

Stability Metrics: Achievement of a final coherence (\gamma^2) of 0.0593 at 45Hz, confirming microKelvin (\mu K) stability.

Industrial Readiness: Validation of the Mean Time To Repair (MTTR) of 4 hours or less through modular MCI architecture.

The data confirms a 'Solid / Invincible' state, outperforming traditional laboratory dilution refrigerators by enabling true industrial mobility and active instability suppression (\nabla B > 0).
DOI: 10.15468/dl.7rw7kb
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptodoras oyakawai",
 "DecimalLatitude is not null",
 "DecimalLongitude is not null"
 ]
}

 The dataset includes 32 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009851-260208012135463/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.31320925
title: Wild ancestors of domesticated barley possess traits to reduce nitrogen pollution

description: The sharp increase in fertilizer use over recent decades has led to severe nitrogen (N) pollution, with less than half of the applied N typically absorbed by crops. We conducted a series of mesocosm experiments comparing an elite barley variety and wild ancestors, representing the progenitors of the HEB-25 population, grown under standard and reduced N fertilization. We focused on two key pathways of N pollution: nitrous oxide (N₂O) emissions and nitrate (NO₃⁻) leaching. The scripts and datasets of this study are included in this file.
DOI: 10.6084/m9.figshare.31320925.v1
title: Wild ancestors of domesticated barley possess traits to reduce nitrogen pollution

description: The sharp increase in fertilizer use over recent decades has led to severe nitrogen (N) pollution, with less than half of the applied N typically absorbed by crops. We conducted a series of mesocosm experiments comparing an elite barley variety and wild ancestors, representing the progenitors of the HEB-25 population, grown under standard and reduced N fertilization. We focused on two key pathways of N pollution: nitrous oxide (N₂O) emissions and nitrate (NO₃⁻) leaching. The scripts and datasets of this study are included in this file.
DOI: 10.5440/1114222
title: Plant Root Characteristics and Dynamics in Arctic Tundra Ecosystems, 1960-2012

description: Plant roots play a critical role in ecosystem function in arctic tundra, but root dynamics in these ecosystems are poorly understood. To address this knowledge gap, we synthesized available literature on tundra roots, including their distribution, dynamics, and contribution to ecosystem carbon and nutrient fluxes, and we highlighted key aspects of their representation in terrestrial biosphere models. Across all tundra ecosystems, belowground plant biomass exceeded aboveground biomass, with the exception of polar desert tundra. Roots were shallowly-distributed in the thin layer of soil that thaws annually, and were often found in surface organic soil horizons. Root traits including distribution, chemistry, anatomy, and resource partitioning play an important role in controlling plant species competition, and therefore ecosystem carbon and nutrient fluxes, under changing climatic conditions, but have only been quantified for a small fraction of tundra plants. Further, the annual production and mortality of fine roots are key components of ecosystem processes in tundra, but extant data are sparse. Tundra root traits and dynamics should be the focus of future research efforts. Better representation of the dynamics and characteristics of tundra roots will improve the utility of models for evaluating the responses of tundra ecosystems to changing environmental conditions. Includes a data file in *.csv, and *.xlsx format and a *.pdf.
The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).
DOI: 10.5440/1167159
title: Airborne Imagery Collections, Utqiagvik (Barrow), Alaska, 2013

description: The data here are orthomosaics, digital surface models (DSMs), and individual frames captured during low altitude airborne flights in 2013 at the Barrow Environmental Observatory. The orthomosaics, thermal IR mosaics, and DSMs were generated from the individual frames using Structure from Motion techniques. Data were collected to characterize the optical and thermal properties of the landscape and how they differ between two points in time with different vegetative and hydrologic conditions. The orthomosaic tiles, thermal IR mosaics, and DSMs are geotiffs in NAD 83 UTM Zone 4 named by their lower-left coordinate. Metadata for the raw imagery are contained in the .exif headers in the files for the optical imagery only. XYZ files contain the IR temperatures at various longitudes and latitudes. Supported by the U.S. DOE Arctic NGEE program and the Alaska Climate Science Center. The LiDAR dataset used for accuracy assessment was provided by Cathy Wilson(cjw@lanl.gov) and Chandana Gangodagamage(chandana@lanl.gov). File types included: *.tif; *.png; *.kmz; *.bmp; *.pgw, *xyz, *.jpg.
The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).
DOI: 10.5440/1526749
title: NGEE Arctic CO2, CH4 and Energy Eddy-Covariance (EC) Flux Tower Auxiliary Measurements, Council Road Mile Marker 71, Seward Peninsula, Alaska, 2017 - 2019

