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All sourcesNASA NTRSDOE OSTI
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ASDC’s Python-Based Metadata Extraction Pipeline for Suborbital Campaigns

The FAIRness of data products, especially findability and accessibility depend on rich metadata which, when extracted, can allow for proper curation. Over the past few years, the Atmospheric Science Data Center (ASDC) suborbital science support team has developed a metadata extraction pipeline to ensure the required metadata can be retrieved systematically, effectively, and efficiently to ensure the data can be used by a broad community. The development of a pipeline has presented many, but necessary, challenges to support archival and distribution of ASDC’s 30+ suborbital missions. Though sufficient metadata is provided by instrument scientists, the metadata may not be readily machine actionable due to different formats and templates. Further complicating metadata extraction, our team has found that the nature of metadata can be quite diverse given the difference in measurement types, instruments, and measurement platforms. A metadata extraction pipeline has been developed to provide an efficient, plugin-in based, method for adding new parsers, a configuration system that lets non-developers customize how files are processed, and a system for identifying and logging metadata quality issues to ensure they are readily found and addressed. The metadata extraction pipeline identifies critical pieces of metadata that are needed to promote data FAIRness, including location, file revision, measurement start/end datetime and can be easily modified to extract further information (such as variables). Given the wide-ranging datasets, the pipeline has been modified to accommodate multiple file formats, including multiple versions of ICARTT (International Consortium for Atmospheric Research on Transport and Transformation), HDF (Hierarchical Data Format), netCDF (network Common Data Form), and multiple versions of the Ames File Format. The pipeline also supports building metadata for file formats that cannot have metadata easily extracted from them, such as PDF (Portable Document Format) and GIF (Graphics Interchange Format). The pipeline has allowed our team to maintain a consistent flow of data and metadata to archival and distribution services, ensuring the ASDC meets the needs of the suborbital science community. This presentation will highlight the ASDC’s suborbital metadata extraction pipeline, its development, how it’s been modified to support data FAIRness, and plans for maintaining the pipeline and adding new features.

Abraham Porter↗
DOE OSTI2023

Transparent application-layer/os deeper packet inspector

A computer-implemented method of deep packet inspection (DPI) in a network is provided. The method comprises collecting data packets comprising a number of traffic flows from a number of devices via a number of traffic taps and classifying each traffic flow according to data about network protocol layers of the packets comprising the traffic flow. Application layer metadata is extracted from the packets. Traffic flow classification data and the extracted metadata are ingested into a data cluster and normalized. The normalized classification data and extracted metadata is then correlated to other data sets.

Urias, Vincent↗
NASA NTRS1991

Automated extraction of metadata from remotely sensed satellite imagery

The paper discusses research in the Intelligent Data Management project at the NASA/Goddard Space Flight Center, with emphasis on recent improvements in low-level feature detection algorithms for performing real-time characterization of images. Images, including MSS and TM data, are characterized using neural networks and the interpretation of the neural network output by an expert system for subsequent archiving in an object-oriented data base. The data show the applicability of this approach to different arrangements of low-level remote sensing channels. The technique works well when the neural network is trained on data similar to the data used for testing.

Cromp, Robert F.↗
DOE OSTI2024

Automated annotation of scientific texts for ML-based keyphrase extraction and validation

Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the data often lack the essential metadata required for researchers to find, curate, and search them effectively. The lack of metadata poses a significant challenge in the utilization of these data sets. Machine learning (ML)–based metadata extraction techniques have emerged as a potentially viable approach to automatically annotating scientific data sets with the metadata necessary for enabling effective search. Text labeling, usually performed manually, plays a crucial role in validating machine-extracted metadata. However, manual labeling is time-consuming and not always feasible; thus, there is a need to develop automated text labeling techniques in order to accelerate the process of scientific innovation. This need is particularly urgent in fields such as environmental genomics and microbiome science, which have historically received less attention in terms of metadata curation and creation of gold-standard text mining data sets. In this paper, we present two novel automated text labeling approaches for the validation of ML-generated metadata for unlabeled texts, with specific applications in environmental genomics. Our techniques show the potential of two new ways to leverage existing information that is only available for select documents within a corpus to validate ML models, which can then be used to describe the remaining documents in the corpus. The first technique exploits relationships between different types of data sources related to the same research study, such as publications and proposals. The second technique takes advantage of domain-specific controlled vocabularies or ontologies. In this paper, we detail applying these approaches in the context of environmental genomics research for ML-generated metadata validation. Our results show that the proposed label assignment approaches can generate both generic and highly specific text labels for the unlabeled texts, with up to 44% of the labels matching with those suggested by a ML keyword extraction algorithm.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2024

