ReactomeGSA: new features to simplify public data reuse.

MOTIVATION: ReactomeGSA is part of the Reactome knowledgebase and one of the leading multi-omics pathway analysis platforms. ReactomeGSA provides access to quantitative pathway analysis methods supporting different 'omics data types. Additionally, ReactomeGSA can process different datasets simultaneously, leading to a comparative pathway analysis that can also be performed across different species. RESULTS: We present a major update to the ReactomeGSA analysis platforms that greatly simplifies the reuse and direct integration of public data. In order to increase the number of available datasets, we developed the new grein_loader Python application that can directly fetch experiments from the GREIN resource. This enabled us to support both EMBL-EBI's Expression Atlas and GEO RNA-seq Experiments Interactive Navigator within ReactomeGSA. To further increase the visibility and simplify the reuse of public datasets, we integrated a novel search function into ReactomeGSA that enables users to search for public datasets across both supported resources. Finally, we completely re-developed ReactomeGSA's web-frontend and R/Bioconductor package to support the new search and loading features, and greatly simplify the use of ReactomeGSA. AVAILABILITY AND IMPLEMENTATION: The new ReactomeGSA web frontend is available at https://www.reactome.org/gsa with an built-in, interactive tutorial. The ReactomeGSA R package (https://bioconductor.org/packages/release/bioc/html/ReactomeGSA.html) is available through Bioconductor and shipped with detailed documentation and vignettes. The grein_loader Python application is available through the Python Package Index (pypi). The complete source code for all applications is available on GitHub at https://github.com/grisslab/grein_loader and https://github.com/reactome.

An Expert-Knowledge-Based Graph Convolutional Network for Skeleton- Based Physical Rehabilitation Exercises Assessment.

Physical therapists play a crucial role in guiding patients through effective and safe rehabilitation processes according to medical guidelines. However, due to the therapist-patient imbalance, it is neither economical nor feasible for therapists to provide guidance to every patient during recovery sessions. Automated assessment of physical rehabilitation can help with this problem, but accurately quantifying patients' training movements and providing meaningful feedback poses a challenge. In this paper, an Expert-knowledge-based Graph Convolutional approach is proposed to automate the assessment of the quality of physical rehabilitation exercises. This approach utilizes experts' knowledge to improve the spatial feature extraction ability of the Graph Convolutional module and a Gated pooling module for feature aggregation. Additionally, a Transformer module is employed to capture long-range temporal dependencies in the movements. The attention scores and weight matrix obtained through this approach can serve as interpretability tools to help therapists understand the assessment model and assist patients in improving their exercises. The effectiveness of the proposed method is verified on the KIMORE dataset, achieving state-of-the-art performance compared to existing models. Experimental results also illustrate the interpretability of the method in both spatial and temporal dimensions.

The development of an EU-wide nutrition and physical activity expert knowledge base to support a personalised mobile application across various EU population groups.

A healthy lifestyle comprising regular physical activity and an adequate diet is imperative for the prevention of non-communicable diseases such as hypertension and some cancers. Advances in information computer technology offer the opportunity to provide personalised lifestyle advice directly to the individual through devices such as smartphones or tablets. The overall aim of the PROTEIN project (Wilson-Barnes et al., 2021) was to develop a smartphone application that could provide tailored and dynamic nutrition and physical activity advice directly to the individual in real time. However, to create this mobile health (m-health) smartphone application, a knowledge base of reference ranges for macro-/micronutrient intake, anthropometry, biochemical, physiological and sleep parameters was required to underpin the parameters of the recommender systems. Therefore, the principal aim of this emerging research paper is to describe the process by which experts in nutrition and physiology from the PROTEIN consortium collaborated to develop the nutritional and physical activity requirements, based upon existing recommendations, for 10 separate population groups living within the EU including, but not limited to healthy adults, adults with type 2 diabetes mellitus, cardiovascular disease, excess weight, obesity and iron deficiency anaemia. A secondary aim is to describe the development of a library of 24-h meal plans appropriate for the same groups and also encompassing various dietary preferences and allergies. Overall, the consortium devised an extensive nutrition and physical activity knowledge base that is pertinent to 10 separate EU user groups, is available in 7 different languages and is practically implemented via a library of culturally appropriate, 24-h meal plans.

On the necessity of specialized knowledge-based models for SBRT prostate treatments plans.

