SEARCH · Engineering Papers

Results for “data repository”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 469 records · Page 26

All sources NASA NTRS DOE OSTI

DOE OSTI2022

Implementation of FAIR principles in the IPCC: the WGI AR6 Atlas repository

The Sixth Assessment Report (AR6) of the Intergovernmental Panel on Climate Change (IPCC) has adopted the FAIR Guiding Principles. We present the Atlas chapter of Working Group I (WGI) as a test case. We describe the application of the FAIR principles in the Atlas, the challenges faced during its implementation, and those that remain for the future. We introduce the open source repository resulting from this process, including coding (e.g., annotated Jupyter notebooks), data provenance, and some aggregated datasets used in some figures in the Atlas chapter and its interactive companion (the Interactive Atlas), open to scrutiny by the scientific community and the general public. We describe the informal pilot review conducted on this repository to gather recommendations that led to significant improvements. Finally, a working example illustrates the re-use of the repository resources to produce customized regional information, extending the Interactive Atlas products and running the code interactively in a web browser using Jupyter notebooks.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis

Abstract Background Many organizations face challenges in managing and analyzing data, especially when relevant datasets arise from multiple sources and methods. Analyzing heterogeneous datasets and additional derived data requires rigorous tracking of their interrelationships and provenance. This task has long been a Grand Challenge of data science and has more recently been formalized in the FAIR principles: that all data objects be Findable, Accessible, Interoperable, and Reusable, both for machines and for people. Adherence to these principles is necessary for proper stewardship of information, for testing regulatory compliance, for measuring the efficiency of processes, and for facilitating reuse of data-analytical frameworks. Findings We present the Contextual Ontology-based Repository Analysis Library (CORAL), a platform that greatly facilitates adherence to all 4 of the FAIR principles, including the especially difficult challenge of making heterogeneous datasets Interoperable and Reusable across all parts of a large, long-lasting organization. To achieve this, CORAL's data model requires that data generators extensively document the context for all data, and our tools maintain that context throughout the entire analysis pipeline. CORAL also features a web interface for data generators to upload and explore data, as well as a Jupyter notebook interface for data analysts, both backed by a common API. Conclusions CORAL enables organizations to build FAIR data types on the fly as they are needed, avoiding the expense of bespoke data modeling. CORAL provides a uniquely powerful platform to enable integrative cross-dataset analyses, generating deeper insights than are possible using traditional analysis tools.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

A customizable data management framework for high-repetition-rate high-energy-density science

The high-energy-density (HED) physics community is moving toward a new paradigm of high-repetition-rate (HRR) operation. To fully leverage the scientific power of HRR HED facilities, all of the components of each subsystem (laser, targetry, and performance diagnostics) must be connected and synchronized in a reliable and robust manner while the data acquired are tagged and archived in real time. To this end, GA has begun developing a generalized NoSQL-database framework, the MongoDB repository for information and archiving. An organizational strategy has been developed that shifts HED data organization from a shot-based to a diagnostic-based approach in order to increase archival and retrieval efficiency that lends itself to optimization applications. This work is a first step in pushing HRR HED science toward data management solutions that emphasize machine actionability and aim to stimulate community engagement to define data standards in HED science.

Instruments & Instrumentation↗

DOE OSTI2023

Verification Testing of OLI Systems Mixed Solvent Electrolyte Model for the Na-K-Mg-Ca-H-Cl-SO 4 -OH-HCO 3 -CO 3 -CO 2 -H 2 ) System to High Ionic Strength at 25°C

