A geospatial database management system for the collection of medicinal plants.

Medicinal plants are increasingly used, both for medical applications and personal healthcare. However, existing herbal database systems for plant retrieval offer only basic information and do not support real-time analysis of the spatial aspects of plantations and distribution sites. Moreover, data records are usually static and not publicly available as they rely on costly proprietary software packages. To address these shortcomings, including limiting the time needed for collection and data processing, a novel medicinal plants geospatial database management system is proposed. The system allows localization of plant sites and data presentation on an interactive heat map displaying spatial information of plants selected by the user within a specific radius from the user's location, including automatic presentation of an itinerary giving the optimal route between user location and plant destinations selected. The approach relies on dynamic and role-based data management, an interactive map that includes graphics and integrated geospatial analyses thanks to cross-platform, geographical a JavaScript library and Google API. Both spatial data and attributes are available in real time. The system would support effective collaboration, among herb farmers, government agencies, private investors, healthcare professionals and the general public with regard to various aspects of medicinal plants and their applications.

CESCR: CP-ABE for efficient and secure sharing of data in collaborative ehealth with revocation and no dummy attribute.

With the rapid advancement of information and communication technologies, there is a growing transformation of healthcare systems. A patient's health data can now be centrally stored in the cloud and be shared with multiple healthcare stakeholders, enabling the patient to be collaboratively treated by more than one healthcare institution. However, several issues, including data security and privacy concerns still remain unresolved. Ciphertext-policy attribute-based encryption (CP-ABE) has shown promising potential in providing data security and privacy in cloud-based systems. Nevertheless, the conventional CP-ABE scheme is inadequate for direct adoption in a collaborative ehealth system. For one, its expressiveness is limited as it is based on a monotonic access structure. Second, it lacks an attribute/user revocation mechanism. Third, the computational burden on both the data owner and data users is linear with the number of attributes in the ciphertext. To address these inadequacies, we propose CESCR, a CP-ABE for efficient and secure sharing of health data in collaborative ehealth systems with immediate and efficient attribute/user revocation. The CESCR scheme is unbounded, i.e., it does not bind the size of the attribute universe to the security parameter, it is based on the expressive and non-restrictive ordered binary decision diagram (OBDD) access structure, and it securely outsources the computationally demanding attribute operations of both encryption and decryption processes without requiring a dummy attribute. Security analysis shows that the CESCR scheme is secure in the selective model. Simulation and performance comparisons with related schemes also demonstrate that the CESCR scheme is expressive and efficient.

The Development and Operation of a Home Management System during the COVID-19 Pandemic: Experience of the Local Government Gyeonggi-do in Korea.

During the three the coronavirus disease 2019 (COVID-19) surges in South Korea, there was a shortage of hospital beds for COVID-19 patients, and as a result, there were cases of death while waiting for hospitalization. To minimize the risk of death and to allow those confirmed with COVID-19 to safely wait for hospitalization at home, the local government of Gyeonggi-do in South Korea developed a novel home management system (HMS). The HMS team, comprised of doctors and nurses, was organized to operate HMS. HMS provided a two-way channel for the taskforce and patients to monitor the severity of patient's condition and to provide healthcare counseling as needed. In addition, the HMS team cooperated with a triage/bed assignment team to expedite the response in case of an emergency, and managed a database of severity for real-time monitoring of patients. The HMS became operational for the first time in August 2020, initially managing only 181 patients; it currently manages a total of 3,707 patients. The HMS supplemented the government's COVID-19 confirmed case management framework by managing patients waiting at home for hospitalization due to lack of hospital and residential treatment center beds. HMS also could contribute a sense of psychological stability in patients and prevented the situation from worsening by efficient management of hospital beds and reduction of workloads on public healthcare centers. To stabilize and improve the management of COVID-19 confirmed cases, governments should organically develop self-treatment and HMS, and implement a decisive division of roles within the local governments.

Ewé: a web-based ethnobotanical database for storing and analysing data.

