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At least 163 records · Page 9

LungMAP Portal Ecosystem: Systems-level Exploration of the Lung

An improved understanding of the human lung necessitates advanced systems models informed by an ever-increasing repertoire of molecular omics, cellular, imaging, and pathological datasets. To centralize and standardize information across broad lung research efforts we expanded the LungMAP.net website into a new gateway portal. This portal connects a broad spectrum of research networks, bulk and single-cell multi-omics data and a diverse collection of image data that span mammalian lung development, and disease. The data are standardized across species and technologies using harmonized data and metadata models that leverage recent advances including those from the Human Cell Atlas, diverse ontologies, and the LungMAP CellCards initiative. To cultivate future discoveries, we have aggregated a diverse collection of single-cell atlases for multiple species (human, rhesus, mouse), to enable consistent queries across technologies, cohorts, age, disease, and drug treatment. These atlases are provided as independent and integrated queryable datasets, with an emphasis on dynamic visualization, figure generation, re-analysis, cell-type curation, and automated reference-based classification of user-provided single-cell genomics datasets (Azimuth). Finally, as this resource grows, we intend to increase the breadth of available interactive interfaces, supported data types, data portals and datasets from LungMAP and external research efforts.

59 BASIC BIOLOGICAL SCIENCES↗

Challenges in predicting protein-protein interactions of understudied viruses: Arenavirus-human interactions

Understanding protein-protein interactions (PPIs) between viruses and host organisms is crucial for uncovering infection mechanisms and identifying potential therapeutic targets. The ability to generalize PPI predictive models across understudied viruses presents a significant challenge. In this work, we use arenavirus-human PPIs to illustrate the difficulties associated with model generalization, which are compounded by a lack of both positive and negative data. We employ a Transfer Learning approach to investigate arenavirus-human PPIs by utilizing models trained on better-studied virus-human and human-human PPIs. Additionally, we curate and assess four types of negative sampling datasets to evaluate their impact on model performance. Despite the overall high accuracies (93–99 %) and AUPRC scores (0.8–0.9) appearing promising, further analysis indicates that these performance metrics can be misleading due to data leakage, data bias, and overfitting, especially concerning under-represented viral proteins. We reveal these gaps and assess the impact of data imbalance using standard k-fold cross-validation and Independent Blind Testing with a Balanced Dataset, resulting in a drop in accuracy below 50 %. We propose a viral protein-specific evaluation framework that categorizes viral proteins into majority and minority classes based on their representation in the dataset, enabling comparison of model performance across these groups using balanced accuracies. This framework offers a more robust evaluation of model generalizability, addressing biases inherent in standard evaluation techniques and paving the way for more reliable PPI prediction models for understudied viruses.

59 BASIC BIOLOGICAL SCIENCES↗

Livewire: A Model Platform for Data Quality Assessment and AI Readiness Across DOE Missions

High-quality, well-governed data is essential for accelerating discovery and achieving operational excellence across DOE and national laboratory missions. The Livewire Data Platform is a DOE-supported platform that offers automated assessments of data quality, standardization, provenance, and Artificial Intelligence (AI) readiness. It allows researchers and data practitioners to systematically and easily evaluate datasets against established governance criteria and prepare them for advanced analytics. Livewire addresses critical challenges in DOE's data ecosystem with integrated capabilities for metadata validation, provenance tracking, and schema alignment. This platform's automated workflows assist users in identifying data quality gaps, enhancing interoperability between datasets collected from various stakeholders, and ensuring compliance with DOE data standards, all while reducing manual curation efforts. Additionally, we will discuss its AI readiness framework, which is being developed to prepare datasets for training models, developing advanced analytic tools, and machine learning applications. Using some of the more than one hundred tabular datasets on Livewire, processed with this open-source methodology, we will demonstrate how Livewire can serve as a model for scalable, standards-driven data management. This approach provides a pathway to leverage existing and future datasets within the DOE, boosting innovation and efficiency across national laboratories.

