A Linked Open Data-Based Terminology to Describe Libre/Free and Open-source Software: Incremental Development Study

BACKGROUND

There is a variety of libre/free and open-source software (LIFOSS) products for medicine and health care. To support health care and IT professionals select an appropriate software product for given tasks, several comparison studies and web platforms, such as Medfloss.org, are available. However, due to the lack of a uniform terminology for health informatics, ambiguous or imprecise terms are used to describe the functionalities of LIFOSS. This makes comparisons of LIFOSS difficult and may lead to inappropriate software selection decisions. Using Linked Open Data (LOD) promises to address these challenges.

OBJECTIVE

We describe LIFOSS systematically with the help of the underlying Health Information Technology Ontology (HITO). We publish HITO and HITO-based software product descriptions using LOD to obtain the following benefits: (1) linking and reusing existing terminologies and (2) using Semantic Web tools for viewing and querying the LIFOSS data on the World Wide Web.

METHODS

HITO was incrementally developed and implemented. First, classes for the description of software products in health IT evaluation studies were identified. Second, requirements for describing LIFOSS were elicited by interviewing domain experts. Third, to describe domain-specific functionalities of software products, existing catalogues of features and enterprise functions were analyzed and integrated into the HITO knowledge base. As a proof of concept, HITO was used to describe 25 LIFOSS products.

RESULTS

HITO provides a defined set of classes and their relationships to describe LIFOSS in medicine and health care. With the help of linked or integrated catalogues for languages, programming languages, licenses, features, and enterprise functions, the functionalities of LIFOSS can be precisely described and compared. We publish HITO and the LIFOSS descriptions as LOD; they can be queried and viewed using different Semantic Web tools, such as Resource Description Framework (RDF) browsers, SPARQL Protocol and RDF Query Language (SPARQL) queries, and faceted searches. The advantages of providing HITO as LOD are demonstrated by practical examples.

CONCLUSIONS

HITO is a building block to achieving unambiguous communication among health IT professionals and researchers. Providing LIFOSS product information as LOD enables barrier-free and easy access to data that are often hidden in user manuals of software products or are not available at all. Efforts to establish a unique terminology of medical and health informatics should be further supported and continued.

RustOnt: An Ontology to Explain Weather Favorable Conditions of the Coffee Rust

Crop disease management in smart agriculture involves applying and using new technologies to reduce the impact of diseases on the quality of products. Coffee rust is a disease that factors such as poor agronomic management activities and climate conditions may favor. Therefore, it is crucial to identify the relationships between these factors and this disease to learn how to face its consequences and build intelligent systems to provide appropriate management or help farmers and experts make decisions accordingly. Nevertheless, there are no studies in the literature that propose ontologies to model these factors and coffee rust. This paper presents a new ontology called RustOnt to help experts more accurately model data, expressions, and samples related to coffee rust and apply it whilst taking into account the geographical location where the ontology is adopted. Consequently, this ontology is crucial for coffee rust monitoring and management by means of smart agriculture systems. RustOnt was successfully evaluated considering quality criteria such as clarity, consistency, modularity, and competence against a set of initial requirements for which it was built.

Monitoring System of the Mar Menor Coastal Lagoon (Spain) and Its Watershed Basin Using the Integration of Massive Heterogeneous Data

The tool created aims at the environmental monitoring of the Mar Menor coastal lagoon (Spain) and the monitoring of the land use of its watershed. It integrates heterogeneous data sources ranging from ecological data obtained from a multiparametric oceanographic sonde to agro-meteorological data from IMIDA's network of stations or hydrological data from the SAIH network as multispectral satellite images from Sentinel and Landsat space missions. The system is based on free and open source software and has been designed to guarantee maximum levels of flexibility and scalability and minimum coupling so that the incorporation of new components does not affect the existing ones. The platform is designed to handle a data volume of more than 12 million records, experiencing exponential growth in the last six months. The tool allows the transformation of a large volume of data into information, offering them through microservices with optimal response times. As practical applications, the platform created allows us to know the ecological state of the Mar Menor with a very high level of detail, both at biophysical and nutrient levels, being able to detect periods of oxygen deficit and delimit the affected area. In addition, it facilitates the detailed monitoring of the cultivated areas of the watershed, detecting the agricultural use and crop cycles at the plot level. It also makes it possible to calculate the amount of water precipitated on the watershed and to monitor the runoff produced and the amount of water entering the Mar Menor in extreme events. The information is offered in different ways depending on the user profile, offering a very high level of detail for research or data analysis profiles, concrete and direct information to support decision-making for users with managerial profiles and validated and concise information for citizens. It is an integrated and distributed system that will provide data and services for the Mar Menor Observatory.

