Comprehensive Interoperability Research Articles

Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR

In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of metadata in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic interchange format across domains but can lead to inconsistency between files in the presentation of metadata. To enable fully autonomous machine actionable data flow, generic elements need to be further specified. We strongly support the merits of the FAIR principles and see the need to facilitate them also through technical implementation specifications. They form a basis for the proposed VCF extensions here. We have learned from the existing application of VCF that the definition of relevant metadata using controlled standards, vocabulary and the consistent use of cross-references via resolvable identifiers (machine-readable) are particularly necessary and propose their encoding. VCF is an established standard for the exchange and publication of genotyping data. Other data formats are also used to capture variant data (for example, the HapMap and the gVCF formats), but none currently have the reach of VCF. For the sake of simplicity, we will only discuss VCF and our recommendations for its use, but these recommendations could also be applied to gVCF. However, the part of the VCF standard relating to metadata (as opposed to the actual variant calls) defines a syntactic format but no vocabulary, unique identifier or recommended content. In practice, often only sparse descriptive metadata is included. When descriptive metadata is provided, proprietary metadata fields are frequently added that have not been agreed upon within the community which may limit long-term and comprehensive interoperability. To address this, we propose recommendations for supplying and encoding metadata, focusing on use cases from plant sciences. We expect there to be overlap, but also divergence, with the needs of other domains.

Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR

In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of metadata in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic interchange format across domains but can lead to inconsistency between files in the presentation of metadata. To enable fully autonomous machine actionable data flow, generic elements need to be further specified. We strongly support the merits of the FAIR principles and see the need to facilitate them also through technical implementation specifications. They form a basis for the proposed VCF extensions here. We have learned from the existing application of VCF that the definition of relevant metadata using controlled standards, vocabulary and the consistent use of cross-references via resolvable identifiers (machine-readable) are particularly necessary and propose their encoding. VCF is an established standard for the exchange and publication of genotyping data. Other data formats are also used to capture variant data (for example, the HapMap and the gVCF formats), but none currently have the reach of VCF. For the sake of simplicity, we will only discuss VCF and our recommendations for its use, but these recommendations could also be applied to gVCF. However, the part of the VCF standard relating to metadata (as opposed to the actual variant calls) defines a syntactic format but no vocabulary, unique identifier or recommended content. In practice, often only sparse descriptive metadata is included. When descriptive metadata is provided, proprietary metadata fields are frequently added that have not been agreed upon within the community which may limit long-term and comprehensive interoperability. To address this, we propose recommendations for supplying and encoding metadata, focusing on use cases from plant sciences. We expect there to be overlap, but also divergence, with the needs of other domains.

Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR.

In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of (meta-) data in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic interchange format across domains but can lead to inconsistency between files in the presentation of metadata. To enable fully autonomous machine actionable data flow, generic elements need to be further specified. We strongly support the merits of the FAIR principles and see the need to facilitate them also through technical implementation specifications. VCF files are an established standard for the exchange and publication of genotyping data. Other data formats are also used to capture variant call data (for example, the HapMap format and the gVCF format), but none currently have the reach of VCF. In VCF, only the sites of variation are described, whereas in gVCF, all positions are listed, and confidence values are also provided. For the sake of simplicity, we will only discuss VCF and our recommendations for its use. However, the part of the VCF standard relating to metadata (as opposed to the actual variant calls) defines a syntactic format but no vocabulary, unique identifier or recommended content. In practice, often only sparse (if any) descriptive metadata is included. When descriptive metadata is provided, proprietary metadata fields are frequently added that have not been agreed upon within the community which may limit long-term and comprehensive interoperability. To address this, we propose recommendations for supplying and encoding metadata, focusing on use cases from the plant sciences. We expect there to be overlap, but also divergence, with the needs of other domains.

A Model-driven Architecture for Collaborative Business Processes

The Model Driven Engineering was developed to make application development more flexible, it provides a comprehensive interoperability framework for defining interconnected systems, and aims to reduce the inherent complexity that partners must face when developing their systems. In collaborative environments where systems are made through the collaboration of several departments or companies, the MDA (Model Driven Architecture) approach seems efficient in maintaining and developing this type of system. This paper show the use of MDE in the context of business process management and present in detail an architecture for the development of collaborative business processes.

Htsget: a protocol for securely streaming genomic data.

SummaryStandardized interfaces for efficiently accessing high-throughput sequencing data are a fundamental requirement for large-scale genomic data sharing. We have developed htsget, a protocol for secure, efficient and reliable access to sequencing read and variation data. We demonstrate four independent client and server implementations, and the results of a comprehensive interoperability demonstration.Availability and implementation http://samtools.github.io/hts-specs/htsget.html Supplementary information Supplementary data are available at Bioinformatics online.