This technical report summarizes model verification results and summary statistics for 41 evaporite mineral solubility cases evaluated by Savannah River National Laboratory using OLI Systems’ aqueous electrolyte thermodynamic modeling software. The 41 verification cases containing a total of 60 solubility curves comprise mineral solubility data from low to high ionic strength at 25°C for the eight-component system Na-K-Mg-Ca-H-Cl-SO 4 -OH-HCO 3 -CO 3 -CO 2 -H 2 O as reported by Harvie et al. (1984). Thermodynamic calculations were executed using OLI Systems’ Stream Analyzer computation module within the OLI Studio software platform (Ver. 11.0, Rev. 11.0.1.9). The Mixed Solvent Electrolyte (MSE) thermodynamic framework was chosen for this investigation because of its superiority in modeling high ionic-strength inorganic salt solutions and actinide redox chemistry and solubility, both of which are relevant to the geological repository conditions at the Waste Isolation Pilot Plant in Carlsbad, New Mexico. Mineral solubility data in various inorganic salt solutions were digitized and extracted from figures generated by Harvie et al. (1984). For each of the 60 solubility curves, a case-specific chemistry model and input file were generated in OLI Studio using OLI Stream Analyzer and the MSE (H 3 O + ion) public databank provided by OLI Systems. Model simulation results were exported to Microsoft Excel to calculate summary statistics and to generate graphs comparing the OLI model predictions to the solubility data. Summary statistics include residuals (model – data) and concordance (accuracy × precision, where precision is indicated by the Pearson correlation coefficient and accuracy accounts for bias and scale differential). Private databanks were not developed, and activity coefficient model regressions were not performed to improve OLI model fits to the data. Of the 41 model verification plots, 83% have a mean of the percent residuals less than or equal to 25%. Similarly, 75% display a concordance greater than or equal to 0.75. Only seven of the 41 verification plots fail to show good agreement between the model and data. Of these seven, three are relevant to the WIPP repository because they involve the Mg-OH-Cl-SO 4 -CO 3 aqueous system. The remaining four address salt solubilities at the pH extremes (strong acid and strong base). It should be noted that in two of the three Mg-OH-Cl-SO 4 -CO 3 system cases, the regressed Harvie et al. (1984) solubility curve also deviated from the data. Lack of agreement between the OLI model-predicted solubility curves and the data is attributable to one or more of the following: specific solid species are not included in the OLI MSE databank; there is significant variation among the different solubility datasets chosen by Harvie et al. (1984); the OLI MSE model’s thermodynamic parameters were determined using different solubility datasets; and the activity coefficient parameters for certain relevant ion-ion and ion-molecule pairs have not been optimized via data regression. Two recommendations for future work are to (1) evaluate solubility data for the Mg-OH-Cl-SO 4 -CO 3 system at high ionic strength and, if necessary, develop a private OLI MSE database that includes missing species and, where necessary, regressed standard state properties and interaction parameters; (2) perform similar verification testing of the OLI model for actinide solubility data.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis -regulatory elements

Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

SCALE 6.2.4 Validation for Light Water Reactor Decay Heat Analysis

Energy release from the decay of radionuclides in nuclear fuel after its discharge from reactor is a critical parameter for design, safety, and licensing analyses of used nuclear fuel storage, transportation, and repository systems. Well-validated computational tools and nuclear data are essential for decay heat prediction. This paper summarizes the validation of the SCALE nuclear analysis code system version 6.2.4, used with ENDF/B-VII.1 libraries, for decay heat analysis of light water reactor used fuel. The experimental data used for validation include full-assembly decay heat measurements that cover assembly burnups of 5 to 51 GWd/tonne U, cooling times after discharge in the 2- to 27-year range, and initial fuel enrichments up to 4 wt% 235U. The comparison between calculated (C) and experimental (E) decay heat showed very good agreement, with an average C/E over all considered measurements of 1.006 (σ = 0.016) for pressurized water reactor and 0.984 (σ = 0.077) for boiling water reactor assembly measurements. The effect of using assembly-average versus axially varying modeling data on the calculated decay heat, important to thermal analyses for used fuel transportation and storage systems, is discussed.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2025

PNNL-CompBio/srpAnalytics

This repository contains the code necessary to process any new data for the Superfund Research Program Analytics Portal.