33 - ADVANCED PROPULSION SYSTEMS↗

VA Determinants of Health Data Curation Documentation FY25-Q2

The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources. With funding from the VA Office of Mental Health and Suicide Prevention (OMHSP), the Determinants of Health (EDH) project has developed innovative datasets associated with specific health outcomes, a methodology for transforming spatiotemporal data from one spatial reference (e.g., a 1km grid) to another (e.g., US Census Tracts), and capabilities for modeling health outcomes. These datasets represent an enhancement of the Agency for Healthcare Research and Quality (AHRQ), addressing key gaps by introducing finer spatial resolution (Census Tract) and additional geographical covariates into existing data. The curation and standardization of these datasets is a complex task since they often originate from various sources and are measured at different spatial and temporal resolutions. For example, US Census data products typically use census blocks, block groups, or counties, while data like weather data are available on 1km grids. Some economic data may only be available at the zip code level. In this context, ‘standardized’ means that all datasets share the same spatial extent (e.g., US Census Tract and/or County), and ‘curated’ implies a repeatable process with data provenance and the use of appropriate methodologies for covariate conversion. The Determinants of Health datasets draw from multiple sources, resulting in variables with varying degrees of availability, patterns of missing data, and methodological considerations across different sources, geographies, and years.

97 MATHEMATICS AND COMPUTING↗

VA Determinants of Health Data Curation Documentation FY25-Q3

The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources. With funding from the VA Office of Mental Health and Suicide Prevention (OMHSP), the Determinants of Health (EDH) project has developed innovative datasets associated with specific health outcomes, a methodology for transforming spatiotemporal data from one spatial reference (e.g., a 1km grid) to another (e.g., US Census Tracts), and capabilities for modeling health outcomes. These datasets represent an enhancement of the Agency for Healthcare Research and Quality (AHRQ), addressing key gaps by introducing finer spatial resolution (Census Tract) and additional geographical covariates into existing data. The curation and standardization of these datasets is a complex task since they often originate from various sources and are measured at different spatial and temporal resolutions. For example, US Census data products typically use census blocks, block groups, or counties, while data like weather data are available on 1km grids. Some economic data may only be available at the zip code level. In this context, ‘standardized’ means that all datasets share the same spatial extent (e.g., US Census Tract and/or County), and ‘curated’ implies a repeatable process with data provenance and the use of appropriate methodologies for covariate conversion. The Determinants of Health datasets draw from multiple sources, resulting in variables with varying degrees of availability, patterns of missing data, and methodological considerations across different sources, geographies, and years.

97 MATHEMATICS AND COMPUTING↗

VA Community Determinants of Health Data Curation Documentation FY25-Q4

The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources. With funding from the VA Office of Mental Health and Suicide Prevention (OMHSP), the Determinants of Health (EDH) project has developed innovative datasets associated with specific health outcomes, a methodology for transforming spatiotemporal data from one spatial reference (e.g., a 1km grid) to another (e.g., US Census Tracts), and capabilities for modeling health outcomes. These datasets represent an enhancement of the Agency for Healthcare Research and Quality (AHRQ), addressing key gaps by introducing finer spatial resolution (Census Tract) and additional geographical covariates into existing data. The curation and standardization of these datasets is a complex task since they often originate from various sources and are measured at different spatial and temporal resolutions. For example, US Census data products typically use census blocks, block groups, or counties, while data like weather data are available on 1km grids. Some economic data may only be available at the zip code level. In this context, standardized’ means that all datasets share the same spatial extent (e.g., US Census Tract and/or County), and ‘curated’ implies a repeatable process with data provenance and the use of appropriate methodologies for covariate conversion. The Determinants of Health datasets draw from multiple sources, resulting in variables with varying degrees of availability, patterns of missing data, and methodological considerations across different sources, geographies, and years.

97 MATHEMATICS AND COMPUTING↗

Graph Generation with a Focusing Lexicon

Reference datasets are an essential part of developing effective data exploration tools. Many reference datasets are synthetic in nature, seeding real-world properties into generation routines. Others are laboriously curated from original source materials. This is a time-consuming process that requires significant domain expertise all along the process. This paper presents a third path: deriving a network from real-world source materials using automated tools. By properly grounding the tools in a small collection of curated documents, a larger corpus be automatically processed with greater confidence. The end system leverages human knowledge (in the initial document curation), but with much less time commitment enabled by automation. Our ultimate goal is to produce reference datasets, derived from real-world data that capture aspects salient to a specific activity in the context of all of the activities in the data-set. Our reference datasets take the form of graphs.