Ethnobotanical databases serve as repositories of traditional knowledge (TK), either at international or local scales. By documenting plant species with traditional use, and most importantly, the applications and modes of use of such species, ethnobotanical databases play a role in the conservation of TK and also provide access to information that could improve hypothesis generation and testing in ethnobotanical studies. Brazil has a rich medicinal flora and a rich cultural landscape. Nevertheless, cultural change and ecological degradation can lead to loss of TK. Here, we present an online database developed with open-source tools with a capacity to include all medicinal flora of Brazil. We present test data for the Leguminosae comprising a total of 2078 records, referred to here as use reports, including data compiled from literature and herbarium sources. Unlike existing databases, Ewé provides tools for the visualization of large datasets, facilitating hypothesis generation and meta-analyses. The Ewé database is currently available at www.ewedb.com.

Metabolic syndrome, metabolic components, and their relation to the risk of pancreatic cancer.

BACKGROUND: Components of the metabolic syndrome (MetS), such as elevated fasting glucose levels and abdominal obesity, have been suggested as potential risk factors for pancreatic cancer. However, data are still insufficient to assure the influence of MetS on incident pancreatic cancer. The objective of the current study was to investigate the association between MetS, metabolic components, and the risk of pancreatic cancer. METHODS: In the Korea National Health Information Database, 223,138 individuals who were without pancreatic cancer in 2009 were enrolled and followed until 2013. They were categorized into 4 groups according to the number of baseline metabolic components (0, 1, 2, 3, and 4-5). A multivariate Cox proportional hazard model was used to calculate the adjusted hazard ratios (HRs) and 95% CIs for incident pancreatic cancer according to the presence of MetS and the number of metabolic components. In addition, the risk of pancreatic cancer was evaluated in individuals who had a single metabolic component. RESULTS: The presence of MetS was significantly associated with incident pancreatic cancer (adjusted HR, 1.47; 95% CI, 1.19-1.81). The group with 4 or 5 baseline metabolic components had a higher risk of pancreatic cancer than the other groups (0 components: reference category; 1 component: adjusted HR, 0.94 [95% CI, 0.61-1.45]; 2 components: adjusted HR, 1.03 [95% CI, 0.68-1.56]; 3 components: adjusted HR, 1.35 [95% CI, 0.89-2.04]; 4-5 components: adjusted HR, 1.64 [95% CI, 1.06-2.51]). Regarding associations between the individual metabolic components and pancreatic cancer, no metabolic component alone had a statistically significant association with pancreatic cancer. CONCLUSIONS: MetS is a potential risk factor for pancreatic cancer. The presence of ≥4 metabolic components leads to a higher risk of pancreatic cancer even within categories of the MetS.

EMIF Catalogue: A collaborative platform for sharing and reusing biomedical data.

OBJECTIVE: The collaboration and knowledge exchange between researchers are often hindered by the nonexistence of accurate information about which databases may support research studies. Even though a considerable amount of patient health information does exist, it is usually distributed and hidden in many institutions. The goal of this project is to provide, for any research community, a holistic view of biomedical datasets of interests, from which researchers can explore several distinct levels of granularity. METHODS: We developed a community-centered approach to facilitate data sharing while ensuring privacy. A dynamic schema allows exposing any metadata model about existing repositories. The framework was developed following a modular plugin-based architecture that facilitates the integration of internal and external tools. RESULTS: The EMIF Catalogue, a web platform for sharing and reusing biomedical data. Through this system, data custodians can publish and share different levels of information, while the researchers can search for databases that fulfill research requirements. CONCLUSIONS: The EMIF Catalogue currently fosters several distinct research communities, with different levels of data governance, combining, for instance, data available in pan-European EHR and Alzheimer cohorts. This portal is publicly available at https://emif-catalogue.eu.

Centralized Clinical Trial Imaging Data Management: Practical Guidance from a Comprehensive Cancer Center's Experience.