Gosline, Sara JC [Pacific Northwest National Labor↗

DOE OSTI2026

SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences

Background Synthetic biology involves combining different DNA fragments, each containing functional biological parts, to address specific problems. Fundamental gene-function research often requires cloning and propagating DNA fragments, such as those from the iGEM Parts Registry or Addgene, typically distributed as circular plasmids. Addgene’s repository alone offers around 150,000 plasmids. To ensure data integrity, cryptographic checksums can be calculated for the sequences. Each sequence has a unique checksum, making checksums useful for validation and quick lookups of associated annotations. For example, the SEGUID checksum uniquely identifies protein sequences with a 27-character string. Objectives The original SEGUID, while effective for protein sequences and single-stranded DNA (ssDNA), is not suitable for circular DNA since there is no natural starting position nor for double-stranded DNA (dsDNA) since two separate sequences are present. Challenges include how to uniquely represent linear dsDNA, circular ssDNA, and circular dsDNA. To meet these needs, we propose SEGUID v2, which extends the original SEGUID to handle additional types of sequences. Conclusions SEGUID v2 produces orientation and rotation invariant checksums for single-stranded, double-stranded, possibly staggered, linear, and circular DNA and RNA sequences. Customizable alphabets allow for other types of sequences. In contrast to the original SEGUID, which uses Base64, SEGUID v2 uses Base64url to encode the SHA-1 hash. This ensures SEGUID v2 checksums can be used as-is in filenames, regardless of platform, and in URLs, with minimal friction. Availability SEGUID v2 is readily available for major programming languages, distributed under the MIT license. JavaScript package seguid is available on npm, Python package seguid on PyPi, R package seguid on CRAN, and a Tcl script on GitHub. These tools, along with documentation, examples, and an online SEGUID Calculator , can be found at https://www.seguid.org .

Pereira, Humberto↗

DOE OSTI2021

Subsurface Characterization and Machine Learning Predictions at Brady Hot Springs Results

Geothermal power plants typically show decreasing heat and power production rates over time. Mitigation strategies include optimizing the management of existing wells - increasing or decreasing the fluid flow rates across the wells - and drilling new wells at appropriate locations. The latter is expensive, time-consuming, and subject to many engineering constraints, but the former is a viable mechanism for periodic adjustment of the available fluid allocations. Data and supporting literature from a study describing a new approach combining reservoir modeling and machine learning to produce models that enable strategies for the mitigation of decreased heat and power production rates over time for geothermal power plants. The computational approach used enables translation of sets of potential flow rates for the active wells into reservoir-wide estimates of produced energy and discovery of optimal flow allocations among the studied sets. In our computational experiments, we utilize collections of simulations for a specific reservoir (which capture subsurface characterization and realize history matching) along with machine learning models that predict temperature and pressure timeseries for production wells. We evaluate this approach using an "open-source" reservoir we have constructed that captures many of the characteristics of Brady Hot Springs, a commercially operational geothermal field in Nevada, USA. Selected results from a reservoir model of Brady Hot Springs itself are presented to show successful application to an existing system. In both cases, energy predictions prove to be highly accurate: all observed prediction errors do not exceed 3.68% for temperatures and 4.75% for pressures. In a cumulative energy estimation, we observe prediction errors that are less than 4.04%. A typical reservoir simulation for Brady Hot Springs completes in approximately 4 hours, whereas our machine learning models yield accurate 20-year predictions for temperatures, pressures, and produced energy in 0.9 seconds. This paper aims to demonstrate how the models and techniques from our study can be applied to achieve rapid exploration of controlled parameters and optimization of other geothermal reservoirs. Includes a synthetic, yet realistic, model of a geothermal reservoir, referred to as open-source reservoir (OSR). OSR is a 10-well (4 injection wells and 6 production wells) system that resembles Brady Hot Springs (a commercially operational geothermal field in Nevada, USA) at a high level but has a number of sufficiently modified characteristics (which renders any possible similarity between specific characteristics like temperatures and pressures as purely random). We study OSR through CMG simulations with a wide range of flow allocation scenarios. Includes a dataset with 101 simulated scenarios that cover the period of time between 2020 and 2040 and a link to the published paper about this project, where we focus on the Machine Learning work for predicting OSR's energy production based on the simulation data, as well as a link to the GitHub repository where we have published the code we have developed (please refer to the repository's readme file to see instructions on how to run the code). Additional links are included to associated work led by the USGS to identify geologic factors associated with well productivity in geothermal fields. Below are the high-level steps for applying the same modeling + ML process to other geothermal reservoirs: 1. Develop a geologic model of the geothermal field. The location of faults, upflow zones, aquifers, etc. need to be accounted for as accurately as possible 2. The geologic model needs to be converted to a reservoir model that can be used in a reservoir simulator, such as, for instance, CMG STARS, TETRAD, or FALCON 3. Using native state modeling, the initial temperature and pressure distributions are evaluated, and they become the initial conditions for dynamic reservoir simulations 4....