A Data Processing Pipeline To Extract A Knowledge Graph From Sec Documents For Socio-technical Analysis Of Critical Infrastructure Influence

The code is written in Python and consists of the following pipeline that is implemented in Apache Airflow. This pipeline intends to understand the companies that are directly or indirectly involved with a type of critical infrastructure system at some point in that system's lifecycle. The pipeline takes a configuration file that specifies a list of initial companies to consider, a geographic region of interest (disk) expressed as a latitude/longitude point and distance, and a set of SEC form types from which to extract entities and relations. There are three main components to this pipeline as currently implemented: Social Network Extraction, Critical Infrastructure Network Extraction, and Inference and Fusion. First, Social Network Extraction, implemented as the `organizations_sec` component of the workflow graph queries the SEC EDGAR webservice using the list of initial companies from the configuration file. Given this, it extracts metadata that documents the number of each type of form for the given set of companies and their location. This forms metadata represents a catalog of data sources for the extracted social network knowledge graph. The pipeline then downloads these forms from the website and saves them in a build directory for further processing. These documents are then parsed for entities and relations. Second, the Critical Network Extraction component extracts entities and relations for a critical infrastructure sector. Currently, we focus on Electric Vehicle charging stations and this information is available via the Department of Energy (DOE) database on fueling stations maintained by NREL. Third, the Inference and Fusion component relates the social network graph to the critical infrastructure graph in order to understand the impact of a company within a geographic region. Relations include ownership of the EV Charging Station asset as well as maintenance/ownership of the EV payment networks. The fused network can be represented in many ways and currently we emit a knowledge graph.

Weaver, GabrielA.↗
NASA NTRS2019

Comprehensive Assessment of Models and Events Using Library Tools (CAMEL) Framework: Time Series Comparisons

The Comprehensive Assessment of Models and Events using Library Tools (CAMEL) framework leverages existing Community Coordinated Modeling Center services: Run on Request post processing tools that generate model time series outputs and the new Community Coordinated Modeling Center Metadata Registry that describes simulation runs using Space Physics Archive Search and Extract metadata. The new CAMEL visualization tool compares the modeled time series with observational data and computes a suite of skill scores such as Prediction Efficiency, Root Mean Square Error, and Symmetric Signed Percentage Bias. Model data pairs used for skill calculations are obtained considering a user selected maximum difference between the time of observation and the nearest model output. The system renders available data for all locations and time periods selected using interactive visualizations that allow the user to zoom, pan, and pick data values along traces. Skill scores are reported for each selected event or aggregated over all events for all participating model runs. Separately, scores are reported for all locations (satellites or stations) and for each location individually. We are building on past experiences with model data comparisons of magnetosphere and ionosphere model outputs from GEM2008, GEMCEDAR Electrodynamics Thermosphere Ionosphere, and the SWPC Operational Space Weather Model challenges. The CAMEL visualization tool is demonstrated using three validation studies: (a) Wang Sheeley Arge heliosphere simulations compared against OMNI solar wind data, (b) ground magnetic perturbations from several magnetosphere and ionosphere electrodynamics models as observed by magnetometers, and (c) electron fluxes from several ring current simulations compared to Radiation Belt Storm Probes Helium Oxygen Proton Electron instrument measurements, integrated over different energy ranges.