PURPOSE: Test whether a well-grounded KBP model trained on moderately hypo-fractionated prostate treatments can be used to satisfactorily drive the optimization of SBRT prostate treatments. MATERIALS AND METHODS: A KBP model (SBRT-model) was developed, trained and validated using the first forty-seven clinically treated VMAT SBRT prostate plans (42.7 Gy/7fx or 36.25 Gy/5fx). The performance and robustness of this model were compared against a high-quality KBP-model (ST-model) that was already clinically adopted for hypo-fractionated (70 Gy/28fx and 60 Gy/20fx) prostate treatments. The two models were compared in terms of their predictions robustness, and the quality of their outcomes were evaluated against a set of reference clinical SBRT plans. Plan quality was assessed using DVH metrics, blinded clinical ranking, and a dedicated Plan Quality Metric algorithm. RESULTS: The plan libraries of the two models were found to share a high degree of anatomical similarity. The overall quality (APQM%) of the plans obtained both with the ST- and SBRT-models was compatible with that of the original clinical plans, namely (93.7 ± 4.1)% and (91.6 ± 3.9)% vs (92.8.9 ± 3.6)%. Plans obtained with the ST-model showed significantly higher target coverage (PTV V95%): (97.9 ± 0.8)% vs (97.1 ± 0.9)% (p < 0.05). Conversely, plans optimized following the SBRT-model showed a small but not-clinically relevant increase in OAR sparing. ST-model generally provided more reliable predictions than SBRT-model. Two radiation oncologists judged as equivalent the plans based on the KBP prediction, which was also judged better that reference clinical plans. CONCLUSION: A KBP model trained on moderately fractionated prostate treatment plans provided optimal SBRT prostate plans, with similar or larger plan quality than an embryonic SBRT-model based on a limited number of cases.

CyclicPepedia: a knowledge base of natural and synthetic cyclic peptides.

Cyclic peptides offer a range of notable advantages, including potent antibacterial properties, high binding affinity and specificity to target molecules, and minimal toxicity, making them highly promising candidates for drug development. However, a comprehensive database that consolidates both synthetically derived and naturally occurring cyclic peptides is conspicuously absent. To address this void, we introduce CyclicPepedia (https://www.biosino.org/iMAC/cyclicpepedia/), a pioneering database that encompasses 8744 known cyclic peptides. This repository, structured as a composite knowledge network, offers a wealth of information encompassing various aspects of cyclic peptides, such as cyclic peptides' sources, categorizations, structural characteristics, pharmacokinetic profiles, physicochemical properties, patented drug applications, and a collection of crucial publications. Supported by a user-friendly knowledge retrieval system and calculation tools specifically designed for cyclic peptides, CyclicPepedia will be able to facilitate advancements in cyclic peptide drug development.

An open source knowledge graph ecosystem for the life sciences.

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoint resources and abstraction algorithms), and benchmarks (e.g., prebuilt KGs). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 different large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability.

Determining the library size for the optimal output plan in the RapidPlan knowledge-based planning system using multicriteria optimization.

OBJECTIVES: The aim of this study was to determine the number of trade-off explored (TO) library plans required for building a RapidPlan (RP) library that would generate the optimal clinical treatment plan. METHODS: We developed 2 RP models, 1 each for the 2 clinical sites, head and neck (HN) and cervix. The models were created using 100 plans and were validated using 70 plans (VP) for each site respectively. Each of the 2 libraries comprising 100 TO plans was divided into 5 different subsets of library plans comprising 20, 40, 60, 80, and 100 plans, leading to 5 different RP models for each site. For every validation patient, a TO plan (TO_VP) was created. For every patient, 5 RP plans were automatically generated using RP models. The dosimetric parameters of the 6 plans (TO_VP + 5 RP plans) were compared using Pearson correlation and Greenhouse-Geisser analysis. RESULTS: Planning target volume (PTV) dose volume parameters PTVD95% in 6 competing plans varied between 97.6 ± 0.7% and 98.1 ± 0.6% in HN cases and 98.8 ± 0.3% and 99.0 ± 0.4% in cervix cases. Overall, for both sites, the mean variations in organ at risk (OAR) doses or volumes were within 50 cGy, 0.5%, and 0.2 cc between library plans, and if TO_VP was included the variations deteriorated to 180 cGy, 0.4%, and 15 cc. All OARs in both sites, except D0.1 ccspine, showed a statistically insignificant variation between all plans. CONCLUSIONS: Dosimetric variation among various output plans generated from 5 RP libraries is minimal and clinically insignificant. The optimal output plan can be derived from the least-weighted library consisting of 20 plans. ADVANCES IN KNOWLEDGE: This article shows that, when the constituent plans are subjected to trade-off exploration, the number of constituent plans for a knowledge-based planning module is not relevant in terms of its dosimetric output.

