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UMLS users and uses: a current overview

Abstract The US National Library of Medicine regularly collects summary data on direct use of Unified Medical Language System (UMLS) resources. The summary data sources include UMLS user registration data, required annual reports submitted by registered users, and statistics on downloads and application programming interface calls. In 2019, the National Library of Medicine analyzed the summary data on 2018 UMLS use. The library also conducted a scoping review of the literature to provide additional intelligence about the research uses of UMLS as input to a planned 2020 review of UMLS production methods and priorities. 5043 direct users of UMLS data and tools downloaded 4402 copies of the UMLS resources and issued 66 130 951 UMLS application programming interface requests in 2018. The annual reports and the scoping review results agree that the primary UMLS uses are to process and interpret text and facilitate mapping or linking between terminologies. These uses align with the original stated purpose of the UMLS.

Amos, Liz↗

Unified Medical Language System resources improve sieve-based generation and Bidirectional Encoder Representations from Transformers (BERT)–based ranking for concept normalization

Concept normalization, the task of linking phrases in text to concepts in an ontology, is useful for many downstream tasks including relation extraction, information retrieval, etc. We present a generate-and-rank concept normalization system based on our participation in the 2019 National NLP Clinical Challenges Shared Task Track 3 Concept Normalization. The shared task provided 13 609 concept mentions drawn from 100 discharge summaries. We first design a sieve-based system that uses Lucene indices over the training data, Unified Medical Language System (UMLS) preferred terms, and UMLS synonyms to generate a list of possible concepts for each mention. We then design a listwise classifier based on the BERT (Bidirectional Encoder Representations from Transformers) neural network to rank the candidate concepts, integrating UMLS semantic types through a regularizer. Our generate-and-rank system was third of 33 in the competition, outperforming the candidate generator alone (81.66% vs 79.44%) and the previous state of the art (76.35%). During postevaluation, the model’s accuracy was increased to 83.56% via improvements to how training data are generated from UMLS and incorporation of our UMLS semantic type regularizer. Analysis of the model shows that prioritizing UMLS preferred terms yields better performance, that the UMLS semantic type regularizer results in qualitatively better concept predictions, and that the model performs well even on concepts not seen during training. Our generate-and-rank framework for UMLS concept normalization integrates key UMLS features like preferred terms and semantic types with a neural network–based ranking model to accurately link phrases in text to UMLS concepts.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Selecting representative geological realizations to model subsurface CO 2 storage under uncertainty

Carbon capture and storage (CCS) is one of the quickest and most effective solutions for reducing carbon emissions. The majority of subsurface storage occurs in saline aquifers, for which geological information is lacking which in turn results in geological uncertainty. To evaluate uncertainty in CO 2 injection projections, the use of multiple geological realizations (GRs) has been practiced very commonly. In this approach, hundreds or thousands of high-resolution GRs is used that quickly becomes computationally expensive. This issue can be addressed with representative geological realizations (RGRs) that preserve the uncertainty domain of the ensemble GRs. Here, in this study, we propose the use of unsupervised machine learning (UML) frameworks, including dissimilarity measurement, dimensionality reduction, clustering and sampling algorithms ta select a predetermined number of RGRs. We compare the simulation outputs of the RGR sets and the ensemble using the Kolmogorov–Smirnov (KS) test to select the best UML. The UML frameworks and their associated selection processes are evaluated using a saline aquifer with a single CO 2 injection well and 200 GRs with varying uncertain petrophysical characteristics. The best UML framework is selected to use only 5% of the GRs while maintaining the uncertainty domain of the ensemble GRs. In addition, the best UML framework is tested using a saline aquifer with three CO 2 injection wells and varied GRs. The results show that our proposed UML framework can be used to choose RGRs, capturing the whole uncertainty domain. Our approach leads to a significant reduction in the computational cost associated with scenario testing, decision-making, and development planning for CO 2 storage sites under geological uncertainty.