15 GEOTHERMAL ENERGY↗

DOE OSTI2025

Dataset: "Widespread Drought-driven Declines in Streamflows and Water quality in the Upper Colorado River Basin (1998-2022)"

This data package contains the associated data and scripts for Nagamoto, E., Ombadi, M., Ciulla, F. et al. Widespread drought-driven declines in streamflows and water quality in the Upper Colorado River Basin during 1998-2022. Commun Earth Environ 7, 734 (2026). https://doi.org/10.1038/s43247-026-03890-5. This purpose of this study was to investigate the impact of the 21st century drought on water quantity and quality at catchments throughout the Upper Colorado River Basin (UCRB). We used stream flow, water temperature, specific conductance, air temperature, precipitation, and catchment attribute data for over 200 sites in the UCRB, collected from the National Water Information System using Basin3D (Varadharajan, 2023), GAGESII (Falcone, 2010), and the Google Earth Engine. We identified years of severe drought between 1998 and 2022 using the Standardized Precipitation Evaporation Index (SPEI), then calculated the relative change percentage of the stream flow, water temperature, and specific conductance from drought versus non-drought years. We used the attribute information from GAGESII to investigate what physical traits of catchments are associated streamflow vulnerability (greater relative change) or resilience to drought. We used land cover data from the National Land Cover Database (USGS, 2024) to assess any changes to physical attributes that may not be represented in the static attributes information in GAGESII. To increase data availability, we modeled stream temperature using methods from Willard, 2023. While the study period is water years 1998 to 2022, the raw water quantity and quality data extends to 1950 and the meteorological data extends to 1980. The data and code can be downloaded via the UCRB_drought.zip. Within the zip, the files are organized as follows: - INPUTS: Contains all input data used in UCRB_Drought_Workflow.ipynb - OUTPUTS: Contains all intermediate data created from UCRB_Drought_Workflow.ipynb as well as final products including the calculated Standardized Evapotranspiration Index (SPEI) - climatic_variables: The code used to collect meteorologic data from Google Earth Engine - feature_importance: The code used for the catchment attributes analysis - preprocessing: Code used in UCRB_Drought_Workflow_Preprocessing.ipynb - pyeto: Code used in UCRB_Drought_Workflow_Preprocessing.ipynb - calculations: Code used in UCRB_Drought_Workflow_Impacts.ipynb - plotting: Code used in UCRB_Drought_Workflow_Impacts.ipynb - README.md - UCRB_Drought_Workflow_Preprocessing.ipynb: The code used to prep raw data for the analysis - UCRB_Drought_Workflow_Impact.ipynb: The code which uses the prepped raw data for analysis, and plots all figures - requirements_ucrb-drought_v2.yml: The requirements file to create a virtual environment and Jupyter Lab kernel to run the code The INPUTS folder is organized into the following major directories and sub-directories. The "RDC_WT_SC_RAW" folder contains raw data for streamflow, water temperature, and specific conductance in a ".h5" file. The "NLCD_RAW" folder