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All sources NASA NTRS DOE OSTI

DOE OSTI2017

EpiK: A Knowledge Base for Epidemiological Modeling and Analytics of Infectious Diseases

Computational epidemiology seeks to develop computational methods to study the distribution and determinants of health-related states or events (including disease), and the application of this study to the control of diseases and other health problems. Recent advances in computing and data sciences have led to the development of innovative modeling environments to support this important goal. The datasets used to drive the dynamic models as well as the data produced by these models presents unique challenges owing to their size, heterogeneity and diversity. These datasets form the basis of effective and easy to use decision support and analytical environments. As a result, it is important to develop scalable data management systems to store, manage and integrate these datasets. In this paper, we develop EpiK —a knowledge base that facilitates the development of decision support and analytical environments to support epidemic science. An important goal is to develop a framework that links the input as well as output datasets to facilitate effective spatio-temporal and social reasoning that is critical in planning and intervention analysis before and during an epidemic. The data management framework links modeling workflow data and its metadata using a controlled vocabulary. The metadata captures information about storage, the mapping between the linked model and the physical layout, and relationships to support services. EpiK is designed to support agent-based modeling and analytics frameworks—aggregate models can be seen as special cases and are thus supported. We use semantic web technologies to create a representation of the datasets that encapsulates both the location and the schema heterogeneity. The choice of RDF as a representation language is motivated by the diversity and growth of the datasets that need to be integrated. A query bank is developed—the queries capture a broad range of questions that can be posed and answered during a typical case study pertaining to disease outbreaks. The queries are constructed using SPARQL Protocol and RDF Query Language (SPARQL) over the EpiK. EpiK can hide schema and location heterogeneity while efficiently supporting queries that span the computational epidemiology modeling pipeline: from model construction to simulation output. As a result, we show that the performance of benchmark queries varies significantly with respect to the choice of hardware underlying the database and resource description framework (RDF) engine.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Materials Data Science Ontology(MDS-Onto): Unifying Domain Knowledge in Materials and Applied Data Science

Ontologies have gained popularity in the scientific community as a way to standardize terminologies in organizations’ data. Although certain cohorts have created frameworks with rules and guidelines on creating ontologies, there exist significant variations in how Materials Science ontologies are currently developed. We seek to provide guidance in the form of a unified automated framework for developing interoperable and modular ontologies for Materials Data Science that simplifies the ontology terms matching by establishing a semantic bridge up to the Basic Formal Ontology(BFO). This framework provides key recommendations on how ontologies should be positioned within the semantic web, what knowledge representation language is recommended, and where ontologies should be published online to boost their findability and interoperability. Two fundamental components of the MDS-Onto framework are the bilingual package called FAIRmaterials for ontology creation and FAIRLinked, for FAIR data creation. To showcase the practical capabilities of FAIRmaterials, we present two exemplar domain ontologies of MDS-Onto: Synchrotron X-Ray Diffraction and Photovoltaics.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2024

GraphAide: Advanced Graph-Assisted Query and Reasoning System

Curating knowledge from multiple siloed sources that contain both structured and unstructured data is a major challenge in many real-world applications. Pattern matching and querying represent fundamental tasks in modern data analytics that leverage this curated knowledge. The development of such applications necessitates overcoming several research challenges, including data extraction, named entity recognition, data modeling, and designing query interfaces. Moreover, the explainability of these functionalities is critical for their broader adoption. The emergence of Large Language Models (LLMs) has accelerated the development lifecycle of new capabilities. Nonetheless, there is an ongoing need for domain-specific tools tailored to user activities. The creation of digital assistants has gained considerable traction in recent years, with LLMs offering a promising avenue to develop such assistants utilizing domain-specific knowledge and assumptions. In this context, we introduce an advanced query and reasoning system, GraphAide, which constructs a knowledge graph (KG) from diverse sources and allows to query and reason over the resulting KG. GraphAide harnesses both the KG and LLMs to rapidly develop domain-specific digital assistants. It integrates design patterns from retrieval augmented generation (RAG) and the semantic web to create an agentic LLM application. GraphAide underscores the potential for streamlined and efficient development of specialized digital assistants, thereby enhancing their applicability across various domains.