Rastätter, Lutz↗
DOE OSTI2023

Building the I (Interoperability) of FAIR for performance reproducibility of large-scale composable workflows in RECUP

Abstract-Scientific computing communities increasingly run their experiments using complex data- and compute-intensive workflows that utilize distributed and heterogeneous architectures targeting numerical simulations and machine learning, often executed on the Department of Energy Leadership Computing Facilities (LCFs). We argue that a principled, systematic approach to implementing FAIR principles at scale, including fine-grained metadata extraction and organization, can help with the numerous challenges to performance reproducibility posed by such workflows. We extract workflow patterns, propose a set of tools to manage the entire life cycle of performance metadata, and aggregate them in an HPC-ready framework for reproducibility (RECUP). We describe the challenges in making these tools interoperable, preliminary work, and lessons learned from this experiment.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2004

Archiving Space Geodesy Data for 20+ Years at the CDDIS

Since 1982, the Crustal Dynamics Data Information System (CDDIS) has supported the archive and distribution of geodetic data products acquired by NASA programs. These data include GPS (Global Positioning System), GLONASS (GLObal NAvigation Satellite System), SLR (Satellite Laser Ranging), VLBI (Very Long Baseline Interferometry), and DORIS (Doppler Orbitography and Radiolocation Integrated by Satellite). The data archive supports NASA's space geodesy activities through the Solid Earth and Natural Hazards (SENH) program. The CDDIS data system and its archive have become increasingly important to many national and international programs, particularly several of the operational services within the International Association of Geodesy (IAG), including the International GPS Service (IGS), the International Laser Ranging Service (ILRS), the International VLBI Service for Geodesy and Astrometry (IVS), the International DORIS Service (IDS), and the International Earth Rotation Service (IERS). The CDDIS provides easy and ready access to a variety of data sets, products, and information about these data. The specialized nature of the CDDIS lends itself well to enhancement and thus can accommodate diverse data sets and user requirements. All data sets and metadata extracted from these data sets are accessible to scientists through ftp and the web; general information about each data set is accessible via the web. The CDDIS, including background information about the system and its user communities, the computer architecture, archive contents, available metadata, and future plans will be discussed.

Noll, Carey E.↗
DOE OSTI2025

Datum: A Scientific Metadata Catalog

The data catalog market is currently flooded with a myriad of different products, but none serve the scientific community well. There are cloud-native tools like Databricks, Snowflake,to on-premise solutions like Collibra and Datahub. The common failing of all these tools however, is their inability to serve the scientific data community directly. Most catalogs are targeted towards financial, health, or user data - not sensor or scientific domain data. They also prioritize integrations that often don’t exist or are just starting to be used in the scientific realm - all while ignoring common scientific tools and file types. Datum is a catalog which targets the scientific data directly, including the tools and networks in which those tools are used. We work with the producers and consumers of the data where they are, targeting cloud and on-premise with a focus on classified networks. Datum is an Erlang/Elixir application. Technical Features Note: The features listed below are still under development and may change, slightly, upon final delivery of the product. File Formats - Datum has the ability to read additional metadata and provides processing pipelines for the following file formats: Plain Text, PDF, LaTeX, HTML, Open Document Format (.odt), XML, CSV/TSV (and other standard delimiters), OpenDocument Database and Spreadsheets, Geo-Referenced TIFF, Common Data Format, HDF/HDF5, LabView TDMS, Excel, DeltaTables, Parquet, Apache Iceberg, Apache Hudi and many others. Metadata Collection - Scanners for the local and networked file systems and cloud storage providers. Network integration with common databases such as MSSQL and MySQL. User Plugin System - Users are able to provide either file processing, metadata extraction, or sampling plugins in the programming language of their choice. Authentication/Authorization -: OIDC integration, SCIM provisioning and EntraID integration out of the box. Full user and group management system with a “least privilege” operating mode. Governance - Customizable data governance platform; dictate and enforce required metadata, enforce data embargos, and enforce user agreements and NDAs before data access. Ability to create health checks on data, rejecting abandoned or poorly curated data and automatically removing it from the search index. Ability for users to submit corrections. Search - Semantic search is a first class citizen. No licenses to expensive, external software required. Integrated use of vectors and vector-based search allows for AI agent integration at all levels of operation. Metadata Model - Display and control data’s lineage and connections to other data and data directories. Data is modeled after a filesystem - an organization instantly recognizable and navigable by most any user. CLI and SDK - Ships with a Command Line Interface (CLI) tool and with a fully-featured Python SDK. This allows for rapid and programmatic use of Datum by every level of user. Minimal Infrastructure - Datum ships as a single executable file and can be run on any operating system and most CPU architectures. Datum has no reliance on external databases, search indexing tools, or other outside services - and it runs equally well on edge computing devices, cloud services, or in a clustered HPC environment.