Chandra Shekar, Mayanka↗

VA Community Determinants of Health Data Curation Documentation FY26-Q1

The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources. With funding from the VA Office of Mental Health and Suicide Prevention (OMHSP), the Community Determinants of Health (EDH) Data project has developed innovative datasets associated with specific health outcomes, a methodology for transforming spatiotemporal data from one spatial reference (e.g., a 1km grid) to another (e.g., US Census Tracts), and capabilities for modeling health outcomes. These datasets represent an enhancement of the Agency for Healthcare Research and Quality (AHRQ), addressing key gaps by introducing finer spatial resolution (Census Tract) and additional geographical covariates into existing data. The curation and standardization of these datasets is a complex task since they often originate from various sources and are measured at different spatial and temporal resolutions. For example, US Census data products typically use census blocks, block groups, or counties, while data like weather data are available on 1km grids. Some economic data may only be available at the zip code level. In this context, ‘standardized’ means that all datasets share the same spatial extent (e.g., US Census Tract and/or County), and ‘curated’ implies a repeatable process with data provenance and the use of appropriate methodologies for covariate conversion. The Community Determinants of Health datasets draw from multiple sources, resulting in variables with varying degrees of availability, patterns of missing data, and methodological considerations across different sources, geographies, and years.

99 GENERAL AND MISCELLANEOUS↗

VA Community Determinants of Health Data Curation Documentation FY26-Q2

The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources. With funding from the VA Office of Mental Health and Suicide Prevention (OMHSP), the Community Determinants of Health (EDH) Data project has developed innovative datasets associated with specific health outcomes, a methodology for transforming spatiotemporal data from one spatial reference (e.g., a 1 km grid) to another (e.g., U.S. Census Tracts), and capabilities for modeling health outcomes. These datasets represent an enhancement of the Agency for Healthcare Research and Quality (AHRQ), addressing key gaps by introducing finer spatial resolution (Census Tract) and additional geographical covariates into existing data. The curation and standardization of these datasets is a complex task since they often originate from various sources and are measured at different spatial and temporal resolutions. For example, U.S. Census data products typically use census blocks, block groups, or counties, while data like weather data are available on 1 km grids. Some economic data may only be available at the ZIP code level. In this context, ‘standardized’ means that all datasets share the same spatial extent (e.g., U.S. Census Tract and/or County), and ‘curated’ implies a repeatable process with data provenance and the use of appropriate methodologies for covariate conversion. The Community Determinants of Health datasets draw from multiple sources, resulting in variables with varying degrees of availability, patterns of missing data, and methodological considerations across different sources, geographies, and years.

99 GENERAL AND MISCELLANEOUS↗

The impact of curation errors in the PDBBind Database on machine learning predictions of protein–protein binding affinity

The PDBBind database has been widely utilized for the computational prediction of protein–protein binding affinities. While the accuracy of the PDBBind-curated equilibrium dissociation constants (K D ) has been reported for the protein–ligand subset of the PDBBind database, the curation accuracy has not been reported for the protein–protein subset. Here, we present a detailed manual analysis for the subset of PDBBind records with PubMed Central Open Access primary publications and find that ~19% of these records had K D values that were not supported by their primary publications. The impact of these putative curation errors on the machine learning-based prediction of K D from experimental protein–protein 3D structures was evaluated and correcting the curation errors improved the Pearson correlation coefficient between measured and random forest-predicted log 10 (K D ) values by ~8 percentage points. This finding underscores the importance of dataset accuracy for computational modelling and highlights the need for more stringent curation processes when extracting information from the scientific literature.

59 BASIC BIOLOGICAL SCIENCES↗

Question-answering system extracts information on injection drug use from clinical notes

Background. Injection drug use (IDU) can increase mortality and morbidity. Therefore, identifying IDU early and initiating harm reduction interventions can benefit individuals at risk. However, extracting IDU behaviors from patients’ electronic health records (EHR) is difficult because there is no other structured data available, such as International Classification of Disease (ICD) codes, and IDU is most often documented in unstructured free-text clinical notes. Although natural language processing can efficiently extract this information from unstructured data, there are no validated tools. Methods. Here, to address this gap in clinical information, we design a question-answering (QA) framework to extract information on IDU from clinical notes for use in clinical operations. Our framework involves two main steps: (1) generating a gold-standard QA dataset and (2) developing and testing the QA model. We use 2323 clinical notes of 1145 patients curated from the US Department of Veterans Affairs (VA) Corporate Data Warehouse to construct the gold-standard dataset for developing and evaluating the QA model. We also demonstrate the QA model’s ability to extract IDU-related information from temporally out-of-distribution data. Results. Here, we show that for a strict match between gold-standard and predicted answers, the QA model achieves a 51.65% F1 score. For a relaxed match between the gold-standard and predicted answers, the QA model obtains a 78.03% F1 score, along with 85.38% Precision and 79.02% Recall scores. Moreover, the QA model demonstrates consistent performance when subjected to temporally out-of-distribution data. Conclusions. Our study introduces a QA framework designed to extract IDU information from clinical notes, aiming to enhance the accurate and efficient detection of people who inject drugs, extract relevant information, and ultimately facilitate informed patient care.