Medical imaging is an integral part of clinical trial research and it must be managed properly to provide accurate data to the sponsor in a timely manner (Clune in Cancer Inform 4:33-56, 2007; Wang et al. in Proc SPIE Int Soc Opt Eng 7967, 2011). Standardized workflows for site qualification, protocol preparation, data storage, retrieval, de-identification, submission, and query resolution are paramount to achieve quality clinical trial data management such as reducing the number of imaging protocol deviations and avoiding delays in data transfer. Centralization of data management and implementation of relational databases and electronic workflows can help maintain consistency and accuracy of imaging data. This technical note aims at sharing the practical implementation of our centralized clinical trial imaging data management processes to avoid the fragmentation of tasks among various disease centers and research staff, and enable us to provide quality, accurate, and timely imaging data to clinical trial sponsors.

Hospital enterprise Architecture Framework (Study of Iranian University Hospital Organization).

BACKGROUNDS: Nowadays developing smart and fast services for patients and transforming hospitals to modern hospitals is considered a necessity. Living in the world inundated with information systems, designing services based on information technology entails a suitable architecture framework. OBJECTIVES: This paper aims to present a localized enterprise architecture framework for the Iranian university hospital. METHODS AND RESULTS: Using two dimensions of implementation and having appropriate characteristics, the best 17 enterprises frameworks were chosen. As part of this effort, five criteria were selected according to experts' inputs. According to these criteria, five frameworks which had the highest rank were chosen. Then 44 general characteristics were extracted from the existing 17 frameworks after careful studying. Then a questionnaire was written accordingly to distinguish the necessity of those characteristics using expert's opinions and Delphi method. The result showed eight important criteria. In the next step, using AHP method, TOGAF was chosen regarding having appropriate characteristics and the ability to be implemented among reference formats. In the next step, enterprise architecture framework was designed by TOGAF in a conceptual model and its layers. For determining architecture framework parts, a questionnaire with 145 questions was written based on literature review and expert's opinions. The results showed during localization of TOGAF for Iran, 111 of 145 parts were chosen and certified to be used in the hospital. CONCLUSION: The results showed that TOGAF could be suitable for use in the hospital. So, a localized Hospital Enterprise Architecture Modelling is developed by customizing TOGAF for an Iranian hospital at eight levels and 11 parts. This new model could be used to be performed in other Iranian hospitals.

Linked Registries: Connecting Rare Diseases Patient Registries through a Semantic Web Layer.

Patient registries are an essential tool to increase current knowledge regarding rare diseases. Understanding these data is a vital step to improve patient treatments and to create the most adequate tools for personalized medicine. However, the growing number of disease-specific patient registries brings also new technical challenges. Usually, these systems are developed as closed data silos, with independent formats and models, lacking comprehensive mechanisms to enable data sharing. To tackle these challenges, we developed a Semantic Web based solution that allows connecting distributed and heterogeneous registries, enabling the federation of knowledge between multiple independent environments. This semantic layer creates a holistic view over a set of anonymised registries, supporting semantic data representation, integrated access, and querying. The implemented system gave us the opportunity to answer challenging questions across disperse rare disease patient registries. The interconnection between those registries using Semantic Web technologies benefits our final solution in a way that we can query single or multiple instances according to our needs. The outcome is a unique semantic layer, connecting miscellaneous registries and delivering a lightweight holistic perspective over the wealth of knowledge stemming from linked rare disease patient registries.

[Design and implementation of information management system for Chinese materia medica resources survey].

By means of the established Information Management System for Chinese materia medica resources survey, the national, provincial and county level organization, personnel and the implementation of the program of Chinese materia medica resources survey, and the survey team of medicinal plant investigation, photos, Chinese herbal medicine market survey, the traditional Chinese materia medica resources knowledge survey, germplasm resources investigation and the data collation and summary specimen have been realised. Throughout the whole working process of the fourth national Chinese materia medica resources survey, it is ensured that all data were no missing, no repeat, and well stored and managed. The Information Management System can improve the standardization degree of Chinese materia medica resources survey, and maintain the continuity.

[Design and implementation of data reporting system for Chinese materia medica resources survey].