Purohit, Sumit [BATTELLE (PACIFIC NW LAB)] (ORCID:↗

DOE OSTI2015

Enhancing the Impact of Science Data: Toward Data Discovery and Reuse

The amount of data produced in support of scientific research continues to grow rapidly. Despite the accumulation and demand for scientific data, relatively little data are actually made available for the broader scientific community. We surmise that one root of this problem is the perceived difficulty of electronically publishing scientific data and associated metadata in a way that makes it discoverable. We propose exploiting Semantic Web technologies and best practices to make metadata both discoverable and easy to publish. We share experiences in curating metadata to illustrate the cumbersome nature of data reuse in the current research environment. We also make recommendations with a real-world example of how data publishers can provide their metadata by adding limited additional markup to HTML pages on the Web. With little additional effort from data publishers, the difficulty of data discovery, access, and sharing can be greatly reduced and the impact of research data greatly enhanced.

Data Curation↗

DOE OSTI2025

Extraction and Analysis of Time Series Data from Building Automation Systems Using Large Language Models

Semantic schemas like Haystack 4, Brick and ASHRAE standard 223 enable the structured, standardized, and machine-readable representation of building data, facilitating interoperability, data integration, and advanced analytics. However, extracting information from these models requires specialized expertise in SPARQL and other programming languages, skills that are not commonly found among building professionals. Recent advancements in Large Language Models (LLMs), such as ChatGPT, enable the construction of queries using natural language, making it easier for individuals to interact with these systems in a manner that resembles everyday speech. However, these methods have not yet been tested on building semantic ontologies. This paper introduces a novel workflow and tool for enabling users to ask questions about a specific building's data, using natural language and receive answers automatically generated by GPT-4o. Our approach integrates semantic ontologies with advanced LLM capabilities to automate three critical steps: (1) generating SPARQL queries to retrieve time series references from ontological models, (2) extracting the corresponding time series data from the Building Automation System, and (3) performing computations and visualizations tailored to the user's query. The proposed method simplifies access to BAS data, allowing both domain experts and non-specialists to conduct sophisticated analyses without needing extensive technical knowledge of semantic web technologies. By demonstrating this pipeline, we facilitate more accessible and scalable data-driven decision-making in building operations and management.

Mulayim, Ozan Baris↗

DOE OSTI2015

Resource Discovery for Extreme Scale Collaboration (RDESC) Final Report - RPI/TWC - Year 3

The amount of data produced in the practice of science is growing rapidly. Despite the accumulation and demand for scientific data, relatively little is actually made available for the broader scientific community. We surmise that the root of the problem is the perceived difficulty to electronically publish scientific data and associated metadata in a way that makes it discoverable. We propose to exploit Semantic Web technologies and practices to make (meta)data discoverable and easy to publish. We share our experiences in curating metadata to illustrate both the flexibility of our approach and the pain of discovering data in the current research environment. We also make recommendations by concrete example of how data publishers can provide their (meta)data by adding some limited, additional markup to HTML pages on the Web. With little additional effort from data publishers, the difficulty of data discovery/access/sharing can be greatly reduced and the impact of research data greatly enhanced.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2020

The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering

The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using a machine-tractable, ontology-backed representation that is built using Semantic Web technologies. While early versions of SBOL focused only on the description of DNA-based components and their sub-components, SBOL can now be used to represent knowledge across multiple scales and throughout the entire synthetic biology workflow, from the specification of a single molecule or DNA fragment through to multicellular systems containing multiple interacting genetic circuits. The third major iteration of the SBOL standard, SBOL3, is an effort to streamline and simplify the underlying data model with a focus on real-world applications, based on experience from the deployment of SBOL in a variety of scientific and industrial settings. Here, we introduce the SBOL3 specification both in comparison to previous versions of SBOL and through practical examples of its use.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Extraction and Analysis of Time Series Data from Building Automation Systems Using Large Language Models

Mulayim, Ozan Baris↗

DOE OSTI2016

The health care and life sciences community profile for dataset descriptions

Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets.

