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BACKGROUND: With an overarching goal of increasing diversity and inclusion in biomedical sciences, the National Research Mentoring Network (NRMN) developed a web-based national mentoring platform (MyNRMN) that seeks to connect mentors and mentees to support the persistence of underrepresented minorities in the biomedical sciences. As of May 15, 2024, the MyNRMN platform, which provides mentoring, networking, and professional development tools, has facilitated more than 12,100 unique mentoring connections between faculty, students, and researchers in the biomedical domain. OBJECTIVE: This study aimed to examine the large-scale mentoring connections facilitated by our web-based platform between students (mentees) and faculty (mentors) across institutional and geographic boundaries. Using an innovative graph database, we analyzed diverse mentoring connections between mentors and mentees across demographic characteristics in the biomedical sciences. METHODS: Through the MyNRMN platform, we observed profile data and analyzed mentoring connections made between students and faculty across institutional boundaries by race, ethnicity, gender, institution type, and educational attainment between July 1, 2016, and May 31, 2021. RESULTS: In total, there were 15,024 connections with 2222 mentees and 1652 mentors across 1625 institutions contributing data. Female mentees participated in the highest number of connections (3996/6108, 65%), whereas female mentors participated in 58% (5206/8916) of the connections. Black mentees made up 38% (2297/6108) of the connections, whereas White mentors participated in 56% (5036/8916) of the connections. Mentees were predominately from institutions classified as Research 1 (R1; doctoral universities-very high research activity) and historically Black colleges and universities (556/2222, 25% and 307/2222, 14%, respectively), whereas 31% (504/1652) of mentors were from R1 institutions. CONCLUSIONS: To date, the utility of mentoring connections across institutions throughout the United States and how mentors and mentees are connected is unknown. This study examined these connections and the diversity of these connections using an extensive web-based mentoring network.

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In the Islamic domain, Hadiths hold significant importance, standing as crucial texts following the Holy Quran. Each Hadith contains three main parts: the ISNAD (chain of narrators), TARAF (starting part, often from Prophet Muhammad), and MATN (Hadith content). ISNAD, a chain of narrators involved in transmitting that particular MATN. Hadith scholars determine the trustworthiness of the transmitted MATN by the quality of the ISNAD. The ISNAD's data is available in its original Arabic language, with narrator names transliterated into English. This paper presents the Multi-IsnadSet (MIS), that has great potential to be employed by the social scientist and theologist. A multi-directed graph structure is used to represents the complex interactions among the narrators of Hadith. The MIS dataset represent directed graph which consists of 2092 nodes, representing individual narrators, and 77,797 edges represent the Sanad-Hadith connections. The MIS dataset represents multiple ISNAD of the Hadith based on the Sahih Muslim Hadith book. The dataset was carefully extracted from online multiple Hadith sources using data scraping and web crawling techniques tools, providing extensive Hadith details. Each dataset entry provides a complete view of a specific Hadith, including the original book, Hadith number, textual content (MATN), list of narrators, narrator count, sequence of narrators, and ISNAD count. In this paper, four different tools were designed and constructed for modeling and analyzing narrative network such as python library (NetworkX), powerful graph database Neo4j and two different network analysis tools named Gephi and CytoScape. The Neo4j graph database is used to represent the multi-dimensional graph related data for the ease of extraction and establishing new relationships among nodes. Researchers can use MIS to explore Hadith credibility including classification of Hadiths (Sahih=perfection in the Sanad/Dhaif=imperfection in the Sanad), and narrators (trustworthy/not). Traditionally, scholars have focused on identifying the longest and shortest Sanad between two Narrators, but in MIS, the emphasis shifts to determining the optimum/authentic Sanad, considering narrator qualities. The graph representation of the authentic and manually curated dataset will open ways for the development of computational models that could identify the significance of a chain and a narrator. The dataset allows the researchers to provide Hadith narrators and Hadith ISNAD that could be used in a wide variety of future research studies related to Hadith authentication and rules extraction. Moreover, the dataset encourages cross-disciplinary research, bridging the gap between Islamic studies, artificial intelligence (AI), social network analysis (SNA), and Graph Neural Network (GNN).

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Inconsistent disease coding standards in medicine create hurdles in data exchange and analysis. This paper proposes a machine learning system to address this challenge. The system automatically matches unstructured medical text (doctor notes, complaints) to ICD-10 codes. It leverages a unique architecture featuring a training layer for model development and a knowledge base that captures relationships between symptoms and diseases. Experiments using data from a large medical research center demonstrated the system's effectiveness in disease classification prediction. Logistic regression emerged as the optimal model due to its superior processing speed, achieving an accuracy of 81.07% with acceptable error rates during high-load testing. This approach offers a promising solution to improve healthcare informatics by overcoming coding standard incompatibility and automating code prediction from unstructured medical text.

