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.

Tri©DB: an integrated platform of knowledgebase and reporting system for cancer precision medicine.

BACKGROUND: With the development of cancer precision medicine, a huge amount of high-dimensional cancer information has rapidly accumulated regarding gene alterations, diseases, therapeutic interventions and various annotations. The information is highly fragmented across multiple different sources, making it highly challenging to effectively utilize and exchange the information. Therefore, it is essential to create a resource platform containing well-aggregated, carefully mined, and easily accessible data for effective knowledge sharing. METHODS: In this study, we have developed "Consensus Cancer Core" (Tri©DB), a new integrative cancer precision medicine knowledgebase and reporting system by mining and harmonizing multifaceted cancer data sources, and presenting them in a centralized platform with enhanced functionalities for accessibility, annotation and analysis. RESULTS: The knowledgebase provides the currently most comprehensive information on cancer precision medicine covering more than 40 annotation entities, many of which are novel and have never been explored previously. Tri©DB offers several unique features: (i) harmonizing the cancer-related information from more than 30 data sources into one integrative platform for easy access; (ii) utilizing a variety of data analysis and graphical tools for enhanced user interaction with the high-dimensional data; (iii) containing a newly developed reporting system for automated annotation and therapy matching for external patient genomic data. Benchmark test indicated that Tri©DB is able to annotate 46% more treatments than two officially recognized resources, oncoKB and MCG. Tri©DB was further shown to have achieved 94.9% concordance with administered treatments in a real clinical trial. CONCLUSIONS: The novel features and rich functionalities of the new platform will facilitate full access to cancer precision medicine data in one single platform and accommodate the needs of a broad range of researchers not only in translational medicine, but also in basic biomedical research. We believe that it will help to promote knowledge sharing in cancer precision medicine. Tri©DB is freely available at www.biomeddb.org , and is hosted on a cutting-edge technology architecture supporting all major browsers and mobile handsets.

Knowledgebase of potential multifaceted solutions to antimicrobial resistance.

Antimicrobial resistance (AMR), a top threat to global health, challenges preventive and treatment strategies of infections. AMR strains of microbial pathogens arise through multiple mechanisms. The underlying "antibiotic resistance genes" (ARGs) spread through various species by lateral gene transfer thereby causing global dissemination. Human methods also augment this process through inappropriate use, non-compliance to treatment schedule, and environmental waste. Worldwide significant efforts are being invested to discover novel therapeutic solutions for tackling resistant pathogens. Diverse therapeutic strategies have evolved over recent years. In this work we have developed a comprehensive knowledgebase by collecting alternative antimicrobial therapeutic strategies from literature data. Therapeutic strategies against bacteria, virus, fungus and parasites were extracted from PubMed literature using text mining. We have used a subjective (sentimental) approach for data mining new strategies, resulting in broad coverage of novel entities and subsequently add objective data like entity name (including IUPAC), potency, and safety information. The extracted data was organized in a freely accessible web platform, KOMBAT. The KOMBAT comprises 1104 Chemical compounds, 220 of newly identified antimicrobial peptides, 42 bacteriophages, 242 phytochemicals, 106 nanocomposites, and 94 novel entities for phototherapy. Entities tested and evaluated on AMR pathogens are included. We envision that this database will be useful for developing future therapeutics against AMR pathogens. The database can be accessed through http://kombat.igib.res.in/.

[Construction of knowledge base of Chinese medicine manufacturing].

Chinese medicine pharmaceutical industry is in the process of digital and intelligent transformation. Intelligent methods are required for efficient analysis and mining of the valuable information in the history data including literature data, pharmaceutical big data, and expert knowledge. Therefore, it is urgent to establish a knowledge-driven intelligent system of pharmaceutical technologies of Chinese medicine for efficient supplying of high-quality Chinese medicinal products. The present study proposed the construction method of the knowledge base of Chinese medicine manufacturing, which was preliminarily established from literature mining, case-based reasoning, and real-time prediction based on vacuum belt drying process optimization. Integrating the technologies(such as deep learning, case-based reasoning, and simulation modeling), pharmaceutical mechanisms, and big data, the knowledge base of Chinese medicine manufacturing can realize knowledge automation and scientific decision-making. It provides an example for upgrading from experience-based manufacturing to intelligent Chinese medicine manufacturing.