Science & Technology - Other Topics↗

NASA NTRS2003

Developing Visualization Techniques for Semantics-based Information Networks

Information systems incorporating complex network structured information spaces with a semantic underpinning - such as hypermedia networks, semantic networks, topic maps, and concept maps - are being deployed to solve some of NASA s critical information management problems. This paper describes some of the human interaction and navigation problems associated with complex semantic information spaces and describes a set of new visual interface approaches to address these problems. A key strategy is to leverage semantic knowledge represented within these information spaces to construct abstractions and views that will be meaningful to the human user. Human-computer interaction methodologies will guide the development and evaluation of these approaches, which will benefit deployed NASA systems and also apply to information systems based on the emerging Semantic Web.

Keller, Richard M.↗

NASA NTRS2008

Standardizing Interfaces for External Access to Data and Processing for the NASA Ozone Product Evaluation and Test Element (PEATE)

NASA's traditional science data processing systems have focused on specific missions, and providing data access, processing and services to the funded science teams of those specific missions. Recently NASA has been modifying this stance, changing the focus from Missions to Measurements. Where a specific Mission has a discrete beginning and end, the Measurement considers long term data continuity across multiple missions. Total Column Ozone, a critical measurement of atmospheric composition, has been monitored for'decades on a series of Total Ozone Mapping Spectrometer (TOMS) instruments. Some important European missions also monitor ozone, including the Global Ozone Monitoring Experiment (GOME) and SCIAMACHY. With the U.S.IEuropean cooperative launch of the Dutch Ozone Monitoring Instrument (OMI) on NASA Aura satellite, and the GOME-2 instrumental on MetOp, the ozone monitoring record has been further extended. In conjunction with the U.S. Department of Defense (DoD) and the National Oceanic and Atmospheric Administration (NOAA), NASA is now preparing to evaluate data and algorithms for the next generation Ozone Mapping and Profiler Suite (OMPS) which will launch on the National Polar-orbiting Operational Environmental Satellite System (NPOESS) Preparatory Project (NPP) in 2010. NASA is constructing the Science Data Segment (SDS) which is comprised of several elements to evaluate the various NPP data products and algorithms. The NPP SDS Ozone Product Evaluation and Test Element (PEATE) will build on the heritage of the TOMS and OM1 mission based processing systems. The overall measurement based system that will encompass these efforts is the Atmospheric Composition Processing System (ACPS). We have extended the system to include access to publically available data sets from other instruments where feasible, including non-NASA missions as appropriate. The heritage system was largely monolithic providing a very controlled processing flow from data.ingest of satellite data to the ultimate archive of specific operational data products. The ACPS allows more open access with standard protocols including HTTP, SOAPIXML, RSS and various REST incarnations. External entities can be granted access to various modules within the system, including an extended data archive, metadata searching, production planning and processing. Data access is provided with very fine grained access control. It is possible to easily designate certain datasets as being available to the public, or restricted to groups of researchers, or limited strictly to the originator. This can be used, for example, to release one's best validated data to the public, but restrict the "new version" of data processed with a new, unproven algorithm until it is ready. Similarly, the system can provide access to algorithms, both as modifiable source code (where possible) and fully integrated executable Algorithm Plugin Packages (APPs). This enables researchers to download publically released versions of the processing algorithms and easily reproduce the processing remotely, while interacting with the ACPS. The algorithms can be modified allowing better experimentation and rapid improvement. The modified algorithms can be easily integrated back into the production system for large scale bulk processing to evaluate improvements. The system includes complete provenance tracking of algorithms, data and the entire processing environment. The origin of any data or algorithms is recorded and the entire history of the processing chains are stored such that a researcher can understand the entire data flow. Provenance is captured in a form suitable for the system to guarantee scientific reproducability of any data product it distributes even in cases where the physical data products themselves have been deleted due to space constraints. We are currently working on Semantic Web ontologies for representing the various provenance information. A new web site focusing on consolidating informaon about the measurement, processing system, and data access has been established to encourage interaction with the overall scientific community. We will describe the system, its data processing capabilities, and the methods the community can use to interact with the standard interfaces of the system.