The collection, summary and sharing of all kinds of survey data are one of the main tasks and achievements in the national census of Chinese materia medica resources organized and implemented by the State Administration of Traditional Chinese Medicine. It is a key link in the implementation of the national census of Chinese materia medica resources. Based on the client / server architecture, the data reporting system for Chinese materia medica resources survey has been established for reporting system application model of geospatial data service based on Web implementation, through the SOA framework, to achieve the data collection summary of the seven aspects of the local data configuration, data reporting, data verification, data reporting, PDA data import and export, APP data import, track instrument data import. The system services include the general investigation, the focus of investigation, specimen information, herbs sample information, market research, germplasm survey, traditional knowledge survey of these seven aspects of the 312 indicators of the report, serving the Chinese materia medica resource survey of field survey data collection and internal data collation. The system provides the technical support for the national census of Chinese materia medica resources, improves the efficiency of the census of Chinese materia medica resources, and is conducive to the long-term preservation of the data of Chinese materia medica resources census, the transformation and sharing of the results.

[Design and implementation of mobile terminal data acquisition for Chinese materia medica resources survey].

In this paper, a data acquisition system based on mobile terminal combining GPS, offset correction, automatic speech recognition and database networking technology was designed implemented with the function of locating the latitude and elevation information fast, taking conveniently various types of Chinese herbal plant photos, photos, samples habitat photos and so on. The mobile system realizes automatic association with Chinese medicine source information, through the voice recognition function it records the information of plant characteristics and environmental characteristics, and record relevant plant specimen information. The data processing platform based on Chinese medicine resources survey data reporting client can effectively assists in indoor data processing, derives the mobile terminal data to computer terminal. The established data acquisition system provides strong technical support for the fourth national survey of the Chinese materia medica resources (CMMR).

[Design and implementation of data checking system for Chinese materia medica resources survey].

The Chinese material medica resources (CMMR) national survey information management system has collected a large amount of data. To help dealing with data recheck, reduce the work of inside, improve the recheck of survey data from provincial and county level, National Resource Center for Chinese Materia Medical has designed a data checking system for Chinese material medica resources survey based on J2EE technology, Java language, Oracle data base in accordance with the SOA framework. It includes single data check, check score, content manage, check the survey data census data with manual checking and automatic checking about census implementation plan, key research information, general survey information, cultivation of medicinal materials information, germplasm resources information the medicine information, market research information, traditional knowledge information, specimen information of this 9 aspects 20 class 175 indicators in two aspects of the quantity and quality. The established system assists in the completion of the data consistency and accuracy, pushes the county survey team timely to complete the data entry arrangement work, so as to improve the integrity, consistency and accuracy of the survey data, and ensure effective and available data, which lay a foundation for providing accurate data support for national survey of the Chinese material medica resources (CMMR) results summary, and displaying results and sharing.

[Design and implementation of Chinese materia medica resources survey results display system].

From the beginning of the fourth national census of traditional Chinese medicine resources in 2011, a large amount of data have been collected and compiled, including wild medicinal plant resource data, cultivation of medicinal plant information, traditional knowledge, and specimen information. The traditional paper-based recording method is inconvenient for query and application. The B/S architecture, JavaWeb framework and SOA are used to design and develop the fourth national census results display platform. Through the data integration and sorting, the users are to provide with integrated data services and data query display solutions. The platform realizes the fine data classification, and has the simple data retrieval and the university statistical analysis function. The platform uses Echarts components, Geo Server, Open Layers and other technologies to provide a variety of data display forms such as charts, maps and other visualization forms, intuitive reflects the number, distribution and type of Chinese material medica resources. It meets the data mapping requirements of different levels of users, and provides support for management decision-making.

[Design and implementation of real-time control of changes to national Chinese medicine resources fill system based on GIS].