Seed and seedling interactions in three tree species from Mediterranean forests as a knowledge base for ecological restoration.

The ecosystems of the Mediterranean regions are severely threatened by human activity, and although we have made progress in physical restoration measures, little is known about the interactions between the plants of these biomes. The objective of this study is to contribute to document interactions between seeds and seedlings of three woody species native to Chile (P. chilensis, Q. saponaria and A. caven), which could be used for restoration actions (e.g., after forest fires). In a first experiment, we evaluated the germination response, the initial elongation and the interactions between the seedlings that germinate exposed to the chemical compounds of the other species. In a second experiment, we compared the survival and growth of seedlings in monospecific versus bispecific mixtures, using a substrate similar to that which is present after a wildfire. Seed extracts of teguments promoted germination of P. chilensis, but cotyledons and whole seed extracts inhibited germination of only one species, Q. saponaria, with very high intensity. The effects of the extracts on initial seedling elongation were more variable, including five inhibitions and one facilitation. Negative effects on germination and elongation included two cases of autotoxicity. The survival of seedlings grown in mixtures showed only two differences between monospecific and bispecific mixtures, both positive, constituting a reciprocal effect between two species. Only in one case was there a significant difference in seedling growth, which was root growth inhibition. Indeed, these results reveal an interaction between species, the type and intensity of which varies according to the condition of the seed or seedling. The negative effect found in seedling root growth reflects an allelopathic interaction that conditions a vital aspect for the establishment of these species, so this information is an opportunity to improve the establishment conditions in future reforestation projects, by avoiding particular species or promoting their proportion in plantation mixtures, either by planting or direct seeding.

Roy Adaptation Model: Theory-Based Knowledge and Nursing Care With a Person Experiencing COVID-19.

Nursing theories shed light and guide nursing care through provision of care to persons based on the specialized knowledge base of the profession. Nurses utilizing Roy's adaptation model deliver holistic care by accounting for people, processes, and the environments. The aim of this article is to illustrate the value of utilizing the Roy adaptation model in the care of a patients by reviewing nursing care provided to a patient diagnosed with COVID-19.

Intention-based and sensory-based predictions.

We inhabit a continuously changing world, where the ability to anticipate future states of the environment is critical for adaptation. Anticipation can be achieved by learning about the causal or temporal relationship between sensory events, as well as by learning to act on the environment to produce an intended effect. Together, sensory-based and intention-based predictions provide the flexibility needed to successfully adapt. Yet it is currently unknown whether the two sources of information are processed independently to form separate predictions, or are combined into a common prediction. To investigate this, we ran an experiment in which the final tone of two possible four-tone sequences could be predicted from the preceding tones in the sequence and/or from the participants' intention to trigger that final tone. This tone could be congruent with both sensory-based and intention-based predictions, incongruent with both, or congruent with one while incongruent with the other. Trials where predictions were incongruent with each other yielded similar prediction error responses irrespectively of the violated prediction, indicating that both predictions were formulated and coexisted simultaneously. The violation of intention-based predictions yielded late additional error responses, suggesting that those violations underwent further differential processing which the violations of sensory-based predictions did not receive.

Knowledge bases and software support for variant interpretation in precision oncology.