A neutral approach for interoperability in the field of 3D measurement data management

Abstract In this paper, a novel approach for a comprehensive measurement data management (MDM) is introduced, that fulfils the technological requirements of industry 4.0 for complex process chains. Today, a variety of measurement equipment, methods and applications are used in the manufacturing industry to ensure a specified level of product quality. That is, in quality management, a large number of devices and processes are used, which differ in terms of performance, functional properties, but also in the adaptability to interdisciplinary PLM processes. Regarding the variety of measurement applications, there is often a tight interweaving between hardware and software, connected via proprietary interfaces. The concept of MDM is to address the quality data management and exchange of measurement-relevant data throughout the quality process. Overall, MDM ensures the data exchange between diverse measurement equipment and measurement software from different software and hardware producers within a company and across company boundaries. The aim is to integrate the flow of information within quality assurance through the use of neutral data formats and achieve a comprehensive interoperability of the individual system components. For this purpose, a measurement data interface is defined, that allows exchanging all relevant information concerning the quality management. In doing so, a comprehensive interoperability of all system components is strived for. In this paper, existing approaches for MDM are introduced and compared. Then, the work of the project group 3D measurement data management (3D MDM) is presented. This group evolves and refines the I++ DMS interface definition using a collaborative approach, involving both users and software suppliers in the field of MDM.

Standardization on for Mastering Healthcare Transformation on - Challenges and Solutions

Background: The ongoing healthcare transformation results in systems medicine and personalized care. This requires advanced interoperability scenarios. Objectives: The paper aims at introducing a reference architecture model to enable the harmonization of existing and future specifications and standards. Methods: For enabling the harmonization of standards and specifications, they have to be correctly and formally represented using a system-theoretical, architecture-centric, ontology-based, policy-driven approach. Results: An Interoperability Reference Architecture Model has been developed and standardized at ISO TC 215 and CEN TC 251. It is used for re-engineering specifications and standards, that way enabling harmonization with any other specification. The proposed modeling methodology has also been introduced in several HL7 specifications. It is demonstrated by re-engineering the ISO 13606 reference model. Conclusion: The approach presented in the paper off ers a solution for comprehensive interoperability at any interoperability level also including user domains and the individual user. That way, never-ending revision cycles and negotiation rounds for integrating diff erent specifications in complex eHealth solutions become obsolete.

Applying Electronic Medical Records in Health Care: Physicians' Perspective.

In order to fulfill comprehensive interoperability and recognize the electronic medical records (EMRs') benefits, physicians' attitudes toward using and applying EMR must be recognized. The purpose of this study was to present an integrated model of applying EMRs by physicians. This was a cross sectional study in which a sample of 330 physicians working in hospitals affiliated to the Tehran University of medical sciences (TUMS) was selected. Physicians' attitudes toward using and accepting EMR in health care have been analyzed by an integrated model of two classical theories i.e. technology acceptance model (TAM) and diffusion of innovation (DOI). The model was tested using an empirical survey. The final model was tested by structural equation modeling (SEM) and represented by Analysis of Moment Structures (AMOS). The results suggest that the hybrid model explains about 43 percent of the variance of using and accepting of EMRs (R2=0.43). The findings also evidenced that Perceived Usefulness (PU), Perceived Ease of Use (PEOU), Relative Advantage, Compatibility, Complicatedness and Trainability have direct and significant effect on physicians' attitudes toward using and accepting EMRs. But concerning observeability, significant path coefficient was not reported. The integrated model supplies purposeful intuition for elucidates and anticipates of physicians' behaviors in EMRs adoption. The study identified six relevant factors that affect using and applying EMRs that should be subsequently the major concern of health organizations and health policy makers.

Standards and solutions for eHealth Interoperability-

There is no doubt that the way to high quality, safe and e cient health services leads to distributed cooperative care (shared care) supported by information and communication technologies [1]. Such approach requires interoperability between all principals (persons, organizations, devices, applications, components) involved [1]. Nevertheless, many papers and organizations (e.g. [2]) dedicated to health care interoperability still refer to the IEEE Dictionary de nition of (semantic) interoperability as ... the ability of two or more systems or components to exchange information and to use the information that has been exchanged [3]. However, the problem of interoperability is not limited to the early days' EDI challenge of harmonized data representation and exchange protocol. Nowadays, it is the challenge of the legally, culturally, socially, educationally and organizationally impacted aspect of commonality regarding business processes and objectives, but also interests, knowledge and skills to cooperate for jointly meeting those business objectives [1]. Those aspects go far beyond ICT ontology and communication protocols as commonly understood today. Depending on the sharing of those common aspects, comprehensive interoperability can be provided at di erent interoperability levels such as structural, syntactic, semantic or services, semantic, or services interoperability depending on the level of shared knowledge and skills [1].

Intelligent security and privacy solutions for enabling personalized telepathology.