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Objective To explore the construction and visualization for knowledge graph of Ling Shu(Spiritual Pivot),with a view to providing ideas for the structured storage and display of the theoretical knowledge of the ancient Chinese medical books.Methods Using the professional idea of constructing knowledge graphs for reference,text mining technology was applied to construct the thesaurus,and then word division,entity recognition,and relationship extraction for the original text of Ling Shu were performed to get the elements of knowledge graph construction.The graph database Neo4j was used for the storage and query of the knowledge graph,and then the visual display of the knowledge graph was achieved.Results The 1 216 high-quality words consisting of the thesaurus of Ling Shu were obtained,and the construction of the knowledge graph of the theory of Ling Shu was realized.The constructed knowledge graph basically displayed the traditional Chinese medicine theories such as the correlation of visceral manifestations with essence qi,and the relationship between emotions and the five-zang organs described in Ling Shu,which made the retrieval and utilization of the related entities and relationships possible,and provided ideas for the structured storage and display of the theoretical knowledge of the ancient books of Chinese medicine.Conclusion The knowledge graph construction technology can be used to obtain the Chinese medicine theoretical knowledge graph of Ling Shu,and to display the knowledge connections of yin-yang and the five elements,and the internal organs and meridians expressed in the Ling Shu.The construction of the knowledge graph and its storage in the graph database enable the knowledge graph involved in the text of Ling Shu to be displayed in the form of visualized semantic network graph,and also make the embedding of other search systems such as the semantic search and semantic wiki possible,which will be helpful for the development of Chinese medicine intelligent medical services.

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The knowledge graph is one of the essential infrastructures of artificial intelligence. It is a challenge for knowledge engineering to construct a high-quality domain knowledge graph for multi-source heterogeneous data. We propose a complete process framework for constructing a knowledge graph that combines structured data and unstructured data, which includes data processing, information extraction, knowledge fusion, data storage, and update strategies, aiming to improve the quality of the knowledge graph and extend its life cycle. Specifically, we take the construction process of an enterprise knowledge graph as an example and integrate enterprise register information, litigation-related information, and enterprise announcement information to enrich the enterprise knowledge graph. For the unstructured text, we improve existing model to extract triples and the F1-score of our model reached 72.77%. The number of nodes and edges in our constructed enterprise knowledge graph reaches 1,430,000 and 3,170,000, respectively. Furthermore, for each type of multi-source heterogeneous data, we apply corresponding methods and strategies for information extraction and data storage and carry out a detailed comparative analysis of graph databases. From the perspective of practical use, the informative enterprise knowledge graph and its timely update can serve many actual business needs. Our proposed enterprise knowledge graph has been deployed in HuaRong RongTong (Beijing) Technology Co., Ltd. and is used by the staff as a powerful tool for corporate due diligence. The key features are reported and analyzed in the case study. Overall, this paper provides an easy-to-follow solution and practice for domain knowledge graph construction, as well as demonstrating its application in corporate due diligence.

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While the continuing decline in genotyping and sequencing costs has largely benefited plant research, some key species for meeting the challenges of agriculture remain mostly understudied. As a result, heterogeneous datasets for different traits are available for a significant number of these species. As gene structures and functions are to some extent conserved through evolution, comparative genomics can be used to transfer available knowledge from one species to another. However, such a translational research approach is complex due to the multiplicity of data sources and the non-harmonized description of the data. Here, we provide two pipelines, referred to as structural and functional pipelines, to create a framework for a NoSQL graph-database (Neo4j) to integrate and query heterogeneous data from multiple species. We call this framework Orthology-driven knowledge base framework for translational research (Ortho_KB). The structural pipeline builds bridges across species based on orthology. The functional pipeline integrates biological information, including QTL, and RNA-sequencing datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. Queries can be written using the Neo4j Cypher language and can, for instance, lead to identify genes controlling a common trait across species. To explore the possibilities offered by such a framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. The proposed model was evaluated by studying the conservation of a flowering-promoting gene. Through a series of queries, we have demonstrated that our knowledge graph base provides an intuitive and powerful platform to support research and development programmes.