Precision oncology is a rapidly evolving interdisciplinary medical specialty. Comprehensive cancer panels are becoming increasingly available at pathology departments worldwide, creating the urgent need for scalable cancer variant annotation and molecularly informed treatment recommendations. A wealth of mainly academia-driven knowledge bases calls for software tools supporting the multi-step diagnostic process. We derive a comprehensive list of knowledge bases relevant for variant interpretation by a review of existing literature followed by a survey among medical experts from university hospitals in Germany. In addition, we review cancer variant interpretation tools, which integrate multiple knowledge bases. We categorize the knowledge bases along the diagnostic process in precision oncology and analyze programmatic access options as well as the integration of knowledge bases into software tools. The most commonly used knowledge bases provide good programmatic access options and have been integrated into a range of software tools. For the wider set of knowledge bases, access options vary across different parts of the diagnostic process. Programmatic access is limited for information regarding clinical classifications of variants and for therapy recommendations. The main issue for databases used for biological classification of pathogenic variants and pathway context information is the lack of standardized interfaces. There is no single cancer variant interpretation tool that integrates all identified knowledge bases. Specialized tools are available and need to be further developed for different steps in the diagnostic process.

Assessing the enrichment of dietary supplement coverage in the Unified Medical Language System.

OBJECTIVE: We sought to assess the need for additional coverage of dietary supplements (DS) in the Unified Medical Language System (UMLS) by investigating (1) the overlap between the integrated DIetary Supplements Knowledge base (iDISK) DS ingredient terminology and the UMLS and (2) the coverage of iDISK and the UMLS over DS mentions in the biomedical literature. MATERIALS AND METHODS: We estimated the overlap between iDISK and the UMLS by mapping iDISK to the UMLS using exact and normalized strings. The coverage of iDISK and the UMLS over DS mentions in the biomedical literature was evaluated via a DS named-entity recognition (NER) task within PubMed abstracts. RESULTS: The coverage analysis revealed that only 30% of iDISK terms can be matched to the UMLS, although these cover over 99% of iDISK concepts. A manual review revealed that a majority of the unmatched terms represented new synonyms, rather than lexical variants. For NER, iDISK nearly doubles the precision and achieves a higher F1 score than the UMLS, while maintaining a competitive recall. DISCUSSION: While iDISK has significant concept overlap with the UMLS, it contains many novel synonyms. Furthermore, almost 3000 of these overlapping UMLS concepts are missing a DS designation, which could be provided by iDISK. The NER experiments show that the specialization of iDISK is useful for identifying DS mentions. CONCLUSIONS: Our results show that the DS representation in the UMLS could be enriched by adding DS designations to many concepts and by adding new synonyms.

Influences of Daily Life Habits on Risk Factors of Stroke Based on Decision Tree and Correlation Matrix.

PURPOSE: To explore the influences of smoking, alcohol consumption, drinking tea, diet, sleep, and exercise on the risk of stroke and relationships among the factors, present corresponding knowledge-based rules, and provide a scientific basis for assessment and intervention of risk factors of stroke. METHODS: The decision tree C4.5 algorithm was optimized and utilized to establish a model for stroke risk assessment; then, the main risk factors of stroke (including hypertension, dyslipidemia, diabetes, atrial fibrillation, body mass index (BMI), history of stroke, family history of stroke, and transient ischemic attack (TIA)) and daily habits (e.g., smoking, alcohol consumption, drinking tea, diet, sleep, and exercise) were analyzed; corresponding knowledge-based rules were finally presented. Establish a correlation matrix of stroke risk factors and analyze the relationship between stroke risk factors. RESULTS: The accuracy of the established model for stroke risk assessment was 87.53%, and the kappa coefficient was 0.8344, which was superior to that of the random forest and Logistic algorithm. Additionally, 37 knowledge-based rules that can be used for prevention of risk factors of stroke were derived and verified. According to in-depth analysis of risk factors of stroke, the values of smoking, exercise, sleep, drinking tea, alcohol consumption, and diet were 6.00, 7.00, 8.67, 9.33, 10.00, 10.60, and 10.75, respectively, indicating that their influence on risk factors of stroke was reduced in turn; on the one hand, smoking and exercise were strongly associated with other risk factors of stroke; on the other hand, sleep, drinking tea, alcohol consumption, and diet were not firmly associated with other risk factors of stroke, and they were relatively tightly associated with smoking and exercise. CONCLUSIONS: Establishment of a model for stroke risk assessment, analysis of factors influencing risk factors of stroke, analysis of relationships among those factors, and derivation of knowledge-based rules are helpful for prevention and treatment of stroke.