darrington, john↗
DOE OSTI2024

Automating the Analysis of Large Language Models Responses through Zero-Shot Question Answering

Recent advancements in Large Language Models (LLMs) have shown significant potential in various applications, yet their evaluation, particularly in zero-shot question answering scenarios, remains a challenging task. In this study, our objective was to explore precision metrics for Large Language Models (LLM) and design and implement a software pipeline to automatically evaluate LLMs' outputs under zero-shot question answering. Zero-shot question answering involves a model providing answers to questions about topics it hasn't seen during training. It leverages the principles of zero-shot learning by relying on semantic understanding and generalization from related knowledge. The data used was metadata from medical databases on congenital heart disease. We explored eleven LLM metrics and selected three for our evaluation: BLEU, BERTScore, and MoverScore. BLEU calculates a score based on the overlap of n-grams (contiguous sequences of n items, typically words) between the machine-generated translation and the reference translations. Higher BLEU scores indicate better correspondence between the machine-generated and human-generated translations. BERTScore is a metric used to evaluate the quality of machine-generated text by measuring the similarity of token embeddings produced by BERT (Bidirectional Encoder Representations from Transformers) between the generated text and reference text. MoverScore is a metric that quantifies the dissimilarity between the distributions of word embeddings from machine-generated text and reference text, emphasizing semantic similarity over exact token overlap. We also introduced HBKI, a composite metric summarizing these approaches. We tested five models —GPT-3, Llama-2, Gemini 1.5 Pro, Solar 10.7B, and Mixtral-8x7b. Our software pipeline, designed and implemented using Object-Oriented Programming principles, allows users to customize the selection and extraction of features for topics of interest in their own research. Our results show that MoverScore delivered the most precise evaluation of the LLM's outputs, while Mixtral-8x7b achieved the best overall performance in extracting metadata from the databases.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Data Center Facility Monitoring with Physics Aware Approach

U.S. Department of Energy's National Renewable Energy Laboratory (NREL) hosts one of the world's most energy-efficient HPC data centers; this system uses component-level warm-water liquid cooling to efficiently remove heat from the data center and capture it for reuse in the building or rejection to the atmosphere. Given the complexity of this system, building data-driven tools for holistically monitoring and operating the entire data center is a priority for ensuring maximal efficiency and resiliency. In this advanced smart facility, over one million metrics are recorded per minute using state-of-the-art streaming data architecture and software to capture and process the state of the system in real time. Here we detail two efforts to effectively analyze, visualize, and interpret this large volume streaming data. We have developed a novel, flexible system for identifying and visualizing individual metric anomalies and component performance across the data center through automatic metadata extraction and physically-motivated visualization for quick interpretation. Additionally, to directly connect system maintenance to data stream processing we explore a physics informed multi-metric drift and anomaly detection application to detect scale-build up in heat exchangers.

anomaly detection↗
DOE OSTI2025

Label-based Virtual Directories In dCache

Traditional filesystems organize data in directories. These directories are typically a collection of files whose grouping is based on a single criterion, e.g., the starting date of an experiment, experiment name, beamline ID, measurement device, or instrument. However, each file in a directory can belong to several logical groups, such as a special event type, experiment condition, or a part of a selected dataset. dCache is a storage system developed to store large amounts of scientific data, used by many HEP and Photon Science experiments. With recent developments in dCache, we have introduced a concept of file tagging, which dynamically groups files with the same label into virtual directories. The file labels can be added, removed, renamed, and deleted through the admin interface or via REST API. The files in virtual directories are exposed through all protocols supported by dCache. This contribution will describe the details of the implementation for file tagging in dCache and present our future development plans on automatic metadata extractions, a feature that will significantly simplify data management. Additionally, we are exploring the future use of virtual directories as a way to translate scientific data catalogs into filesystem views for direct data analysis.