Validity and Absolute Reliability of the Cobb Angle in Idiopathic Scoliosis with TraumaMeter Software

The Cobb angle value is a critical parameter for evaluating adolescent idiopathic scoliosis (AIS) patients. This study aimed to evaluate a software’s validity and absolute reliability to determine the Cobb angle in AIS digital X-rays, with two different degrees of experienced observers. Four experts and four novice evaluators measured 35 scoliotic curves with the software on three separate occasions, one month apart. The observers re-measured the same radiographic studies on three separate occasions three months later but on conventional X-ray films. The differences between the mean bias errors (MBE) within the experience groups were statistically significant between the experts (software) and novices (manual) (p < 0.001) and between the novices (software) and novices (manual) (p = 0.005). When measured with the software, the intra-group error in the expert group was MBE = 1.71 ± 0.61° and the intraclass correlation coefficient (ICC (2,1)) = 0.986, and in the novice group, MBE = 1.9 ± 0.67° and ICC (2,1) = 0.97. There was almost a perfect concordance among the two measurement methods, ICC (2,1) = 0.998 and minimum detectable change (MCD95) < 0.4°. Control of the intrinsic error sources enabled obtaining inter- and intra-observer MDC95 < 0.5° in the two experience groups and with the two measurement methods. The computer-aided software TraumaMeter increases the validity and reliability of Cobb angle measurements concerning manual measurement.

Validity and reliability of a computer-assisted system method to measure axial vertebral rotation

BACKGROUND

Axial vertebral rotation and Cobb's angle are essential parameters for analysing adolescent idiopathic scoliosis. This study's scope evaluates the validity and absolute reliability of application software based on a new mathematical equation to determine the axial vertebral rotation in digital X-rays according to Raimondi's method in evaluators with different degrees of experience.

METHODS

Twelve independent evaluators with different experience levels measured 33 scoliotic curves in 21 X-rays with the software on three separate occasions, separated one month. Using the same methodology, the observers re-measured the same radiographic studies three months later but on X-ray films and in a conventional way.

RESULTS

Both methods show good validity and reliability, and the intraclass correlation coefficients are almost perfect. According to our results, the software increases 1.7 times the validity and 1.9 times the absolute reliability of axial vertebral rotation on digital X-rays according to Raimondi's method, compared to the conventional manual measurement.

CONCLUSIONS

The intra-group and inter-group agreement of the measurements with the software shows equal or minor variations than with the manual method, among the different measurement sessions and in the three experience groups. There is almost perfect agreement between the two measurement methods, so the equation and the software may be helpful to increase the accuracy in the axial vertebral rotation assessment.

Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide Analysis

Intact glycopeptide identification has long been known as a key and challenging barrier to the comprehensive and accurate understanding the role of glycosylation in an organism. Intact glycopeptide analysis is a blossoming field that has received increasing attention in recent years. MS-based strategies and relative software tools are major drivers that have greatly facilitated the analysis of intact glycopeptides, particularly intact N-glycopeptides. This article provides a systematic review of the intact glycopeptide-identification process using MS data generated in shotgun proteomic experiments, which typically focus on N-glycopeptide analysis. Particular attention is paid to the software tools that have been recently developed in the last decade for the interpretation and quality control of glycopeptide spectra acquired using different MS strategies. The review also provides information about the characteristics and applications of these software tools, discusses their advantages and disadvantages, and concludes with a discussion of outstanding tools.