The Alzheimer's Knowledge Base: A Knowledge Graph for Alzheimer Disease Research.

BACKGROUND: As global populations age and become susceptible to neurodegenerative illnesses, new therapies for Alzheimer disease (AD) are urgently needed. Existing data resources for drug discovery and repurposing fail to capture relationships central to the disease's etiology and response to drugs. OBJECTIVE: We designed the Alzheimer's Knowledge Base (AlzKB) to alleviate this need by providing a comprehensive knowledge representation of AD etiology and candidate therapeutics. METHODS: We designed the AlzKB as a large, heterogeneous graph knowledge base assembled using 22 diverse external data sources describing biological and pharmaceutical entities at different levels of organization (eg, chemicals, genes, anatomy, and diseases). AlzKB uses a Web Ontology Language 2 ontology to enforce semantic consistency and allow for ontological inference. We provide a public version of AlzKB and allow users to run and modify local versions of the knowledge base. RESULTS: AlzKB is freely available on the web and currently contains 118,902 entities with 1,309,527 relationships between those entities. To demonstrate its value, we used graph data science and machine learning to (1) propose new therapeutic targets based on similarities of AD to Parkinson disease and (2) repurpose existing drugs that may treat AD. For each use case, AlzKB recovers known therapeutic associations while proposing biologically plausible new ones. CONCLUSIONS: AlzKB is a new, publicly available knowledge resource that enables researchers to discover complex translational associations for AD drug discovery. Through 2 use cases, we show that it is a valuable tool for proposing novel therapeutic hypotheses based on public biomedical knowledge.

The biomarkers ATLAS: An audit on 1100 non-small cell lung cancer from an Italian knowledge-based database.

AIMS: To date, precision medicine has revolutionized the clinical management of Non-Small Cell Lung Cancer (NSCLC). International societies approved a rapidly improved mandatory testing biomarkers panel for the clinical stratification of NSCLC patients, but harmonized procedures are required to optimize the diagnostic workflow. In this context a knowledge-based database (Biomarkers ATLAS, https://biomarkersatlas.com/) was developed by a supervising group of expert pathologists and thoracic oncologists collecting updated clinical and molecular records from about 80 referral Italian institutions. Here, we audit molecular and clinical data from n = 1100 NSCLC patients collected from January 2019 to December 2020. METHODS: Clinical and molecular records from NSCLC patients were retrospectively collected from the two coordinating institutions (University of Turin and University of Naples). Molecular biomarkers (KRAS, EGFR, BRAF, ROS1, ALK, RET, NTRK, MET) and clinical data (sex, age, histological type, smoker status, PD-L1 expression, therapy) were collected and harmonized. RESULTS: Clinical and molecular data from 1100 (n = 552 mutated and n = 548 wild-type) NSCLC patients were systematized and annotated in the ATLAS knowledge-database. Molecular records from biomarkers testing were matched with main patients' clinical variables. CONCLUSIONS: Biomarkers ATLAS (https://biomarkersatlas.com/) represents a unique, easily managing, and reliable diagnostic tool aiming to integrate clinical records with molecular alterations of NSCLC patients in the real-word Italian scenario.

Knowledge-based planning for Gamma Knife.