Introducing the concept of virtual control groups into preclinical toxicology testing.

Sharing legacy data from in vivo toxicity studies offers the opportunity to analyze the variability of control groups stratified for strain, age, duration of study, vehicle and other experimental conditions. Historical animal control group data may lead to a repository, which could be used to construct virtual control groups (VCGs) for toxicity studies. VCGs are an established concept in clinical trials, but the idea of replacing living beings with virtual data sets has so far not been introduced into the design of regulatory animal studies. The use of VCGs has the potential of a 25% reduction in animal use by replacing the control group animals with existing randomized data sets. Prerequisites for such an approach are the availability of large and well-structured control data sets as well as thorough statistical evaluations. the foundation of data sharing has been laid within the Innovative Medicines Initiatives projects eTOX and eTRANSAFE. For a proof of principle participating companies have started to collect control group data for subacute (4-week) GLP studies with Wistar rats (the strain preferentially used in Europe) and are characterizing these data for its variability. In a second step, the control group data will be shared among the companies and cross-company variability will be investigated. In a third step, a set of studies will be analyzed to assess whether the use of VCG data would have influenced the outcome of the study compared to the real control group.

iDISK: the integrated DIetary Supplements Knowledge base.

OBJECTIVE: To build a knowledge base of dietary supplement (DS) information, called the integrated DIetary Supplement Knowledge base (iDISK), which integrates and standardizes DS-related information from 4 existing resources. MATERIALS AND METHODS: iDISK was built through an iterative process comprising 3 phases: 1) establishment of the content scope, 2) development of the data model, and 3) integration of existing resources. Four well-regarded DS resources were integrated into iDISK: The Natural Medicines Comprehensive Database, the "About Herbs" page on the Memorial Sloan Kettering Cancer Center website, the Dietary Supplement Label Database, and the Natural Health Products Database. We evaluated the iDISK build process by manually checking that the data elements associated with 50 randomly selected ingredients were correctly extracted and integrated from their respective sources. RESULTS: iDISK encompasses a terminology of 4208 DS ingredient concepts, which are linked via 6 relationship types to 495 drugs, 776 diseases, 985 symptoms, 605 therapeutic classes, 17 system organ classes, and 137 568 DS products. iDISK also contains 7 concept attribute types and 3 relationship attribute types. Evaluation of the data extraction and integration process showed average errors of 0.3%, 2.6%, and 0.4% for concepts, relationships and attributes, respectively. CONCLUSION: We developed iDISK, a publicly available standardized DS knowledge base that can facilitate more efficient and meaningful dissemination of DS knowledge.

Molecular expression profiles of morphologically defined hippocampal neuron types: Empirical evidence and relational inferences.

Gene and protein expressions are key determinants of cellular function. Neurons are the building blocks of brain circuits, yet the relationship between their molecular identity and the spatial distribution of their dendritic inputs and axonal outputs remains incompletely understood. The open-source knowledge base Hippocampome.org amasses such transcriptomic data from the scientific literature for morphologically defined neuron types in the rodent hippocampal formation: dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex. Positive, negative, or mixed expression reports were initially obtained from published articles directly connecting molecular evidence to neurons with known axonal and dendritic patterns across hippocampal layers. Here, we supplement this information by collating, formalizing, and leveraging relational expression inferences that link a gene or protein expression or lack thereof to that of another molecule or to an anatomical location. With these additional interpretations, we freely release online a comprehensive human- and machine-readable molecular profile for more than 100 neuron types in Hippocampome.org. Analysis of these data ascertains the ability to distinguish unequivocally most neuron types in each of the major subdivisions of the hippocampus based on currently known biochemical markers. Moreover, grouping neuron types by expression similarity reveals eight superfamilies characterized by a few defining molecules.