description: Measurements began in July 2017 and are made year-round (2017 seasonal only) on the tussock tundra with discontinuous permafrost at the Council Road Site on the Seward Peninsula. CO2, CH4 and energy fluxes using the Eddy Covariance (EC) technique (Baldocchi 2003) and meteorological measurements are reported as 30-minute averages. The tower site is registered with AmeriFlux as US-NGC. See http://ameriflux.lbl.gov/sites/siteinfo/US-NGC for more information. Reported data include: (1) additional/extra meteorological and eddy covariance CO2, CH4 and energy flux data, (2) binned spectra for the three wind components, the sonic temperature and gas densities together with the binned cospectra for covariances of w (vertical wind component) and gas densities, (3) binned ogives (cumulative (co)spectra) for the three wind components, the sonic temperature and gas densities, and (4) tower site footprint matrices. The majority of the files are *.csv with paired visualization footprint files as *.jpg. Meteorological and eddy covariance CO2, CH4 and energy flux data (AmeriFlux BASE data product) are available from AmeriFlux BASE US-NGC NGEE Arctic Council (Torn, 2020) https://doi.org/10.17190/AMF/1634883.
The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) near Utqiagvik (Barrow), Alaska and 2) multiple areas in the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).
DOI: 10.5440/1545603
title: Evaluating Integrated Surface/Subsurface Permafrost Thermal Hydrology Models in ATS (v0.88) Against Observations from a Polygonal Tundra Site: Modeling Archive

description: This Modeling Archive supports the NGEE Arctic publication "Evaluating integrated surface/subsurface permafrost thermal hydrology models in ATS (v0.88) against observations from a polygonal tundra site" available in the Geoscientific Model Development journal.
We evaluated the integrated surface/subsurface permafrost thermal hydrology models in the Advanced Terrestrial Simulator (ATS) against field observations in polygonal tundra at the Barrow Environmental Observatory. We simulated thermal hydrology of three-dimensional ice-wedge polygons with generic but broadly representative surface microtopography. We drove the simulations with meteorological data and observed water table elevations in ice-wedge polygon troughs. With limited calibration of the soil properties and evaporation model parameters, the simulations were found to be consistent with observed water tables, active layer thickness, snowpack depth, evaporation, and observed soil temperatures at several depths in trough, rim, and center. The study builds confidence in the emerging class of integrated surface/subsurface permafrost simulators and provides an optimized set of model parameters for use in projections of permafrost dynamics in a warming climate. This dataset includes python, html, pdf, EXO, H5, xlsx, and csv files.
The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).
DOI: 10.5440/1579361
title: Modeling Present and Future Permafrost Distribution at Seward Peninsula, Alaska: Modeling Archive

description: This dataset contains results from two GIPL runs for RCP4.5 and RCP8.5 across the Seward Peninsula. The model was run on 500 m by 500 m resolution for the period 1901-2100. Meteo variables include forcing air temperature and precipitation as well as modeled maxim and average snow height. This dataset also includes ground temperature at 10 different depths for every grid cell, active layer depth and talik thickness. Auxillary variables include ecotype map and projected latitude and longitude. Ground temperature borehole data that is used for model calibration and validation of GIPL2 for Seward Peninsula 500 m resolution model runs for 1901-2100 time period. Dataset also includes calibrated model parameters for future use. The main purpose of this dataset is the reproducibility of research. Data were produced for regional permafrost distribution assessment for present and future, in addition, model parameters can be used for future model runs on adjacent territories. This dataset contains *.pdf, *.txt, *.csv, and *.nc. files. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).