58 GEOSCIENCES↗

Sequence Diagrams & PFMEA Table - VGI [SWR-25-107]

As part of the VGI work under the National Charging Experience (ChargeX) Consortium, reliability analysis of communication interfaces for multiple SCM/VGI use-cases was performed using a Process Failure Modes and Analysis (PFMEA) style framework. This repository hosts all the relevant files for each of these use-cases which include: *A visual representation of their communication architecture: Image file (.png) *UML sequence diagram: Plant-UML source file (.puml). Visio file (.vsdx) and image file (.png) derived from the UML sourceX` *The PFMEA table: Excel file (.xlsx) These files are meant to serve as a starting point and can be adapted to company / organization specific SCM implementation.

Gadamsetty, Pranav [National Renewable Energy Labo↗

A pre-training and self-training approach for biomedical named entity recognition

Named entity recognition (NER) is a key component of many scientific literature mining tasks, such as information retrieval, information extraction, and question answering; however, many modern approaches require large amounts of labeled training data in order to be effective. This severely limits the effectiveness of NER models in applications where expert annotations are difficult and expensive to obtain. In this work, we explore the effectiveness of transfer learning and semi-supervised self-training to improve the performance of NER models in biomedical settings with very limited labeled data (250-2000 labeled samples). We first pre-train a BiLSTM-CRF and a BERT model on a very large general biomedical NER corpus such as MedMentions or Semantic Medline, and then we fine-tune the model on a more specific target NER task that has very limited training data; finally, we apply semi-supervised self-training using unlabeled data to further boost model performance. We show that in NER tasks that focus on common biomedical entity types such as those in the Unified Medical Language System (UMLS), combining transfer learning with self-training enables a NER model such as a BiLSTM-CRF or BERT to obtain similar performance with the same model trained on 3x-8x the amount of labeled data. We further show that our approach can also boost performance in a low-resource application where entities types are more rare and not specifically covered in UMLS.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Uncertainty Quantification in CO2 Trapping Mechanisms: A Case Study of PUNQ-S3 Reservoir Model Using Representative Geological Realizations and Unsupervised Machine Learning

Evaluating uncertainty in CO2 injection projections often requires numerous high-resolution geological realizations (GRs) which, although effective, are computationally demanding. This study proposes the use of representative geological realizations (RGRs) as an efficient approach to capture the uncertainty range of the full set while reducing computational costs. A predetermined number of RGRs is selected using an integrated unsupervised machine learning (UML) framework, which includes Euclidean distance measurement, multidimensional scaling (MDS), and a deterministic K-means (DK-means) clustering algorithm. In the context of the intricate 3D aquifer CO2 storage model, PUNQ-S3, these algorithms are utilized. The UML methodology selects five RGRs from a pool of 25 possibilities (20% of the total), taking into account the reservoir quality index (RQI) as a static parameter of the reservoir. To determine the credibility of these RGRs, their simulation results are scrutinized through the application of the Kolmogorov–Smirnov (KS) test, which analyzes the distribution of the output. In this assessment, 40 CO2 injection wells cover the entire reservoir alongside the full set. The end-point simulation results indicate that the CO2 structural, residual, and solubility trapping within the RGRs and full set follow the same distribution. Simulating five RGRs alongside the full set of 25 GRs over 200 years, involving 10 years of CO2 injection, reveals consistently similar trapping distribution patterns, with an average value of Dmax of 0.21 remaining lower than Dcritical (0.66). Using this methodology, computational expenses related to scenario testing and development planning for CO2 storage reservoirs in the presence of geological uncertainties can be substantially reduced.

Mahjour, Seyed Kourosh↗

Blockchain smart contracts for energy markets

A successful architecture that depicts the relationship between the energy market engineering requirements and blockchain requirements (shown as enablers). Software includes sequential and relational architectures supported by the UML flow diagrams. For a successful blockchain agnostic implementation of energy markets, the proposed architecture/blueprint supported by prototype implementation is very efficient. The proposed invention also depicts various means of the use of blockchain technology for energy market systems.