Promoting the use of self-management in patients with spine pain managed by chiropractors and chiropractic interns: barriers and design of a theory-based knowledge translation intervention.

Background: The literature supports the effectiveness of self-management support (SMS) to improve health outcomes of patients with chronic spine pain. However, patient engagement in SMS programs is suboptimal. The objectives of this study were to: 1) assess participation in self-care (i.e. activation) among patients with spine pain, 2) identify patients' barriers and enablers to using SMS, and 3) map behaviour change techniques (BCTs) to key barriers to inform the design of a knowledge translation (KT) intervention aimed to increase the use of SMS. Methods: In summer 2016, we invited 250 patients with spine pain seeking care at the Canadian Memorial Chiropractic College in Ontario, Canada to complete the Patient Activation Measure (PAM) survey to assess the level of participation in self-care. We subsequently conducted individual interviews, in summer 2017, based on the Theoretical Domains Framework (TDF) in a subset of patients to identify potential challenges to using SMS. The interview guide included 20 open-ended questions and accompanying probes. Findings were deductively analysed guided by the TDF. A panel of 7 experts mapped key barriers to BCTs, designed a KT intervention, and selected the modes of delivery. Results: Two hundred and twenty-three patients completed the PAM. Approximately 24% of respondents were not actively involved in their care. Interview findings from 13 spine pain patients suggested that the potential barriers to using SMS corresponded to four TDF domains: Environmental Context and Resources; Emotion; Memory, Attention & Decision-Making; and Behavioural Regulation. The proposed theory-based KT intervention includes paper-based educational materials, webinars and videos, summarising and demonstrating the therapeutic recommendations including exercises and other lifestyle changes. In addition, the KT intervention includes Brief Action Planning, a SMS strategy based on motivational interviewing, along with a SMART plan and reminders. Conclusions: Almost one quarter of study participants were not actively engaged in their spine care. Key barriers likely to influence uptake of SMS among patients were identified and used to inform the design of a theory-based KT intervention to increase their participation level. The proposed multi-component KT intervention may be an effective strategy to optimize the quality of spine pain care and improve patients' health-outcomes.

Clinical Decision-Support Systems for Detection of Systemic Inflammatory Response Syndrome, Sepsis, and Septic Shock in Critically Ill Patients: A Systematic Review.