BACKGROUND: Current methods for Gamma Knife (GK) treatment planning utilizes either manual forward planning, where planners manually place shots in a tumor to achieve a desired dose distribution, or inverse planning, whereby the dose delivered to a tumor is optimized for multiple objectives based on established metrics. For other treatment modalities like IMRT and VMAT, there has been a recent push to develop knowledge-based planning (KBP) pipelines to address the limitations presented by forward and inverse planning. However, no complete KBP pipeline has been created for GK. PURPOSE: To develop a novel (KBP) pipeline, using inverse optimization (IO) with 3D dose predictions for GK. METHODS: Data were obtained for 349 patients from Sunnybrook Health Sciences Centre. A 3D dose prediction model was trained using 322 patients, based on a previously published deep learning methodology, and dose predictions were generated for the remaining 27 out-of-sample patients. A generalized IO model was developed to learn objective function weights from dose predictions. These weights were then used in an inverse planning model to generate deliverable treatment plans. A dose mimicking (DM) model was also implemented for comparison. The quality of the resulting plans was compared to their clinical counterparts using standard GK quality metrics. The performance of the models was also characterized with respect to the dose predictions. RESULTS: Across all quality metrics, plans generated using the IO pipeline performed at least as well as or better than the respective clinical plans. The average conformity and gradient indices of IO plans was 0.737 ± $\pm$ 0.158 and 3.356 ± $\pm$ 1.030 respectively, compared to 0.713 ± $\pm$ 0.124 and 3.452 ± $\pm$ 1.123 for the clinical plans. IO plans also performed better than DM plans for five of the six quality metrics. Plans generated using IO also have average treatment times comparable to that of clinical plans. With regards to the dose predictions, predictions with higher conformity tend to result in higher quality KBP plans. CONCLUSIONS: Plans resulting from an IO KBP pipeline are, on average, of equal or superior quality compared to those obtained through manual planning. The results demonstrate the potential for the use of KBP to generate GK treatment with minimal human intervention.

EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing.

The lengthy and expensive process of developing new drugs from scratch, coupled with a high failure rate, has prompted the emergence of drug repurposing/repositioning as a more efficient and cost-effective approach. This approach involves identifying new therapeutic applications for existing approved drugs, leveraging the extensive drug-related data already gathered. However, the diversity and heterogeneity of data, along with the limited availability of known drug-disease interactions, pose significant challenges to computational drug design. To address these challenges, this study introduces EKGDR, an end-to-end knowledge graph-based approach for computational drug repurposing. EKGDR utilizes the power of a drug knowledge graph, a comprehensive repository of drug-related information that encompasses known drug interactions and various categorization information, as well as structural molecular descriptors of drugs. EKGDR employs graph neural networks, a cutting-edge graph representation learning technique, to embed the drug knowledge graph (nodes and relations) in an end-to-end manner. By doing so, EKGDR can effectively learn the underlying causes (intents) behind drug-disease interactions and recursively aggregate and combine relational messages between nodes along different multihop neighborhood paths (relational paths). This process generates representations of disease and drug nodes, enabling EKGDR to predict the interaction probability for each drug-disease pair in an end-to-end manner. The obtained results demonstrate that EKGDR outperforms previous models in all three evaluation metrics: area under the receiver operating characteristic curve (AUROC = 0.9475), area under the precision-recall curve (AUPRC = 0.9490), and recall at the top-200 recommendations (Recall@200 = 0.8315). To further validate EKGDR's effectiveness, we evaluated the top-20 candidate drugs suggested for each of Alzheimer's and Parkinson's diseases.

Bayesian-knowledge driven ontologies: A framework for fusion of semantic knowledge under uncertainty and incompleteness.

The modeling of uncertain information is an open problem in ontology research and is a theoretical obstacle to creating a truly semantic web. Currently, ontologies often do not model uncertainty, so stochastic subject matter must either be normalized or rejected entirely. Because uncertainty is omnipresent in the real world, knowledge engineers are often faced with the dilemma of performing prohibitively labor-intensive research or running the risk of rejecting correct information and accepting incorrect information. It would be preferable if ontologies could explicitly model real-world uncertainty and incorporate it into reasoning. We present an ontology framework which is based on a seamless synthesis of description logic and probabilistic semantics. This synthesis is powered by a link between ontology assertions and random variables that allows for automated construction of a probability distribution suitable for inferencing. Furthermore, our approach defines how to represent stochastic, uncertain, or incomplete subject matter. Additionally, this paper describes how to fuse multiple conflicting ontologies into a single knowledge base that can be reasoned with using the methods of both description logic and probabilistic inferencing. This is accomplished by using probabilistic semantics to resolve conflicts between assertions, eliminating the need to delete potentially valid knowledge and perform consistency checks. In our framework, emergent inferences can be made from a fused ontology that were not present in any of the individual ontologies, producing novel insights in a given domain.

Centralized Interactive Phenomics Resource: an integrated online phenomics knowledgebase for health data users.