The dynamic monitoring data of traditional Chinese medicine resources is one of the important tasks of the dynamic monitoring system of Chinese medicine resources,the system has formed a periodic monitoring data reporting mechanism. Data authenticity and accuracy are the basis for the sustainable and healthy development of Chinese medicine resources dynamic monitoring,information technology is an effective means to improve the efficiency of data reporting, reporting quality. Data production based on dynamic monitoring is of great significance for grasp the trend of change and development of Chinese medicine resources. In order to achieve the real-time control of changes to the national Chinese medicine resources, we build the Chinese medicine resources dynamic monitoring system. In order to solve the problems in practice, we have upgraded the fill system by using the data of GIS. In order to achieve the multidimensional, improve safety, practicality and standardization of the data, which laid a foundation for subsequent processing of data. The system can collect the information of the cultivation of Chinese herbal medicines,production and sales of daily reporting data, provide the Chinese herbal medicine market,fast growing industry environment such as positioning center. In this paper, the design and implementation of the system are expounded.According to the business requirements, we designed 12 forms, 98 collection indicators to meet the needs of dynamic monitoring of traditional Chinese medicine resources. This paper will introduce the development content, design and implementation, main function characteristics and application effect of the national Chinese medicine resources fill System. To explain the role that GIS technology plays in the system and how to realize the cultivation of Chinese herbal medicines, production and sales of daily reporting data, provide the Chinese herbal medicine market,fast growing industry environment such as positioning center,and information collecting.

[Study on spatial distribution characteristics of traditional Chinese medicine resource species richness based on national census of Chinese medicine resources (pilot)].

Based on the data collected by the census team in the national census information management system, the spatial autocorrelation analysis method was used to analyze the similarity of the richness of Chinese herbal medicine resources in the investigated counties. The results showed that the species richness in the investigated counties appeared a tendency to focus on the distribution of the characteristics. Among them, the areas with sparse resources are concentrated in most areas of the north of the Yangtze River, northwest and most areas of Tibet. The areas with abundant resources are concentrated in the areas south of the Yangtze River. The results showed that there were significant differences in the abundance of traditional Chinese medicine resources between regions. The results showed that there were significant differences in the abundance of traditional Chinese medicine resources between regions. Due to the large differences in the land area between the county and the richness of the types of traditional Chinese medicine resources, it is proposed to increase the land area of the traditional Chinese medicine resource census when allocating the fourth national census of Chinese medicine resources by the "factor method", and the richness of traditional Chinese medicine and other indicators, in order to give full play to the efficiency of transfer payment system. Based on the county area and the rich variety of traditional Chinese medicine resources, combined with the national drug resources census pilot work carried out, it is recommended to focus on attention and support in the national medicine resources census work, personnel team, funding, summary of results on the western and southern provinces.

SPIRIT: Systematic Planning of Intelligent Reuse of Integrated Clinical Routine Data. A Conceptual Best-practice Framework and Procedure Model.

BACKGROUND: Secondary use of clinical routine data is receiving an increasing amount of attention in biomedicine and healthcare. However, building and analysing integrated clinical routine data repositories are nontrivial, challenging tasks. As in most evolving fields, recognized standards, well-proven methodological frameworks, or accurately described best-practice approaches for the systematic planning of solutions for secondary use of routine medical record data are missing. OBJECTIVE: We propose a conceptual best-practice framework and procedure model for the systematic planning of intelligent reuse of integrated clinical routine data (SPIRIT). METHODS: SPIRIT was developed based on a broad literature overview and further refined in two case studies with different kinds of clinical routine data, including process-oriented nursing data from a large hospital group and high-volume multimodal clinical data from a neurologic intensive care unit. RESULTS: SPIRIT aims at tailoring secondary use solutions to specific needs of single departments without losing sight of the institution as a whole. It provides a general conceptual best-practice framework consisting of three parts: First, a secondary use strategy for the whole organization is determined. Second, comprehensive analyses are conducted from two different viewpoints to define the requirements regarding a clinical routine data reuse solution at the system level from the data perspective (BOTTOM UP) and at the strategic level from the future users perspective (TOP DOWN). An obligatory clinical context analysis (IN BETWEEN) facilitates refinement, combination, and integration of the different requirements. The third part of SPIRIT is dedicated to implementation, which comprises design and realization of clinical data integration and management as well as data analysis solutions. CONCLUSIONS: The SPIRIT framework is intended to be used to systematically plan the intelligent reuse of clinical routine data for multiple purposes, which often was not intended when the primary clinical documentation systems were implemented. SPIRIT helps to overcome this gap. It can be applied in healthcare institutions of any size or specialization and allows a stepwise setup and evolution of holistic clinical routine data reuse solutions.