BACKGROUND: The design of computerized systems able to support automated detection of threatening conditions in critically ill patients such as systemic inflammatory response syndrome (SIRS) and sepsis has been fostered recently. The increase of research work in this area is due to both the growing digitalization in health care and the increased appreciation of the importance of early sepsis detection and intervention. To be able to understand the variety of systems and their characteristics as well as performances, a systematic literature review is required. Existing reviews on this topic follow a rather restrictive searching methodology or they are outdated. As much progress has been made during the last 5 years, an updated review is needed to be able to keep track of current developments in this area of research. OBJECTIVES: To provide an overview about current approaches for the design of clinical decision-support systems (CDSS) in the context of SIRS, sepsis, and septic shock, and to categorize and compare existing approaches. METHODS: A systematic literature review was performed in accordance with the preferred reporting items for systematic reviews and meta-analyses (PRISMA) statement. Searches for eligible articles were conducted on five electronic bibliographic databases, including PubMed/MEDLINE, IEEE Xplore, Embase, Scopus, and ScienceDirect. Initial results were screened independently by two reviewers based on clearly defined eligibility criteria. A backward as well as an updated search enriched the initial results. Data were extracted from included articles and presented in a standardized way. Articles were classified into predefined categories according to characteristics extracted previously. The classification was performed according to the following categories: clinical setting including patient population and mono- or multicentric study, support type of the system such as prediction or detection, systems characteristics such as knowledge- or data-driven algorithms used, evaluation of methodology, and results including ground truth definition, sensitivity, and specificity. All results were assessed qualitatively by two reviewers. RESULTS: The search resulted in 2,373 articles out of which 55 results were identified as eligible. Over 80% of the articles describe monocentric studies. More than 50% include adult patients, and only four articles explicitly report the inclusion of pediatric patients. Patient recruitment often is very selective, which can be observed from highly varying inclusion and exclusion criteria. The task of disease detection is covered in 62% of the articles; prediction of upcoming conditions in 33%. Sepsis is covered in 67% of the articles, SIRS as sole entity in only 4%, whereas 27% focus on severe sepsis and/or septic shock. The most common combinations of categories "algorithm used" and "support type" are knowledge-based detection of sepsis and data-driven prediction of sepsis. In evaluations, manual chart review (38%) and diagnosis coding (29%) represent the most frequently used ground truth definitions; most studies present a sample size between 10,001 and 100,000 cases (31%) and performances highly differ with only five articles presenting sensitivities and specificities above 90%; four of them using knowledge-based rather than machine learning algorithms. The presentations of holistic CDSS approaches, including technical implementation details, system interfaces, and data and interoperability aspects enabling the use of CDSS in routine settings are missing in nearly all articles. CONCLUSIONS: The review demonstrated the high variety of research in this context successfully. A clear trend is observable toward the use of data-driven algorithms, and a lack of research could be identified in covering the pediatric population as well as acknowledging SIRS as an independent and threatening condition. The quality as well as the significance of the presented evaluations for assessing the performances of the algorithms in clinical routine settings are often not meeting the current standard of scientific work. Our future interest will be concentrated on these realistic settings by implementing and evaluating SIRS detection approaches as well as considering factors to make the CDSS useable in clinical routine from both technical and medical perspectives.

Midwives' Perception of Using a Knowledge Base on Fetal Impact of Drugs.

A non-commercial knowledge base providing assessments of fetal risks of medicinal drugs is a useful tool in the everyday work of midwives. The information is freely available on the internet, and according to a questionnaire study, nearly 95% of the midwives are familiar with the database, 30% use the information weekly, and 80% express that it affects their medical decisions. A vast majority of the midwives also state that it is time-saving.

An ontological framework for the formalization, organization and usage of TCM-Knowledge.

BACKGROUND: The traditional Chinese Medicine Language System (TCMLS) is a large-scale terminology system, developed from 2002 on by the Institute of Information of Traditional Chinese Medicine (IITCM). Until now, more than 120,000 concepts, 300,000 terms and 1.27 million semantic relational links are included. Its top-level framework, called TCMLS-semantic network (SN), provides an important basis for the standardization and mapping of traditional Chinese Medicine (TCM) terminology systems. Though, many data produced and stored in TCMLS have poor quality for historical reasons or because of human factors. There is a large number of classification errors or inconsistent expressions of terms remained in the current TCMLS- SN, which hamper an efficient utilization of the data stored in TCMLS in practical applications. METHODS: We start with analyzing the technical specification based on TCMLS, considering some obvious classification errors and problems of ambiguity of semantic expressions in TCMLS-SN, followed with using a top-down approach for building a middle level ontology which is based on the framework General Formal Ontology (GFO), take into account the compatibility with TCM related concepts, turn out the results of a modification of the current TCMLS-SN, called GFO-TCM. RESULTS: Through comparison with TCMLS-SN, according to viewpoints of GFO, some semantic types and relations were reconstructed within GFO-TCM. We propose a middle level ontology for TCMLS which may support entailment and ensure coherence, we also draw out a mapping which possess a more reasonable framework with a unified semantic criterion, it is application scenarios oriented and can be further updated and extended. CONCLUSIONS: The goal is to construct a formal middle-level ontology that is compatible with both the traditional medical terminology system and modern medical terminology standards. it is intended to satisfy functional requirements which are relevant for natural language processing, information extraction, semantic retrieval, clinical decision support in the field of traditional Chinese medicine. It also provides a foundation and methodology for building a large-scale, unified semantic and extensible knowledge graph platform.