contains ".csv" files with annual land cover percentages for counties within the UCRB. The "MET_RAW" folder contains a ".csv" file with monthly meteorological data (air temperature and precipitation) for the sites in the UCRB which was obtained from code in the climatic_variables folder. The "GAGESII" folder contains ".csv" files with physical catchment attribute variables for catchments across the country. The "WT_LSTM_data" folder contains ".csv" files with calculated WT (Willard, 2023) and the associated RMSEs. The "Upper_Colorado_River_Basin_Boundary" folder contains geographic data including a shapefile for plotting in the UCRB_Drought_Workflow.ipynb. The "RESERVOIRS_RAW" folder contains ".csv" files for each reservoir in the UCRB with daily reservoir storage. There are also two files in the INPUTS folder that have combined reservoir storage data and reservoir metadata. The OUTPUTS folder is organized into the following major directories and sub-directories. The "RDC_WT_SC_data" folder contains a folder "Water_year" with the associated cleaned data, metadata, and data availability information in ".csv" files, a folder "Median_Relchange" with the relative change comparing drought to non-drought years in ".csv" files, and a folder "Peak95_Min5_Relchange" that has ".csv" files for the relative change in peak (95th %) and minimum (5th %) variables. The "NLCD_data" folder contains the difference in land cover from the beginning to end of the study period and the percentage of the county that is within UCRB bounds can be found in Nagamoto et al (2025)). The "MET_data" folder contains separated monthly air temperature and precipitation data and the calculated PET in ".csv" files. The "SPEI_data" folder contains ".csv" files with calculated SPEI values (one restricted to the study period and the other with information from the entire MET data period). The "Paper_Tables" folder contains two ".csv" files containing site information and data availability and information about the GAGESII trait aggregated categories. The base directory includes the file “flmd.csv” for a list and description of all files and the file “dd.csv” for data dictionaries. Scripts for preprocessing, analysis, and figure generation are located in the associated GitHub repository found at [https://github.com/iNAIADS/drought-impacts/tree/develop/UCRB-drought]. UPDATE 1: Title and code file updated to match submitted manuscript 10-15-2025. UPDATE 2: Code and data files updated to match revised manuscript 3-4-2026. UPDATE 3: Code and data files updated to match revised manuscript 6-7-2026. ** NOTE: DD and FLMD have not been updated yet. UPDATE 4: Added associated Manuscript information and DD and FLMD have been updated. To cite this code, please use the following BibTeX: @misc{nagamoto2025drought, author = {Emily Nagamoto and Fabio Ciulla and Mohammad Ombadi and Jared Willard and Rosemary Carroll and Charuleka Varadharajan}, title = {Dataset: "Widespread Drought-driven Declines in Streamflows and Water quality in the Upper Colorado River Basin (1998-2022)"}, year = {2025}, doi = {10.15485/2551894}, publisher = {ESS-DIVE Repository}, url = {https://data.ess-dive.lbl.gov/datasets/doi:10.15485/2551894} }