Gourisetti, Sri Nikhil Gupta↗

Enabling Data Exchange and Data Integration with the Common Information Model: An Introduction for Power Systems Engineers and Application Developers

The Common Information Model (CIM) is an open-source information model that is used to model an electrical network and the various equipment used on the network. CIM is widely used for data exchange of bulk transmission power systems and is finding increasing use for distribution systems. Use of a non-proprietary information model (such as CIM) that has been agreed upon and adopted by numerous utilities, vendors, and researchers allows significant reduction in the effort and cost of data integration. Likewise, adoption of open data platforms built around the CIM increases available functionalities for managing and optimizing the smart grid of the future. This report is intended as an introduction to CIM for utility engineers, power systems researchers, and application developers, providing a broad view of the CIM and how particular profiles can be adapted for various use cases. Unlike most other CIM introduction documents and the International Electrotechnical Commission (IEC) standards (which are mostly targeted to an audience of data scientists, enterprise database managers, and platform developers), this report is intended for users of traditional power systems analysis software and other readers without any prior experience with canonical information models, data profiles, or UML modeling.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Smart Contract Architectures and Templates for Blockchain-based Energy Markets (V.1.0)

Within the field of Transactive Energy Systems (TES), there is an active need for tools that can support and accelerate the development of these new grid solutions. Among the many tools available, blockchain stands out as a viable instrument that can help researchers develop decentralized, autonomous, and tamper-resistant grid applications. In this work, we explore the use of smart contracts (SCs), a subset of blockchain technology, and analyze their applicability to facilitating the implementation of TES solutions. In particular, we focus on presenting areas of opportunity and potential drawbacks, along with use cases that can benefit from this technology building upon previous research developed by Pacific Northwest National Laboratory and other research organizations. This work builds upon the fundamentals of TES and smart contract technology to develop a series of software templates that can be used by industry to build TES-oriented grid solutions. These templates are intended to be platform agnostic and take into consideration the unique properties of SCs and distributed ledger storage mechanisms to ensure actual code implementations remain aware of the limitations of the technology. The proposed templates have the potential to enable software architects to mix and match components to satisfy their application requirements, thereby reducing the number of resources required to implement blockchain-based solutions. These templates are divided into two main components—data and behavioral models. The data models are intended to help software engineers represent the underlying grid objects along with their properties in a ledger-based storage system. The behavioral models are used to describe the processes and actions that actors within a system must perform to achieve a given outcome such as registering an asset, placing a bid, and performing bid clearances. These two components are documented in a Unified Modeling Language (UML) format and are intended for use in SC-based implementations, with special behavioral considerations to account for the asynchronous properties of the underlying ledger and the typical execution model of smart contracts. Finally, future research ideas and potential extensions to this work are discussed. In particular, known limitations and potential improvements of the developed product are identified and expected to be addressed in future revisions of the template model.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Development of Low-Cost, High-Performance, Easy-To-Apply, Non-Flammable, Inorganic Phase Change Material (PCM) Technology (Project Final Report)