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Navigating through a real-world map can be represented in a bi-directed graph with a group of nodes representing the intersections and edges representing the roads between them. In cycling, we can plan training as a group of nodes and edges the athlete must cover. Optimizing routes using artificial intelligence is a well-studied phenomenon. Much work has been done on finding the quickest and shortest paths between two points. In cycling, the solution is not necessarily the shortest and quickest path. However, the optimum path is the one where a cyclist covers the suitable distance, ascent, and descent based on his/her training parameters. This paper presents a Neo4j graph-based dataset of cycling routes in Slovenia. It consists of 152,659 nodes representing individual road intersections and 410,922 edges representing the roads between them. The dataset allows the researchers to develop and optimize cycling training generation algorithms, where distance, ascent, descent, and road type are considered.

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Semantic interoperability establishes intercommunications and enables data sharing across disparate systems. In this study, we propose an ostensive information architecture for healthcare information systems to decrease ambiguity caused by using signs in different contexts for different purposes. The ostensive information architecture adopts a consensus-based approach initiated from the perspective of information systems re-design and can be applied to other domains where information exchange is required between heterogeneous systems. Driven by the issues in FHIR (Fast Health Interoperability Resources) implementation, an ostensive approach that supplements the current lexical approach in semantic exchange is proposed. A Semantic Engine with an FHIR knowledge graph as the core is constructed using Neo4j to provide semantic interpretation and examples. The MIMIC III (Medical Information Mart for Intensive Care) datasets and diabetes datasets have been employed to demonstrate the effectiveness of the proposed information architecture. We further discuss the benefits of the separation of semantic interpretation and data storage from the perspective of information system design, and the semantic reasoning towards patient-centric care underpinned by the Semantic Engine.

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The German Medical Informatics Initiative (MII) aims to increase the interoperability and reuse of clinical routine data for research purposes. One important result of the MII work is a German-wide common core data set (CDS), which is to be provided by over 31 data integration centers (DIZ) following a strict specification. One standard format for data sharing is HL7/FHIR. Locally, classical data warehouses are often in use for data storage and retrieval. We are interested to investigate the advantages of a graph database in this setting. After having transferred the MII CDS into a graph, storing it in a graph database and subsequently enriching it with accompanying meta-information, we see a great potential for more sophisticated data exploration and analysis. Here we describe the extract-transform-load process which we set up as a proof of concept to achieve the transformation and to make the common set of core data accessible as a graph.

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BACKGROUND: Graph databases enable efficient storage of heterogeneous, highly-interlinked data, such as clinical data. Subsequently, researchers can extract relevant features from these datasets and apply machine learning for diagnosis, biomarker discovery, or understanding pathogenesis. METHODS: To facilitate machine learning and save time for extracting data from the graph database, we developed and optimized Decision Tree Plug-in (DTP) containing 24 procedures to generate and evaluate decision trees directly in the graph database Neo4j on homogeneous and unconnected nodes. RESULTS: Creation of the decision tree for three clinical datasets directly in the graph database from the nodes required between 0.059 and 0.099 s, while calculating the decision tree with the same algorithm in Java from CSV files took 0.085-0.112 s. Furthermore, our approach was faster than the standard decision tree implementations in R (0.62 s) and equal to Python (0.08 s), also using CSV files as input for small datasets. In addition, we have explored the strengths of DTP by evaluating a large dataset (approx. 250,000 instances) to predict patients with diabetes and compared the performance against algorithms generated by state-of-the-art packages in R and Python. By doing so, we have been able to show competitive results on the performance of Neo4j, in terms of quality of predictions as well as time efficiency. Furthermore, we could show that high body-mass index and high blood pressure are the main risk factors for diabetes. CONCLUSION: Overall, our work shows that integrating machine learning into graph databases saves time for additional processes as well as external memory, and could be applied to a variety of use cases, including clinical applications. This provides user with the advantages of high scalability, visualization and complex querying.

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PURPOSE: In this work, we present a subsystem of a robotic circulating nurse, that produces recommendations for the next supplied sterile item based on incomplete requests from the sterile OR staff, the current situation, predefined knowledge and experience from previous surgeries. We describe a structure to store and query the underlying information in terms of entities and their relationships of varying strength. METHODS: For the implementation, the graph database Neo4j is used as a core component together with its querying language Cypher. We outline a specific structure of nodes and relationships, i.e., a graph. Primarily, it allows to represent entities like surgeons, surgery types and items, as well as their complex interconnectivity. In addition, it enables to match given situations and partial requests in the OR with corresponding subgraphs. The subgraphs provide suitable sterile items and allow to prioritize them according to their utilization frequency. RESULTS: The graph database was populated with existing data from 854 surgeries describing the intraoperative use of sterile items. A test scenario is evaluated in which a request for "Prolene" is made during a cholecystectomy. The software identifies a specific "Prolene" suture material as the most probable requested sterile item, because of its utilization frequency from over 95%. Other "Prolene" suture materials were used in less than 15% of the cholecystectomies. CONCLUSION: We have proposed a graph database for the selection of sterile items in the operating room. The example shows how the partial information from different sources can be easily integrated in a query, leading to an unique result. Eventually, we propose possible enhancements to further improve the quality of the recommendations. In the next step, the recommendations of the software will be evaluated in real time during surgeries.