OBJECTIVE: Development of clinical phenotypes from electronic health records (EHRs) can be resource intensive. Several phenotype libraries have been created to facilitate reuse of definitions. However, these platforms vary in target audience and utility. We describe the development of the Centralized Interactive Phenomics Resource (CIPHER) knowledgebase, a comprehensive public-facing phenotype library, which aims to facilitate clinical and health services research. MATERIALS AND METHODS: The platform was designed to collect and catalog EHR-based computable phenotype algorithms from any healthcare system, scale metadata management, facilitate phenotype discovery, and allow for integration of tools and user workflows. Phenomics experts were engaged in the development and testing of the site. RESULTS: The knowledgebase stores phenotype metadata using the CIPHER standard, and definitions are accessible through complex searching. Phenotypes are contributed to the knowledgebase via webform, allowing metadata validation. Data visualization tools linking to the knowledgebase enhance user interaction with content and accelerate phenotype development. DISCUSSION: The CIPHER knowledgebase was developed in the largest healthcare system in the United States and piloted with external partners. The design of the CIPHER website supports a variety of front-end tools and features to facilitate phenotype development and reuse. Health data users are encouraged to contribute their algorithms to the knowledgebase for wider dissemination to the research community, and to use the platform as a springboard for phenotyping. CONCLUSION: CIPHER is a public resource for all health data users available at https://phenomics.va.ornl.gov/ which facilitates phenotype reuse, development, and dissemination of phenotyping knowledge.

Empowering personalized pharmacogenomics with generative AI solutions.

OBJECTIVE: This study evaluates an AI assistant developed using OpenAI's GPT-4 for interpreting pharmacogenomic (PGx) testing results, aiming to improve decision-making and knowledge sharing in clinical genetics and to enhance patient care with equitable access. MATERIALS AND METHODS: The AI assistant employs retrieval-augmented generation (RAG), which combines retrieval and generative techniques, by harnessing a knowledge base (KB) that comprises data from the Clinical Pharmacogenetics Implementation Consortium (CPIC). It uses context-aware GPT-4 to generate tailored responses to user queries from this KB, further refined through prompt engineering and guardrails. RESULTS: Evaluated against a specialized PGx question catalog, the AI assistant showed high efficacy in addressing user queries. Compared with OpenAI's ChatGPT 3.5, it demonstrated better performance, especially in provider-specific queries requiring specialized data and citations. Key areas for improvement include enhancing accuracy, relevancy, and representative language in responses. DISCUSSION: The integration of context-aware GPT-4 with RAG significantly enhanced the AI assistant's utility. RAG's ability to incorporate domain-specific CPIC data, including recent literature, proved beneficial. Challenges persist, such as the need for specialized genetic/PGx models to improve accuracy and relevancy and addressing ethical, regulatory, and safety concerns. CONCLUSION: This study underscores generative AI's potential for transforming healthcare provider support and patient accessibility to complex pharmacogenomic information. While careful implementation of large language models like GPT-4 is necessary, it is clear that they can substantially improve understanding of pharmacogenomic data. With further development, these tools could augment healthcare expertise, provider productivity, and the delivery of equitable, patient-centered healthcare services.

Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse.

Mouse Genome Informatics (MGI) is a federation of expertly curated information resources designed to support experimental and computational investigations into genetic and genomic aspects of human biology and disease using the laboratory mouse as a model system. The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are core MGI databases that share data and system architecture. MGI serves as the central community resource of integrated information about mouse genome features, variation, expression, gene function, phenotype, and human disease models acquired from peer-reviewed publications, author submissions, and major bioinformatics resources. To facilitate integration and standardization of data, biocuration scientists annotate using terms from controlled metadata vocabularies and biological ontologies (e.g. Mammalian Phenotype Ontology, Mouse Developmental Anatomy, Disease Ontology, Gene Ontology, etc.), and by applying international community standards for gene, allele, and mouse strain nomenclature. MGI serves basic scientists, translational researchers, and data scientists by providing access to FAIR-compliant data in both human-readable and compute-ready formats. The MGI resource is accessible at https://informatics.jax.org. Here, we present an overview of the core data types represented in MGI and highlight recent enhancements to the resource with a focus on new data and functionality for MGD and GXD.

Research on the relationship between CEO career variety, digital knowledge base extension, and digital transformation in the context of digital merger and acquisition: The case of China's new generation of information technology firms.