Electronic reporting of all reference laboratory results: An important step toward a truly all-encompassing, integrated health record.

Results from reference laboratories are often not easily available in electronic health records. This article describes a multi-pronged, long-term approach that includes bringing send-out tests in-house, upgrading the laboratory information system, interfacing more send-out tests and more reference laboratories, utilizing the "miscellaneous assay" option offered by some reference laboratories, and scanning all remaining paper reports from reference laboratories for display in the electronic health record. This allowed all laboratory results obtained in association with a patient visit, whether performed in-house or at a reference laboratory, to be available in the integrated electronic health record. This was achieved without manual data entry of reference laboratory results, thereby avoiding the risk of transcription errors. A fully integrated electronic health record that contains all laboratory results can be achieved by maximizing the number of interfaced reference laboratory assays and making all non-interfaced results available as scanned documents.

Low Osteoporosis Treatment Initiation Rate in Women after Distal Forearm or Proximal Humerus Fracture: A Healthcare Database Nested Cohort Study.

Treatment initiation rates following fragility fractures have often been reported to be low and in recent years numerous programs have been implemented worldwide to increase them. This study aimed at describing osteoporosis (OP) treatment initiation in a representative sample of women who were hospitalized for a distal forearm fracture (DFF) or proximal humerus fracture (PHF) in 2009-2011 in France. The data source was a nationwide sample of 600,000 individuals, extracted from the French National Insurance Healthcare System database. All women aged 50 years and older who were hospitalized for a DFF or PHF between 2009 and 2011 and who had not received any OP treatment in the preceding 12 months were included in a retrospective cohort study. OP treatments initiated during the year following the fracture were analyzed. From 2009 to 2011, 729 women were hospitalized for a DFF or a PHF and 284 were on OP treatment at the time of the fracture occurrence. Among the 445 women who had no prevalent OP treatment, 131 (29.4%) received supplementation treatment only (vitamin D and/or calcium) and 42 (9.4%) received a pharmacologic OP treatment in the year following their fracture. Pharmacological OP treatments included bisphosphonates (n = 21), strontium ranelate (n = 14), hormone replacement therapy (n = 4), or raloxifene (n = 3). General practitioners prescribed 75% of initial OP treatments. Despite the guidelines published in 2006 and the numerous initiatives to promote post-fracture OP treatment, OP treatment initiation rate in women who were hospitalized for a fragility fracture remained low in 2009-2011 in France.

PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine.

Despite the growing attention given to Traditional Medicine (TM) worldwide, there is no well-known, publicly available, integrated bio-pharmacological Traditional Korean Medicine (TKM) database for researchers in drug discovery. In this study, we have constructed PharmDB-K, which offers comprehensive information relating to TKM-associated drugs (compound), disease indication, and protein relationships. To explore the underlying molecular interaction of TKM, we integrated fourteen different databases, six Pharmacopoeias, and literature, and established a massive bio-pharmacological network for TKM and experimentally validated some cases predicted from the PharmDB-K analyses. Currently, PharmDB-K contains information about 262 TKMs, 7,815 drugs, 3,721 diseases, 32,373 proteins, and 1,887 side effects. One of the unique sets of information in PharmDB-K includes 400 indicator compounds used for standardization of herbal medicine. Furthermore, we are operating PharmDB-K via phExplorer (a network visualization software) and BioMart (a data federation framework) for convenient search and analysis of the TKM network. Database URL: http://pharmdb-k.org, http://biomart.i-pharm.org.