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The current management of patients with multimorbidity is suboptimal, with either a single-disease approach to care or treatment guideline adaptations that result in poor adherence due to their complexity. Although this has resulted in calls for more holistic and personalized approaches to prescribing, progress toward these goals has remained slow. With the rapid advancement of machine learning (ML) methods, promising approaches now also exist to accelerate the advance of precision medicine in multimorbidity. These include analyzing disease comorbidity networks, using knowledge graphs that integrate knowledge from different medical domains, and applying network analysis and graph ML. Multimorbidity disease networks have been used to improve disease diagnosis, treatment recommendations, and patient prognosis. Knowledge graphs that combine different medical entities connected by multiple relationship types integrate data from different sources, allowing for complex interactions and creating a continuous flow of information. Network analysis and graph ML can then extract the topology and structure of networks and reveal hidden properties, including disease phenotypes, network hubs, and pathways; predict drugs for repurposing; and determine safe and more holistic treatments. In this article, we describe the basic concepts of creating bipartite and unipartite disease and patient networks and review the use of knowledge graphs, graph algorithms, graph embedding methods, and graph ML within the context of multimorbidity. Specifically, we provide an overview of the application of graph theory for studying multimorbidity, the methods employed to extract knowledge from graphs, and examples of the application of disease networks for determining the structure and pathways of multimorbidity, identifying disease phenotypes, predicting health outcomes, and selecting safe and effective treatments. In today's modern data-hungry, ML-focused world, such network-based techniques are likely to be at the forefront of developing robust clinical decision support tools for safer and more holistic approaches to treating older patients with multimorbidity.

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BACKGROUND: Medical databases normally contain large amounts of data in a variety of forms. Although they grant significant insights into diagnosis and treatment, implementing data exploration into current medical databases is challenging since these are often based on a relational schema and cannot be used to easily extract information for cohort analysis and visualization. As a consequence, valuable information regarding cohort distribution or patient similarity may be missed. With the rapid advancement of biomedical technologies, new forms of data from methods such as Next Generation Sequencing (NGS) or chromosome microarray (array CGH) are constantly being generated; hence it can be expected that the amount and complexity of medical data will rise and bring relational database systems to a limit. DESCRIPTION: We present Graph4Med, a web application that relies on a graph database obtained by transforming a relational database. Graph4Med provides a straightforward visualization and analysis of a selected patient cohort. Our use case is a database of pediatric Acute Lymphoblastic Leukemia (ALL). Along routine patients' health records it also contains results of latest technologies such as NGS data. We developed a suitable graph data schema to convert the relational data into a graph data structure and store it in Neo4j. We used NeoDash to build a dashboard for querying and displaying patients' cohort analysis. This way our tool (1) quickly displays the overview of patients' cohort information such as distributions of gender, age, mutations (fusions), diagnosis; (2) provides mutation (fusion) based similarity search and display in a maneuverable graph; (3) generates an interactive graph of any selected patient and facilitates the identification of interesting patterns among patients. CONCLUSION: We demonstrate the feasibility and advantages of a graph database for storing and querying medical databases. Our dashboard allows a fast and interactive analysis and visualization of complex medical data. It is especially useful for patients similarity search based on mutations (fusions), of which vast amounts of data have been generated by NGS in recent years. It can discover relationships and patterns in patients cohorts that are normally hard to grasp. Expanding Graph4Med to more medical databases will bring novel insights into diagnostic and research.

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This paper presents the development process of a graph database that connects statements posted by disabled people on various web-based platforms with accessibility requirements in the Danish Building Regulations (BR18). The aim is to bring the lived experience of disabled people into a vocabulary of space-making for architects. By elevating the missing voices of disabled people - describing what matters, how and why - the project supports the decision-making processes of architects to make the built environment more inclusive. The developed database relates statements posted by disabled people with sentences from paragraphs of BR18 through specific architectural features of room, element, and object. Using the architectural features as point of reference, the database not only highlights some of the most common building situations encountered by disabled people, but also allows anyone interested to explore their relationship to the real lives of disabled users and the statutory requirements.