This study examines the relationship between CEO career variety, digital knowledge base extension, and digital transformation in a digital M&A context. An empirical test was conducted using regression analysis with the digital M&A events of the new generation of information technology firms in China as the research sample. The results reveal that CEO career variety has a positive effect on digital transformation in the digital M&A context and that digital knowledge-base extension plays a mediating role. Moreover, the heterogeneity impact analysis indicated that the moderating effects of geographical distance, knowledge disparity, and cultural difference between target and acquirer firms on the above relationships vary greatly: geographical distance has a negative moderating effect, cultural difference has a positive moderating effect, and the moderating effects of both geographical distance and cultural difference are realized through mediating effects, but none of the moderating effects of knowledge disparity are significant.

Detecting mental and physical disorders using multi-task learning equipped with knowledge graph attention network.

Mental and physical disorders (MPD) are inextricably linked in many medical cases; psychosomatic diseases can be induced by mental concerns and psychological discomfort can ensue from physiological diseases. However, existing medical informatics studies focus on identifying mental or physical disorders from a unilateral perspective. Consequently, no existing domain knowledge base, corpus, or detection modeling approach considers mental as well as physical aspects concurrently. This paper proposes a joint modeling approach to detect MPD. First, we crawl through online medical consultation records of patients from websites and build an MPD knowledge ontology by extracting the core conceptual features of the text. Based on the ontology, an MPD knowledge graph containing 12,673 nodes and 82,195 relations is obtained using term matching with a domain thesaurus of each concept. Subsequently, an MPD corpus with fine-grained severities (None, Mild, Moderate, Severe, Dangerous) and 8909 records is constructed by formulating MPD classification criteria and a data annotation process under the guidance of domain experts. Taking the knowledge graph and corpus as the dataset, we design a multi-task learning model to detect the MPD severity, in which a knowledge graph attention network (KGAT) is embedded to better extract knowledge features. Experiments are performed to demonstrate the effectiveness of our model. Furthermore, we employ ontology-based and centrality-based methods to discover additional potential inferred knowledge, which can be captured by KGAT so as to improve the prediction performance and interpretability of our model. Our dataset has been made publicly available, so it can be further used as a medical informatics reference in the fields of psychosomatic medicine, psychiatrics, physical co-morbidity, and so on.

Enriching the FIDEO ontology with food-drug interactions from online knowledge sources.

The increasing number of articles on adverse interactions that may occur when specific foods are consumed with certain drugs makes it difficult to keep up with the latest findings. Conflicting information is available in the scientific literature and specialized knowledge bases because interactions are described in an unstructured or semi-structured format. The FIDEO ontology aims to integrate and represent information about food-drug interactions in a structured way. This article reports on the new version of this ontology in which more than 1700 interactions are integrated from two online resources: DrugBank and Hedrine. These food-drug interactions have been represented in FIDEO in the form of precompiled concepts, each of which specifies both the food and the drug involved. Additionally, competency questions that can be answered are reviewed, and avenues for further enrichment are discussed.

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning.

MOTIVATION: Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrarily complex nested knowledge schemas. RESULTS: Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against an LLM to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for matched elements. We present examples of applying SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease relationships. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction methods, but greatly surpasses an LLM's native capability of grounding entities with unique identifiers. SPIRES has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any new training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. AVAILABILITY AND IMPLEMENTATION: SPIRES is available as part of the open source OntoGPT package: https://github.com/monarch-initiative/ontogpt.

Hippocampome.org 2.0 is a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits.

Hippocampome.org is a mature open-access knowledge base of the rodent hippocampal formation focusing on neuron types and their properties. Previously, Hippocampome.org v1.0 established a foundational classification system identifying 122 hippocampal neuron types based on their axonal and dendritic morphologies, main neurotransmitter, membrane biophysics, and molecular expression (Wheeler et al., 2015). Releases v1.1 through v1.12 furthered the aggregation of literature-mined data, including among others neuron counts, spiking patterns, synaptic physiology, in vivo firing phases, and connection probabilities. Those additional properties increased the online information content of this public resource over 100-fold, enabling numerous independent discoveries by the scientific community. Hippocampome.org v2.0, introduced here, besides incorporating over 50 new neuron types, now recenters its focus on extending the functionality to build real-scale, biologically detailed, data-driven computational simulations. In all cases, the freely downloadable model parameters are directly linked to the specific peer-reviewed empirical evidence from which they were derived. Possible research applications include quantitative, multiscale analyses of circuit connectivity and spiking neural network simulations of activity dynamics. These advances can help generate precise, experimentally testable hypotheses and shed light on the neural mechanisms underlying associative memory and spatial navigation.