Tilmes, Curt A.↗

NASA NTRS2008

Provenance in Data Interoperability for Multi-Sensor Intercomparison

As our inventory of Earth science data sets grows, the ability to compare, merge and fuse multiple datasets grows in importance. This requires a deeper data interoperability than we have now. Efforts such as Open Geospatial Consortium and OPeNDAP (Open-source Project for a Network Data Access Protocol) have broken down format barriers to interoperability; the next challenge is the semantic aspects of the data. Consider the issues when satellite data are merged, cross-calibrated, validated, inter-compared and fused. We must match up data sets that are related, yet different in significant ways: the phenomenon being measured, measurement technique, location in space-time or quality of the measurements. If subtle distinctions between similar measurements are not clear to the user, results can be meaningless or lead to an incorrect interpretation of the data. Most of these distinctions trace to how the data came to be: sensors, processing and quality assessment. For example, monthly averages of satellite-based aerosol measurements often show significant discrepancies, which might be due to differences in spatio- temporal aggregation, sampling issues, sensor biases, algorithm differences or calibration issues. Provenance information must be captured in a semantic framework that allows data inter-use tools to incorporate it and aid in the intervention of comparison or merged products. Semantic web technology allows us to encode our knowledge of measurement characteristics, phenomena measured, space-time representation, and data quality attributes in a well-structured, machine-readable ontology and rulesets. An analysis tool can use this knowledge to show users the provenance-related distrintions between two variables, advising on options for further data processing and analysis. An additional problem for workflows distributed across heterogeneous systems is retrieval and transport of provenance. Provenance may be either embedded within the data payload, or transmitted from server to client in an out-of-band mechanism. The out of band mechanism is more flexible in the richness of provenance information that can be accomodated, but it relies on a persistent framework and can be difficult for legacy clients to use. We are prototyping the embedded model, incorporating provenance within metadata objects in the data payload. Thus, it always remains with the data. The downside is a limit to the size of provenance metadata that we can include, an issue that will eventually need resolution to encompass the richness of provenance information required for daata intercomparison and merging.

Lynnes, Chris↗

NASA NTRS2007

Defining the Core Archive Data Standards of the International Planetary Data Alliance (IPDA)

A goal of the International Planetary Data Alliance (lPDA) is to develop a set of archive data standards that enable the sharing of scientific data across international agencies and missions. To help achieve this goal, the IPDA steering committee initiated a six month proj ect to write requirements for and draft an information model based on the Planetary Data System (PDS) archive data standards. The project had a special emphasis on data formats. A set of use case scenarios were first developed from which a set of requirements were derived for the IPDA archive data standards. The special emphasis on data formats was addressed by identifying data formats that have been used by PDS nodes and other agencies in the creation of successful data sets for the Planetary Data System (PDS). The dependency of the IPDA information model on the PDS archive standards required the compilation of a formal specification of the archive standards currently in use by the PDS. An ontology modelling tool was chosen to capture the information model from various sources including the Planetary Science Data Dictionary [I] and the PDS Standards Reference [2]. Exports of the modelling information from the tool database were used to produce the information model document using an object-oriented notation for presenting the model. The tool exports can also be used for software development and are directly accessible by semantic web applications.

ontology↗

NASA NTRS2008

An Ontology-Based Archive Information Model for the Planetary Science Community

The Planetary Data System (PDS) information model is a mature but complex model that has been used to capture over 30 years of planetary science data for the PDS archive. As the de-facto information model for the planetary science data archive, it is being adopted by the International Planetary Data Alliance (IPDA) as their archive data standard. However, after seventeen years of evolutionary change the model needs refinement. First a formal specification is needed to explicitly capture the model in a commonly accepted data engineering notation. Second, the core and essential elements of the model need to be identified to help simplify the overall archive process. A team of PDS technical staff members have captured the PDS information model in an ontology modeling tool. Using the resulting knowledge-base, work continues to identify the core elements, identify problems and issues, and then test proposed modifications to the model. The final deliverables of this work will include specifications for the next generation PDS information model and the initial set of IPDA archive data standards. Having the information model captured in an ontology modeling tool also makes the model suitable for use by Semantic Web applications.