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

CSD 2078665: Experimental Crystal Structure Determination

An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Cell Parameters↗

DOE OSTI2024

CSD 2312746: Experimental Crystal Structure Determination

Cell Parameters↗

DOE OSTI2024

CSD 2374310: Experimental Crystal Structure Determination

Cell Parameters↗

DOE OSTI2023

NSRDB (National Solar Radiation Database Software) [SWR-23-77]

This repository contains all of the methods for the NSRDB data processing pipeline. The NSRDB is a serially complete collection of hourly and half-hourly values of meteorological data and the three most common measurements of solar radiation: global horizontal, direct normal and diffuse horizontal irradiance.

Benton, Brandon↗

DOE OSTI2025

Neural Network Analysis of Nuclear Magnetic Resonance and Infrared Spectra

Nuclear magnetic resonance (NMR) spectroscopy and infrared (IR) spectroscopy are powerful chemical characterization techniques with broad general usage. However, the manual evaluation of the resulting spectra is time-consuming and requires significant expertise, preventing insights from being used in real-time applications. With recent advances in computation and artificial intelligence (AI), new tools are available for automating spectral interpretation. In this work, machine learning (ML) algorithms using 1-dimensional convolutional neural networks (CNNs) were applied to identify common functional groups from spectral information. Raw spectra were collected virtually from the Human Metabolome Database (HMDB) and National Institute of Standards and Technology (NIST) Chemistry WebBook and processed into a suitable standard. Algorithm design was tailored to best fit the nature of the problem, with built-in flexibility to accommodate relevant parameters beyond the raw spectral input, specifically solvent identity and magnetic frequency for NMR. The predictive capability of the algorithm in identifying functional groups is displayed in several examples. This methodology has been compiled into a code repository and could easily be modified to adapt alternative data sources, including other spectrum types. To mitigate overfitting, a common problem in mathematical modeling where overfamiliarity with training data produces trends that are not representative of the general data, a novel metric was developed, referred to as Accufit. Accufit includes a parameter that penalizes substantial differences in the training accuracy and the accuracy of an independent validation set. Examples are presented showing the effectiveness of Accufit in maintaining the model’s predictive capability while controlling the overfitting when used as a custom metric for hyperparameter tuning.

Sturgill, James↗

DOE OSTI2023

The Importance of Sharing Data in Systems Biology

Systems biology research spans a range of biological scales and science domains, and often requires a collaborative effort to collect and share data so that integration is possible. However, sharing data effectively is a challenging task that requires effort and alignment between collaborative partners, as well as coordination between organizations, repositories, and journals. As a community of systems biology researchers, we must get better at efficiently sharing data, and ensuring that shared data comes with the recognition and citations it deserves.

Wood-Charlson, Elisha M. (ORCID:0000000195577715)↗

DOE OSTI2023

Field surveying data of low-cost networked flood sensors in southeast Texas

Floods are common natural disasters worldwide and pose substantial risks to life, property, food production, and natural resources. Effective measures for flood mitigation and warning are essential. Southeast Texas is still at significant risk of flooding, and Lamar University is assisting the region with asset management of a flood sensor network for flooding events. This network provides real-time water stage information. Lamar University developed a survey program to measure elevation and coordinates at each sensor site location to make this data more useful for flood monitoring and mapping. This paper overviews the measurement of the elevation and coordinates of 74 networked flood sensors and various flood stage thresholds at critical points that flood decision-makers can use for reference at each site. In the first phase of this program, these sensors were deployed throughout a 7-county region spanning nearly 6,000 square miles in Southeast Texas. The latitude and longitude of the sensors and their elevations were determined using survey-grade Global Navigation Satellite System (GNSS) technology. Various Continually Operating Reference Stations (CORS) were utilized for post-processing to achieve sub-inch resolution. The flood stage thresholds, water level sensors elevation, and the elevations and positions of other critical surrounding points are viewable to the public through two online repositories and a web-based sensor management dashboard. The data is used to aid with decisions related to road closures or modeling efforts by mitigation decision-makers, emergency managers, and the public, including the Texas Department of Transportation, Houston Transtar, the National Weather Service, and the Sabine River Authority of Texas (SRA).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

MINE 2.0: enhanced biochemical coverage for peak identification in untargeted metabolomics

Abstract Summary Although advances in untargeted metabolomics have made it possible to gather data on thousands of cellular metabolites in parallel, identification of novel metabolites from these datasets remains challenging. To address this need, Metabolic in silico Network Expansions (MINEs) were developed. A MINE is an expansion of known biochemistry which can be used as a list of potential structures for unannotated metabolomics peaks. Here, we present MINE 2.0, which utilizes a new set of biochemical transformation rules that covers 93% of MetaCyc reactions (compared to 25% in MINE 1.0). This results in a 17-fold increase in database size and a 40% increase in MINE database compounds matching unannotated peaks from an untargeted metabolomics dataset. MINE 2.0 is thus a significant improvement to this community resource. Availability and implementation The MINE 2.0 website can be accessed at https://minedatabase.ci.northwestern.edu. The MINE 2.0 web API documentation can be accessed at https://mine-api.readthedocs.io/en/latest/. The data and code underlying this article are available in the MINE-2.0-Paper repository at https://github.com/tyo-nu/MINE-2.0-Paper. MINE 2.0 source code can be accessed at https://github.com/tyo-nu/MINE-Database (MINE construction), https://github.com/tyo-nu/MINE-Server (backend web API) and https://github.com/tyo-nu/MINE-app (web app). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