60 APPLIED LIFE SCIENCES↗

An Open-Access Repository of Synchrophasor Data Quality Examples: Curation and Example Applications

Synchrophasor measurements are critical in providing wide-area situational awareness to power system operators. However, data artifacts may be introduced due to various issues such as loss of communication, loss of GPS signal, internal clock error, and vendor-specific implementation of phasor estimation algorithms. Tools designed to provide actionable insights from synchrophasor data, hence, must be designed to be robust to these data quality issues. In this work, two years of synchrophasor data sourced from multiple electric utilities in the United States were analyzed to identify examples of data quality problems. These examples were then labeled and published in the Grid Event Signature Library, a publicly available repository of power system measurements hosted by the Oak Ridge National Laboratory. This paper describes the data curation process, and illustrates two application use cases where the dataset can be valuable to the research community. In the first use case, a random forest classifier is trained to distinguish power system disturbance signatures from data anomalies introduced in synchrophasor measurements due to clock errors. The second use case studies the impact of data quality issues on an example synchrophasor application (specifically, event start time determination). The choice of data quality problems investigated is informed by the examples in the repository curated in this work.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Expanding Repository Data Available For Sharing and Knowledge Discovery

Some of the hardest space biology and space health challenges require data-intensive, bioinformatic, meta-analytical, and computer-assisted research approaches. These challenges include examining interdisciplinary space life science research across experiments and across interacting spaceflight hazards (radiation, altered gravity, confinement, hostile-closed environments, distance-duration from Earth). The approaches to confront these challenges involve mining multiple datasets simultaneously from various hierarchical organizations of biological complexity, all while concurrently evaluating how experimental design factors affect endpoints of standard assays. To enable this field, it is essential that principal investigators (PIs) submit data in a structure so it can be maximally re-used. The purpose of the NASA Ames Life Sciences Data Archive (ALSDA) is to collect, curate, and make publicly available all non-human space-relevant biological data. ALSDA must also ensure data are open-access, and maximally findable, accessible, interoperable, and reusable (FAIR). The scope of ALSDA data collected and submitted by PIs include subject and study design metadata, assay metadata parameters, raw and processed assay data, assay imagery/video, and subject-experienced mission data telemetry (radiation, temperature, humidity, acoustics, vibrations, etc.). ALSDA recently integrated into a collaborative group of Open Science projects to facilitate a suite of new tools and workflows that will improve data submission, accessibility, and reusability by implementing digital data submission agreements, and adopting the data management system originally developed by NASA GeneLab. ALSDA intends to bring current biological repository data and all future collected data into this new scientific data reuse reality. This new suite of tools will enable ALSDA to deploy a science curation system using scientific assay configurations for the data submission portal. It will capture essential assay parameters according to established standards in each sub-field within biology. The submission portal expedites data collection by enhancing ease of PI data submission, providing a user interface and specificity for which data is to be submitted. Data submissions can be brought into cutting-edge informatic analysis portals to enable mining of physiological, behavioral, biochemical, and imaging datasets in conjunction with ‘omics-level datasets. As ALSDA datasets are submitted, curated, and published (e.g., micro-computed tomography, histology, pulse oximetry, serum metabolites, magnetic resonance imaging, intraocular pressure, novel object recognition, etc.), the merging together of spaceflight data along this multi-hierarchical complexity of biology will enable informatics and data-intensive approaches resulting in knowledge discoveries across missions, space hazards, and biological disciplines.