Visual function, digital behavior and the vision performance index

Historically, visual acuity has been the benchmark for visual function. It is used to measure therapeutic outcomes for vision-related services, products and interventions. Quantitative measurement of suboptimal visual acuity can potentially be corrected optically with proper refraction in some cases, but in many cases of reduced vision there is something else more serious that can potentially impact other aspects of visual function such as contrast sensitivity, color discrimination, peripheral field of view and higher-order visual processing. The measurement of visual acuity typically requires stimuli subject to some degree of standardization or calibration and has thus often been limited to clinical settings. However, we are spending increasing amounts of time interacting with devices that present high-resolution, full color images and video (hereafter, digital media) and can record our responses. Most of these devices can be used to measure visual acuity and other aspects of visual function, not just with targeted testing experiences but from typical device interactions. There is growing evidence that prolonged exposure to digital media can lead to various vision-related issues (eg, computer vision syndrome, dry eye, etc.). Our regular, daily interactions (digital behavior) can also be used to assess our visual function, passively and continuously. This allows us to expand vision health assessment beyond the clinic, to collect vision-related data in the whole range of settings for typical digital behavior from practically any population(s) of interest and to further explore just how our increasingly virtual interactions are affecting our vision. We present a tool that can be easily integrated into digital media to provide insights into our digital behavior.

Wireless Capsule Endoscopy in Correlation with Software Application in Gastrointestinal Diseases

Wireless capsule endoscopy is one of the most recent investigation techniques of gastrointestinal pathology. Unlike conventional upper and lower endoscopy, it has the advantages of being a noninvasive and painless procedure. One of the capsule endoscopy disadvantages is represented by the necessary time to analyze the video frames obtained. Software applications proposed in this purpose could offer support in the images evaluation. Different algorithms have been described in the literature, but further research is needed to establish the practical value of computer vision tools in gastroenterology.

A lot of action, but not in the right direction: systematic review and content analysis of smartphone applications for the prevention, detection, and management of cancer

Background

Mobile phones have become nearly ubiquitous, offering a promising means to deliver health interventions. However, little is known about smartphone applications (apps) for cancer.

Objective

The purpose of this study was to characterize the purpose and content of cancer-focused smartphone apps available for use by the general public and the evidence on their utility or effectiveness.

Methods

We conducted a systematic review of the official application stores for the four major smartphone platforms: iPhone, Android, Nokia, and BlackBerry. Apps were included in the review if they were focused on cancer and available for use by the general public. This was complemented by a systematic review of literature from MEDLINE, Embase, and the Cochrane Library to identify evaluations of cancer-related smartphone apps.

Results

A total of 295 apps from the smartphone app stores met the inclusion criteria. The majority of apps targeted breast cancer (46.8%, 138/295) or cancer in general (28.5%, 84/295). The reported app purpose was predominantly to raise awareness about cancer (32.2%, 95/295) or to provide educational information about cancer (26.4%, 78/295), followed by apps to support fundraising efforts (12.9%, 38/295), assist in early detection (11.5%, 34/295), promote a charitable organization (10.2%, 30/295), support disease management (3.7%, 11/295), cancer prevention (2.0%, 6/295), or social support (1.0%, 3/295). The majority of the apps did not describe their organizational affiliation (64.1%, 189/295). Apps affiliated with non-profit organizations were more likely to be free of cost (χ²₁=16.3, P<.001) and have a fundraising or awareness purpose (χ²₂=13.3, P=.001). The review of the health literature yielded 594 articles, none of which reported an evaluation of a cancer-focused smartphone application.

Conclusions

There are hundreds of cancer-focused apps with the potential to enhance efforts to promote behavior change, to monitor a host of symptoms and physiological indicators of disease, and to provide real-time supportive interventions, conveniently and at low cost. However, there is a lack of evidence on their utility, effectiveness, and safety. Future efforts should focus on improving and consolidating the evidence base into a whitelist for public consumption.