This report describes a 45-months long research program focused on the development of novel, easy-to-apply, non-flammable, and high-performance inorganic phase change materials (PCMs) for building and industrial applications. The University of Massachusetts Lowell (UML) formed a world-class team consisting of researchers form InsolCorp (only N. American manufacturer of inorganic PCM systems for building applications), and a group of industrial advisors, to develop a universal/multipurpose, simple-to-manufacture and cost-effective PCM technology. The project team expects that the results of this work will spur in the future the adoption of thermal storage materials – a key building energy saving technology as identified by DOE BTO – for a variety of building envelope applications. The main goal of this project was to demonstrate a suite of low-cost, multipurpose, and durable inorganic PCM formulations with phase transition temperatures encompassing typical building applications (between +5 o C and +55 o C). The first objective was to design, fabricate, and experimentally validate a performance of inexpensive, durable, highly efficient, non-flammable, and easy to manufacture PCMs. To allow a variety of building applications, the project team focused on formulations that exhibit repeatable phase transitions between +5 o C and +55 o C. To follow the DOE BTO cost efficiency target without compromising thermal performance, our work was based on inorganic compounds (mostly salt hydrates) and their blends, which represent a fraction of the cost of most of organic PCMs with about twice as high density as well as significantly higher thermal conductivity and phase change enthalpy. The second objective was to develop easy-to-manufacture and -install packaging/encapsulation designs that are 1) a superior barrier to current state-of-the-art macro-packaging, which significantly reduces the risk of loss of hydration water and PCM leak, and 2) optimal in enhancing the heat exchange rates with the surroundings and within the PCM core to ensure complete charging/discharging of the entire PCM within the product. Finally, the project’s intend was to scale-up the fabrication process to demonstrate installation on system-scale applications, and to validate the performance under field conditions. This work aimed at developing low-cost, high-energy storage, and reliable latent heat storage technology for building applications. This development was realized by formulating and integrating the following two technology components: 1) inorganic salt hydrate based PCMs that have high latent enthalpies and are low-cost and durable, and 2) PCM encapsulation (packaging) technology that maximizes PCM concentration and enhances heat transport characteristics in the product and with the external environment/materials. High thermal storage capacity, low cost and fire resistance are key to the building market entry for PCM technology. Therefore, the project’s focus was on salt-hydrate-based formulations which satisfy all these criteria. Packaging and/or encapsulation of PCM is a key processing step. The project team recognized that a low-cost and simple-to-manufacture salt hydrate-based PCM technology holds the best chance to be successful in the building construction market, a market which is traditionally extremely sensitive to cost and where commodity thermal insulations are the benchmark for envelope-related energy saving measures. That is why, in this project, the main intention was to minimize the production cost and maximize the product energy storage density without sacrificing the PCM performance. It was achieved through: 1. Minimizing the non-PCM components (plastics, additives, packaging/encapsulation materials, etc.) because they are significantly more expensive than salt hydrates, 2. Using highly thermally conductive and lightweight PCM carrier (packaging material) to facilitate more complete phase cycling, and 3. Optimizing the thickness and minimizing air spaces in product design (such as in pouched PCM). For this purpose, our approach was to enable an easy system design, including selection of the PCM operating temperatures, optimizing the necessary heat storage capacity (by stacking together several layers of PCM products), and if needed, a synchronized usage of PCM products of different temperatures. A specially designed, robust, highly thermally conducting and highly impermeable packaging (to retain salt hydrate water during phase transition cycles) was designed and tested to increase the overall system thermal performance and durability. All PCM products developed during this project were tested in both lab scale and in full scale field conditions. It is expected that, after further developments and commercialization, the developed PCM technologies may be also applied in space conditioning, energy storage technologies, and heat transfer applications.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Visual Modeling for Complex System Valuation: Implementation Guidance

Within the Transactive Systems Program (TSP) at Pacific Northwest National Laboratory (PNNL) the need to incorporate a valuation analysis design early within the research process of transactive energy systems led to development of a valuation methodology. This methodology allows the modeling of economic exchanges within a complex system and supports the evaluation of individual stakeholder economic outcomes in addition to systemwide costs and benefits. The use of visual modeling practices enables the research team to reach common understanding and agreement on the analysis design within the complex system. While this methodology was developed for the valuation of transactive energy systems, it can be applied to any complex system where a granular economic analysis is desired. It allows for the inclusion of equity analyses and ties individual activities and microeconomic outcomes with the systemwide macroeconomic impacts. This document serves as implementation guidance for analysts planning to deploy the methodology within a research study. The appendixes provide specific guidance on how this methodology is deployed within the TSP at PNNL for analysts seeking guidance for deployment within that context.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