Biology↗

Expanding Repository Data Available For Sharing And Knowledge Discovery

Some of the hardest space biology and space health challenges require data-intensive, bioinformatic, meta-analytical, and computer-assisted research approaches. These challenges include examining interdisciplinary space life science research across experiments and across interacting spaceflight hazards (radiation, altered gravity, confinement, hostile-closed environments, distance-duration from Earth). The approaches to confront these challenges involve mining multiple datasets simultaneously from various hierarchical organizations of biological complexity, all while concurrently evaluating how experimental design factors affect endpoints of standard assays. To enable this field, it is essential that principal investigators (PIs) submit data in a structure so it can be maximally re-used. The purpose of the NASA Ames Life Sciences Data Archive (ALSDA) is to collect, curate, and make publicly available all non-human space-relevant biological data. ALSDA must also ensure data are open-access, and maximally findable, accessible, interoperable, and reusable (FAIR). The scope of ALSDA data collected and submitted by PIs include subject and study design metadata, assay metadata parameters, raw and processed assay data, assay imagery/video, and subject-experienced mission data telemetry (radiation, temperature, humidity, acoustics, vibrations, etc.). ALSDA recently integrated into a collaborative group of Open Science projects to facilitate a suite of new tools and workflows that will improve data submission, accessibility, and reusability by implementing digital data submission agreements, and adopting the data management system originally developed by NASA GeneLab. ALSDA intends to bring current biological repository data and all future collected data into this new scientific data reuse reality. This new suite of tools will enable ALSDA to deploy a science curation system using scientific assay configurations for the data submission portal. It will capture essential assay parameters according to established standards in each sub-field within biology. The submission portal expedites data collection by enhancing ease of PI data submission, providing a user interface and specificity for which data is to be submitted. Data submissions can be brought into cutting-edge informatic analysis portals to enable mining of physiological, behavioral, biochemical, and imaging datasets in conjunction with ‘omics-level datasets. As ALSDA datasets are submitted, curated, and published (e.g., micro-computed tomography, histology, pulse oximetry, serum metabolites, magnetic resonance imaging, intraocular pressure, novel object recognition, etc.), the merging together of spaceflight data along this multi-hierarchical complexity of biology will enable informatics and data-intensive approaches resulting in knowledge discoveries across missions, space hazards, and biological disciplines.

life science↗

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

Background: Exploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure. Results: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena’s usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset. Conclusions: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena, together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data.

59 BASIC BIOLOGICAL SCIENCES↗

Fostering Geothermal Machine Learning Success: Elevating Big Data Accessibility and Automated Data Standardization in the Geothermal Data Repository

The Department of Energy's (DOE) Geothermal Data Repository (GDR) has implemented improvements to both its data lakes and its data standards and automated data pipelines. The GDR data lakes have reduced storage and compute-related barriers to using large geothermal datasets, enabling these large datasets to be accessed by anyone with a modern computer and internet access. More recently, the GDR has been working to further reduce barriers through streamlining the data intake process, educating users on the process and requirements, and aiding users in accessing data from the data lakes. These improvements have augmented the quantity of datasets the GDR is able to accept into its data lakes and have enabled users who are new to cloud tools to access these datasets more easily, overall increasing the accessibility of big geothermal data for use in machine learning and other projects. In addition, the GDR now has built-in data standards and pipelines for drilling data, geospatial data, and distributed acoustic sensing (DAS) data. These standardization efforts aim to enhance the real-world applicability of geothermal machine learning outcomes by improving the quality of training data. Specifically, through standardizing high-value datasets, the GDR is reducing project-specific data curation requirements, thus allowing more time for actual research. By automating this process, the burden of standardization is lifted from the user, ultimately increasing the availability of standardized data.

15 GEOTHERMAL ENERGY↗

Infusion of AI/ML Technology into Operational NASA Data Systems

NASA has been developing a variety of Artificial Intelligence / Machine Learning technologies related to Earth Observations. In most cases, the full value of such a technology is realized when it is infused into an operational system. NASA’s Earth Science Data Systems program has been formulating repeatable methods to execute technology infusion. These efforts include the Advancing Collaborative Connections for Earth System Science (ACCESS) program, a Technology Infusion Playbook, and an assemblage of working groups investigating methods for infusion collaboration, community development, and capacity building. ESDS has also been executing a pathfinder activity to infuse a machine-learning-driven recommender of science keywords for Earth Observation datasets, which is intended to be used for metadata curation in the Earth Observation System Data and Information System.

C Lynnes↗

An Update on the Geothermal Data Repository's Data Standards and Pipelines: Geospatial Data and Distributed Acoustic Sensing Data: Preprint

The Department of Energy's (DOE) Geothermal Data Repository (GDR) team has implemented data standards and automated data pipelines for the following data types: 1) drilling data, 2) geospatial datasets, and 3) DAS data. An additional data pipeline is proposed for stimulation data. These data standards and pipelines are intended to improve the real-world applicability of geothermal machine learning outputs through improving the quality of data. More specifically, through standardizing high-value datasets, the GDR is reducing project-specific data curation requirements, allowing more time to be spent on actual research. By automating this process, the burden of standardization is taken off of the user, overall increasing the availability of standardized data. This paper provides an update on the GDR's transition toward data standardization through automated data pipelines and calls for feedback from the community on how we can improve this process.

cloud-optimized↗