Sahakyan, Marina [DESY]↗
NASA NTRS1997

Unsupervised, Robust Estimation-based Clustering for Multispectral Images

To prepare for the challenge of handling the archiving and querying of terabyte-sized scientific spatial databases, the NASA Goddard Space Flight Center's Applied Information Sciences Branch (AISB, Code 935) developed a number of characterization algorithms that rely on supervised clustering techniques. The research reported upon here has been aimed at continuing the evolution of some of these supervised techniques, namely the neural network and decision tree-based classifiers, plus extending the approach to incorporating unsupervised clustering algorithms, such as those based on robust estimation (RE) techniques. The algorithms developed under this task should be suited for use by the Intelligent Information Fusion System (IIFS) metadata extraction modules, and as such these algorithms must be fast, robust, and anytime in nature. Finally, so that the planner/schedule module of the IlFS can oversee the use and execution of these algorithms, all information required by the planner/scheduler must be provided to the IIFS development team to ensure the timely integration of these algorithms into the overall system.

Netanyahu, Nathan S.↗
NASA NTRS2008

HDF-EOS Web Server

A shell script has been written as a means of automatically making HDF-EOS-formatted data sets available via the World Wide Web. ("HDF-EOS" and variants thereof are defined in the first of the two immediately preceding articles.) The shell script chains together some software tools developed by the Data Usability Group at Goddard Space Flight Center to perform the following actions: Extract metadata in Object Definition Language (ODL) from an HDF-EOS file, Convert the metadata from ODL to Extensible Markup Language (XML), Reformat the XML metadata into human-readable Hypertext Markup Language (HTML), Publish the HTML metadata and the original HDF-EOS file to a Web server and an Open-source Project for a Network Data Access Protocol (OPeN-DAP) server computer, and Reformat the XML metadata and submit the resulting file to the EOS Clearinghouse, which is a Web-based metadata clearinghouse that facilitates searching for, and exchange of, Earth-Science data.

Ullman, Richard↗
NASA NTRS2011

Generic, Extensible, Configurable Push-Pull Framework for Large-Scale Science Missions

The push-pull framework was developed in hopes that an infrastructure would be created that could literally connect to any given remote site, and (given a set of restrictions) download files from that remote site based on those restrictions. The Cataloging and Archiving Service (CAS) has recently been re-architected and re-factored in its canonical services, including file management, workflow management, and resource management. Additionally, a generic CAS Crawling Framework was built based on motivation from Apache s open-source search engine project called Nutch. Nutch is an Apache effort to provide search engine services (akin to Google), including crawling, parsing, content analysis, and indexing. It has produced several stable software releases, and is currently used in production services at companies such as Yahoo, and at NASA's Planetary Data System. The CAS Crawling Framework supports many of the Nutch Crawler's generic services, including metadata extraction, crawling, and ingestion. However, one service that was not ported over from Nutch is a generic protocol layer service that allows the Nutch crawler to obtain content using protocol plug-ins that download content using implementations of remote protocols, such as HTTP, FTP, WinNT file system, HTTPS, etc. Such a generic protocol layer would greatly aid in the CAS Crawling Framework, as the layer would allow the framework to generically obtain content (i.e., data products) from remote sites using protocols such as FTP and others. Augmented with this capability, the Orbiting Carbon Observatory (OCO) and NPP (NPOESS Preparatory Project) Sounder PEATE (Product Evaluation and Analysis Tools Elements) would be provided with an infrastructure to support generic FTP-based pull access to remote data products, obviating the need for any specialized software outside of the context of their existing process control systems. This extensible configurable framework was created in Java, and allows the use of different underlying communication middleware (at present, both XMLRPC, and RMI). In addition, the framework is entirely suitable in a multi-mission environment and is supporting both NPP Sounder PEATE and the OCO Mission. Both systems involve tasks such as high-throughput job processing, terabyte-scale data management, and science computing facilities. NPP Sounder PEATE is already using the push-pull framework to accept hundreds of gigabytes of IASI (infrared atmospheric sounding interferometer) data, and is in preparation to accept CRIMS (Cross-track Infrared Microwave Sounding Suite) data. OCO will leverage the framework to download MODIS, CloudSat, and other ancillary data products for use in the high-performance Level 2 Science Algorithm. The National Cancer Institute is also evaluating the framework for use in sharing and disseminating cancer research data through its Early Detection Research Network (EDRN).