Design Considerations for a Knowledge Graph: The WATRIMed Use Case.

The World Health Organization estimates that as much as 80% of the population uses Traditional Medicine (TM) in some form, and in particular, herbal-based Traditional Medicine (HTM). However, TM is mostly orally transmitted and suffers from lack of standardizations and lack of computable TM data. Shareable standards could enable computational support of TM data management. In this paper, we outline the design and development of the West African Herbal Traditional Medicine (WATRIMed) Knowledge Graph (KG), which is an effort for bringing West Africa TM to the digital world and help establishing bridges with conventional medicine. WATRIMed entities have been enriched with knowledge from external publicly available knowledge bases and further mapped with the BioTopLite Upper Level Ontology. As of result, the model of the publicly available KG currently comprises 472 Concepts and 75 Properties (57 object properties and 18 data properties). It describes formally 115 medicinal plants, 179 chemical compounds and 67 recipes.

Updates in Rhea: SPARQLing biochemical reaction data.

Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of over 11 000 expert-curated biochemical reactions that uses chemical entities from the ChEBI ontology to represent reaction participants. Originally designed as an annotation vocabulary for the UniProt Knowledgebase (UniProtKB), Rhea also provides reaction data for a range of other core knowledgebases and data repositories including ChEBI and MetaboLights. Here we describe recent developments in Rhea, focusing on a new resource description framework representation of Rhea reaction data and an SPARQL endpoint (https://sparql.rhea-db.org/sparql) that provides access to it. We demonstrate how federated queries that combine the Rhea SPARQL endpoint and other SPARQL endpoints such as that of UniProt can provide improved metabolite annotation and support integrative analyses that link the metabolome through the proteome to the transcriptome and genome. These developments will significantly boost the utility of Rhea as a means to link chemistry and biology for a more holistic understanding of biological systems and their function in health and disease.

Toward a normalized clinical drug knowledge base in China-applying the RxNorm model to Chinese clinical drugs.

Objective: In recent years, electronic health record systems have been widely implemented in China, making clinical data available electronically. However, little effort has been devoted to making drug information exchangeable among these systems. This study aimed to build a Normalized Chinese Clinical Drug (NCCD) knowledge base, by applying and extending the information model of RxNorm to Chinese clinical drugs. Methods: Chinese drugs were collected from 4 major resources-China Food and Drug Administration, China Health Insurance Systems, Hospital Pharmacy Systems, and China Pharmacopoeia-for integration and normalization in NCCD. Chemical drugs were normalized using the information model in RxNorm without much change. Chinese patent drugs (i.e., Chinese herbal extracts), however, were represented using an expanded RxNorm model to incorporate the unique characteristics of these drugs. A hybrid approach combining automated natural language processing technologies and manual review by domain experts was then applied to drug attribute extraction, normalization, and further generation of drug names at different specification levels. Lastly, we reported the statistics of NCCD, as well as the evaluation results using several sets of randomly selected Chinese drugs. Results: The current version of NCCD contains 16 976 chemical drugs and 2663 Chinese patent medicines, resulting in 19 639 clinical drugs, 250 267 unique concepts, and 2 602 760 relations. By manual review of 1700 chemical drugs and 250 Chinese patent drugs randomly selected from NCCD (about 10%), we showed that the hybrid approach could achieve an accuracy of 98.60% for drug name extraction and normalization. Using a collection of 500 chemical drugs and 500 Chinese patent drugs from other resources, we showed that NCCD achieved coverages of 97.0% and 90.0% for chemical drugs and Chinese patent drugs, respectively. Conclusion: Evaluation results demonstrated the potential to improve interoperability across various electronic drug systems in China.