Starting with the paradigm change of health systems towards personalized health services, the paper introduces the technical paradigms to be met for enabling ubiquitous pHealth including ePathology. The system-theoretical, architecture-centric approach to mobile, pervasive and autonomous solutions has to be based on an open component system framework such as the Generic Component Model. The crucial challenge to be met for comprehensive interoperability is multi-disciplinary knowledge representation, which must be integrated into the aforementioned framework. The approach is demonstrated for security and privacy services fundamental for any eHealth or ePathology environment.

GIS Design: A Review of Current Issues in Interoperability

AbstractThe evolution of Geographic Information Systems (GIS) has witnessed an important step towards achieving interoperability through the communication, exchange, cooperation and sharing of resources between systems. The main developments in interoperability include the use of standards for transfer and exchange of geographical information, the integration of different data types up to the development of comprehensive interoperability models. This article aims to review the main advances in interoperability of GIS and provide a basis to identify the future research issues in this field. It first considers the various points of view from which interoperability can be defined and then examines the concept of interoperability itself. An overview is provided on how interoperability can be modelled by discussing the main aspects that directly have an effect on how interoperability levels have been created according to different contexts and purposes of use. It also points out the significant advances in terms of measures that can determine the ability of a GIS to interoperate with other systems, predict the resources needed for successful interoperation, and discover techniques useful to achieving interoperability. We conclude with some suggestions where the research will go next.

Simulation interoperability — where are the challenges?

AbstractThis paper will discuss and review the nature of simulation interoperability. It will analyse the scope of interoperability in terms of basic intercommunication features (technical interoperability), fitness for purpose (functional interoperability) and suitability for use in distributed training (training interoperability). Only technical interoperability has received close attention, through DIS and HLA standards. Other aspects still present many challenges. The ability to create a common ‘outside world’ database is frequently cited as the dominant component and principal challenge in any discussion of interoperability. While this is often true, this paper identifies how interactions among all participants in the shared operational space (‘battlespace’) should be the starting point in defining interoperability, these interactions of course being dictated by the training requirement. Interactions are accomplished through ‘sensors’, which could be the human eye, night vision goggles (NVGs), radios, data links, radar, FLIR etc. Comprehensive interoperability demands comparable levels of modelling among all participants, including the effect of the environment (whether terrain or meteorology) on the performance of each simulator’s sensor suite. The paper will identify these significant effects and discuss where simulation technology is challenged and needs to advance, particularly in the context of mission simulation of future joint (Air/Land/Maritime) operations. The paper concludes with some discussion of the way ahead, including how guidelines based on experience could augment the use of standards.

From the field

Widespread adoption of information technology is now regarded as a pathway to improving health care and achieving the Institute of Medicine’s highly regarded six aims for redesigning care. Achieving these aims requires fresh approaches to health system design, including continuous healing relationships between physicians and patients and provision of tools to help patients be more active participants in their own care. Personal health records (PHRs) might allow patients and providers to develop new ways of collaborating and provide the basis for broader transformation of the health care system. Federal policies can be key catalysts in accelerating PHR development and adoption. F our years have pas sed s ince the Institute of Medicine (IOM) issued its six aims for redesigning health care for the twenty-first century: providing safe, effective, patient-centered, timely, efficient, and equitable health care.1 The current enthusiasm for adoption of electronic health records (EHRs) and broad connectivity across the health care system reflects the belief that information technology (IT) can hasten the nation’s ability to achieve these six aims. Less often mentioned are the IOM’s ten design rules: care based on continuous healing relationships; customization based on patients’ needs and values; the patient as the source of control; shared knowledge and the free flow of information; evidence-based decision making; safety as a system property; the need for transparency; anticipation of needs; continuous decrease in waste; and cooperation among clinicians. The first four of these rules imply that the IOM’s worthy aims will not be achieved unless we build a system in which patients share information and control with professionals. The mere installation of EHRs—even with comprehensive interoperability—will not sufficiently engage patients in the health system. Patients As ‘Copilots’ In Their Care Patients have little access to information and knowledge that can help them participate in, let alone guide, their own care. The IOM design rules propose that patients have shared knowledge and free flow of information. At a minimum, they need access to information from their providers’ EHRs—their own diagnoses, medications, allergies, lab test results, visit summaries, and other findings over time. A continuous healing relationship is a twoway interaction (whether electronic or faceto-face) between patients and their providers. 1 2 9 0 S e p t e m b e r / O c t o b e r 2 0 0 5 H e a l t h T r a c k i n g DOI 10.1377/hlthaff.24.5.1290 ©2005 Project HOPE–The People-to-People Health Foundation, Inc. Paul Tang (tang@smi.stanford.edu) is the chief medical information officer at the Palo Alto Medical Foundation in Palo Alto, California. David Lansky is director of the Health Program at the Markle Foundation in New York