Information Model↗

NASA NTRS2018

ESIP Documentation Cluster Session: GCMD Keyword Update

The Global Change Master Directory (GCMD) Keywords are a hierarchical set of controlled Earth Science vocabularies that help ensure Earth science data and services are described in a consistent and comprehensive manner and allow for the precise searching of collection-level metadata and subsequent retrieval of data and services. Initiated over twenty years ago, the GCMD Keywords are periodically analyzed for relevancy and will continue to be refined and expanded in response to user needs. This talk explores the current status of the GCMD keywords, the value and usage that the keywords bring to different tools/agencies as it relates to data discovery, and how the keywords relate to SWEET (Semantic Web for Earth and Environmental Terminology) Ontologies.

data discover↗

NASA NTRS2015

The Open Data Repository's Data Publisher

We have quickly gathered a diverse set of databases that have significant activity. Researchers are using them on a daily basis from collection through all phases of research. Focus on: (1) Linked data and semantic web integration are fundamental to our long term plans. (2) Citation system is critical before our first full release. Snapshot-based citation generation for data sets or objects. As we expand our feature set, expect the system will: (1) Provide a very high level of provenance for any data housed in the software. (2) Make data management beneficial to the researcher throughout the research process. (3) Create living archives that allow citable snapshots of data and summaries of the changes since the snapshot was created.

Stone, N.↗

NASA NTRS2016

Ontologies for Aviation Data Management

Managing complex aviation data can be a significant challenge for any enterprise – whether a government agency, airline, airframe manufacturer, or aviation service provider. To handle this challenge, data models are typically developed to characterize and manage the data generated, used, and stored by a given enterprise. Unfortunately, different data providers employ qualitatively different data models, and this gives rise to problems exchanging data across organizational boundaries. Over the past decade, these problems have motivated data producers and consumers to look toward standardized data exchange models to address data interoperability. In this paper we examine some of these standardized data exchange models and compare them with a new type of data model based on ontologies. Ontology models have emerged in recent years from a confluence of research in the artificial intelligence, semantic web, and information science communities. This paper introduces ontology models, provides several use cases for ontologies relevant to aviation data management, and summarizes state of the art aviation prototype applications that utilize ontologies.

artificial intelligence↗

NASA NTRSDate not supplied

Modeling Atmospheric Science Knowledge from Research Publications

NASA Earth Science Data Centers contain enormous amounts of remote sensing digital data. It is often a significant challenge for users to find data suitable for their research topic in these vast archives. One of the approaches is the usage-driven dataset discovery, where users seek publications on projects similar to their intended study. For this approach to be effective, users need a clear connection between the underlying data in the publications and the study objectives; this is not often apparent to non-expert users. Tools and methodologies that can help facilitate and organize these connections are therefore valuable for creating improved knowledge mappings, which can be further used by search engines to suggest data or publications best tailored to a user’s specific research goal. As an illustration of these challenges, in this work we focus on the atmospheric chemistry processes related to Earth environmental impacts such as ozone depletion, aerosols, smog formation, acid rain, and radiative forcing. We further limit our study to publications that use data from the Microwave Limb Sounder (MLS) instrument flown on the Aura Earth Observing System. To create knowledge representations of science carried out in these publications, we use existing ontologies such as the Global Change Master Directory (GCMD) and Semantic Web for Earth and Environmental Terminology (SWEET). These ontologies together encompass term dictionaries that include measured variables, names of molecules or radicals, mission and instrument names, locations, action words, among many others. Based on these terms acknowledge graph database was populated with the terms retrieved from scientific publications that study atmospheric chemistry. These databases can be used to further enhance the automation of knowledge discovery and facilitate machine learning and artificial intelligence algorithms or applications. These tools and methods can also be extended to apply to content from other related Earth science domains.

Irina Gerasimov↗