Foster, Brian M.↗
NASA NTRS2011

Improvements in Space Geodesy Data Discovery at the CDDIS

The Crustal Dynamics Data Information System (CDDIS) supports data archiving and distribution activities for the space geodesy and geodynamics community. The main objectives of the system are to store space geodesy and geodynamics related data products in a central data bank. to maintain information about the archival of these data, and to disseminate these data and information in a timely manner to a global scientific research community. The archive consists of GNSS, laser ranging, VLBI, and DORIS data sets and products derived from these data. The CDDIS is one of NASA's Earth Observing System Data and Information System (EOSDIS) distributed data centers; EOSDIS data centers serve a diverse user community and arc tasked to provide facilities to search and access science data and products. Several activities are currently under development at the CDDIS to aid users in data discovery, both within the current community and beyond. The CDDIS is cooperating in the development of Geodetic Seamless Archive Centers (GSAC) with colleagues at UNAVCO and SIO. TIle activity will provide web services to facilitate data discovery within and across participating archives. In addition, the CDDIS is currently implementing modifications to the metadata extracted from incoming data and product files pushed to its archive. These enhancements will permit information about COOlS archive holdings to be made available through other data portals such as Earth Observing System (EOS) Clearinghouse (ECHO) and integration into the Global Geodetic Observing System (GGOS) portal.

Noll, C.↗
NASA NTRS2012

An Update on the CDDIS

The Crustal Dynamics Data Inforn1ation System (CoorS) supports data archiving and distribution activities for the space geodesy and geodynamics community. The main objectives of the system are to store space geodesy and geodynamics related data products in a central data bank, to maintain infom1ation about the archival of these data, and to disseminate these data and information in a timely mam1er to a global scientific research community. The archive consists of GNSS, laser ranging, VLBI, and OORIS data sets and products derived from these data. The coors is one of NASA's Earth Observing System Oata and Infom1ation System (EOSorS) distributed data centers; EOSOIS data centers serve a diverse user community and are tasked to provide facilities to search and access science data and products. The coors data system and its archive have become increasingly important to many national and international science communities, in pal1icular several of the operational services within the International Association of Geodesy (lAG) and its project the Global Geodetic Observing System (GGOS), including the International OORIS Service (IDS), the International GNSS Service (IGS), the International Laser Ranging Service (ILRS), the International VLBI Service for Geodesy and Astrometry (IVS), and the International Earth Rotation Service (IERS). The coors has recently expanded its archive to supp011 the IGS Multi-GNSS Experiment (MGEX). The archive now contains daily and hourly 3D-second and subhourly I-second data from an additional 35+ stations in RINEX V3 fOm1at. The coors will soon install an Ntrip broadcast relay to support the activities of the IGS Real-Time Pilot Project (RTPP) and the future Real-Time IGS Service. The coors has also developed a new web-based application to aid users in data discovery, both within the current community and beyond. To enable this data discovery application, the CDDIS is currently implementing modifications to the metadata extracted from incoming data and product files pushed to its archive. This poster will include background information about the system and its user communities, archive contents and updates, enhancements for data discovery, new system architecture, and future plans.

Noll, Carey↗