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In this study, we utilized ontology and machine learning methods to analyze the current results on vaccine adverse events. With the VAERS (Vaccine Adverse Event Reporting System) Database, the side effects of COVID-19 vaccines are summarized, and a relational/graph database was implemented for further applications and analysis. The adverse effects of COVID-19 vaccines up to March 2022 were utilized in the study. With the built network of the adverse effects of COVID-19 vaccines, the API can help provide a visualized interface for patients, healthcare providers and healthcare officers to quickly find the information of a certain patient and the potential relationships of side effects of a certain vaccine. In the meantime, the model was further applied to predict the key feature symptoms that contribute to hospitalization and treatment following receipt of a COVID-19 vaccine and the performance was evaluated with a confusion matrix method. Overall, our study built a user-friendly visualized interface of the side effects of vaccines and provided insight on potential adverse effects with ontology and machine learning approaches. The interface and methods can be expanded to all FDA (Food and Drug Administration)-approved vaccines.

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The ability to estimate the probability of a drug to receive approval in clinical trials provides natural advantages to optimizing pharmaceutical research workflows. Success rates of clinical trials have deep implications for costs, duration of development, and under pressure due to stringent regulatory approval processes. We propose a machine learning approach that can predict the outcome of the trial with reliable accuracies, using biological activities, physicochemical properties of the compounds, target-related features, and NLP-based compound representation. In the above list, biological activities have never been used as an independent variable towards the prediction of clinical trial outcomes. We have extracted the drug-disease pair from clinical trials and mapped target(s) to that pair using multiple data sources. Empirical results demonstrate that ensemble learning outperforms independently trained, small-data ML models. We report results and inferences derived from a Random forest classifier with an average accuracy of 93%, and an F1 score of 0.96 for the "Pass" class. "Pass" refers to one of the two classes (Pass/Fail) of all clinical trials, and the model performed well in predicting the "Pass" category. Through the analysis of feature contributions to predictive capability, we have demonstrated that bioactivity plays a statistically significant role in predicting clinical trial outcome. A significant effort has gone into the production of the dataset that, for the first time, integrates clinical trial information with protein targets. Cleaned, organized, integrated data and code to map these entities, created as a part of this work, are available open-source. This reproducibility and the freely available code ensure that researchers with access to deep curated and proprietary clinical trial databases (we only use open-source data in this study) can further expand the scope of the results.

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CovidGraph, developed by the HealthECCO community, is a platform designed to foster research and data exploration to fight COVID-19. It is built on a graph database and encompasses data sources from different biomedical data domains including publications, clinical trials, patents, case statistics, molecular data and systems biology models. The tool provides multiple interfaces for data exploration and thus serves as a single point of entry for data driven COVID-19 research. Availability and Implementation: CovidGraph is available from the project website: https://healthecco.org/covidgraph/. The source code and documentation are provided on GitHub: https://github.com/covidgraph.

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OBJECTIVES: A novel graph data model of non-small cell lung cancer clinical and genomic data has been constructed with two aims: (1) provide a suitable model for facilitating graph analytics within the Neo4j framework or through tools which can interact through existing Neo4j APIs; and (2) provide a base model extensible to other cancer types and additional datasets such as those derived from electronic health records and other real world sources. DATA DESCRIPTION: Clinical and genomic data integrated with a novel property graph database schema from publicly available datasets and analyses based on The Cancer Genome Atlas lung cancer datasets augmented by with subgraphs patient-patient social network from similarity and correlation as well as individual based biological networks.

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Objective@#To establish the knowledge graph of “disease-syndrome-symptom-method-formula” in Treatise on Febrile Diseases (Shang Han Lun,《伤寒论》) for reducing the fuzziness and uncertainty of data, and for laying a foundation for later knowledge reasoning and its application.@*Methods@#Under the guidance of experts in the classical formula of traditional Chinese medicine (TCM), the method of “top-down as the main, bottom-up as the auxiliary” was adopted to carry out knowledge extraction, knowledge fusion, and knowledge storage from the five aspects of the disease, syndrome, symptom, method, and formula for the original text of Treatise on Febrile Diseases, and so the knowledge graph of Treatise on Febrile Diseases was constructed. On this basis, the knowledge structure query and the knowledge relevance query were realized in a visual manner. @*Results@#The knowledge graph of “disease-syndrome-symptom-method-formula” in the Treatise on Febrile Diseases was constructed, containing 6 469 entities and 10 911 relational triples, on which the query of entities and their relationships can be carried out and the query result can be visualized. @*Conclusion@#The knowledge graph of Treatise on Febrile Diseases systematically realizes its digitization of the knowledge system, and improves the completeness and accuracy of the knowledge representation, and the connection between “disease-syndrome-symptom-treatment-formula”, which is conducive to the sharing and reuse of knowledge can be obtained in a clear and efficient way.