XML-based Format Research Articles

Enhancing scientific publishing: automatic conversion to JATS XML

JATS XML (Journal Article Tag Suite) is an XML-based format used for publishing scholarly content. It has multiple advantages over traditional publishing methods but faces adoption challenges due to the need for relatively expensive tools and/or manual work. In 2023, the HRČAK Portal’s team enabled automatic full-text con-version from DOCX to JATS XML which does not require prior knowledge of XML nor additional tools. Created JATS facilitates content and reference mining as well as transformation to HTML. It also improves cross-device compatibility and produces interactive links for an enhanced reading experience.

Ontology-Based Laboratory Data Acquisition With EnzymeML for Process Simulation of Biocatalytic Reactors

The presented work explores the use of ontologies and standardized enzymatic data to set up enzymatic reactions in process simulators, such as DWSIM. Setting up an automated workflow to start a process simulation based on enzymatic data obtained from the laboratory can help save costs and time during the development phase. Standardized conditions are crucial for accurate comparison and analysis of enzymatic data, where ontologies provide a standardized vocabulary and semantic relations between relevant concepts. To ensure standardized data, an electronic lab notebook (ELN) is used based on EnzymeML, an open standard XML-based format for enzyme kinetics data. Furthermore, two ontologies are merged and the result is extended for the use in the Python-based workflow. The resulting data is stored in a knowledge graph for research data in a machine-accessible and human-readable format. Thus, the study demonstrates a workflow that allows for the direct translation of ELN data into a process simulation via ontologies.

XLUM: an open data format for exchange and long-term preservation of luminescence data

Abstract. The concept of open data has become the modern science meme, and major funding bodies and publishers support open data. On a daily basis, however, the open data mandate frequently encounters technical obstacles, such as a lack of a suitable data format for data sharing and long-term data preservation. Such issues are often community-specific and best addressed through community-tailored solutions. In Quaternary sciences, luminescence dating is widely used for constraining the timing of event-based processes (e.g. sediment transport). Every luminescence dating study produces a vast body of primary data that usually remains inaccessible and incompatible with future studies or adjacent scientific disciplines. To facilitate data exchange and long-term data preservation (in short, open data) in luminescence dating studies, we propose a new XML-based structured data format called XLUM. The format applies a hierarchical data storage concept consisting of a root node (node 0), a sample (node 1), a sequence (node 2), a record (node 3), and a curve (node 4). The curve level holds information on the technical component (e.g. photomultiplier, thermocouple). A finite number of curves represent a record (e.g. an optically stimulated luminescence curve). Records are part of a sequence measured for a particular sample. This design concept allows the user to retain information on a technical component level from the measurement process. The additional storage of related metadata fosters future data mining projects on large datasets. The XML-based format is less memory-efficient than binary formats; however, its focus is data exchange, preservation, and hence XLUM long-term format stability by design. XLUM is inherently stable to future updates and backwards-compatible. We support XLUM through a new R package xlum, facilitating the conversion of different formats into the new XLUM format. XLUM is licensed under the MIT licence and hence available for free to be used in open- and closed-source commercial and non-commercial software and research projects.

ECG Standards and Formats for Interoperability between mHealth and Healthcare Information Systems: A Scoping Review.

Interoperability is defined as the ability of a system or device to communicate between different technologies and software applications. This allows the exchange and use of data in an efficient, precise, and robust way. The present article gives researchers and healthcare information systems developers a qualitative and quantitative synthesis of the state of knowledge related to data formats and data standards proposed for mHealth devices interoperability in healthcare information systems that retrieve and store ECG data. We carry out a scoping review to answer to following questions: (1) What digital data formats or data standards have been proposed for the interoperability of electrocardiograph data between traditional healthcare information systems and mobile healthcare information systems? (2) What are the advantages and disadvantages of these data formats or data standards? The scoping review was conducted in four databases in accordance with the JBI methodology for scoping reviews, and in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). A total of 4018 studies were identified of which 30 studies met the inclusion criteria. Based on our findings, we identify four standards and nine formats for capturing and storing streaming ECG data in mobile health applications. The standards used were HL7, SCP-ECG, x73-PHD, and PDF/A. Formats include CSV, PDF-ECG, and seven XML-based formats. These are ECG-XML, HL7-XML, mPCG-XML, mECGML, JSON, SaECG, and CDA R2.

SBML to bond graphs: From conversion to composition

The Systems Biology Markup Language (SBML) is a popular software-independent XML-based format for describing models of biological phenomena. The BioModels Database is the largest online repository of SBML models. Several tools and platforms are available to support the reuse and composition of SBML models. However, these tools do not explicitly assess whether models are physically plausible or thermodynamically consistent. This often leads to ill-posed models that are physically impossible, impeding the development of realistic complex models in biology. Here, we present a framework that can automatically convert SBML models into bond graphs, which imposes energy conservation laws on these models. The new bond graph models are easily mergeable, resulting in physically plausible coupled models. We illustrate this by automatically converting and coupling a model of pyruvate distribution to a model of the pentose phosphate pathway.

Open-source feature detection for non-target LC-MS analytics.

Non-target screening techniques using high-resolution mass spectrometers become more and more important for environmental sciences. Highly reliable and sophisticated software solutions are required to deal with the large amount of data obtained from such analyses. Processing of high-resolution LC-HRMS data was performed upon conversion into an open, XML-based data format followed by an automated assignment of chromatographic peaks using the open-source programming language R. Raw data from three different LC-HRMS systems were processed as a proof of principle. We present a simple and straightforward algorithm to extract chromatographic peaks from previously m/z-centroided data based on the open-source programming language R and C++. The working principle and processing parameters are explained in detail. A ready-to-use script is provided in the supporting information. The developed algorithm enables a comprehensible automated peak picking of non-target LC-MS data. Application to three completely different HRMS raw data files showed reasonable False Positives and False Negatives detection and moderate calculation times.

What Does Diggs Do For Me? Better, Faster, Cheaper Is the Goal!

For the past decade, the Ohio Department of Transportation (ODOT) has been at the forefront of advancing geotechnical data management associated with its investment and leadership related to DIGGS (Data Interchange for Geotechnical and Geoenvironmental Specialists). DIGGS is a robust, open standard, XML-based format for sharing with project partners a wide variety of geotechnical data related to site investigations. It’s currently being expanded to handle other types of geotechnical data from sources such as pile load testing, performance monitoring instrumentation, and geo-environmental site monitoring. DIGGS is compliant with industry standards and best practices for exchanging data.

AQT—A Query Template for AutomationML

This article proposes the AutomationML query template (AQT) for accessing engineering data stored in the XML-based data format AutomationML (IEC 62714). The motivation of AQT is to facilitate query construction for domain experts who are familiar with AutomationML but unskilled in programming. The contribution of the article is threefold. First, AQT has an AutomationML-based syntax, which allows constructing queries using conventional AutomationML tools, e.g., the AutomationML Editor. Second, the formal semantics of AQT is defined based on the notion of tree pattern queries , which are a fundamental concept for querying tree-structured data, including XML. Finally, algorithms are presented for the automated translation from AQTs to XPath and XQuery programs, which can be executed on any standard-conform XQuery processors. We show that AQT covers the essential query requirements for AutomationML and provide a prototype implementation in Java.

OBDMR: An Ontology-Based Data Model for Railways

The domain of the railway system is vast and complex since it includes several sub-domains hierarchy in it. These sub-domains include different branches of technology and operational hierarchy. Many types of research are running on and have happened in this vast domain along with different technologies. Among all available technologies ontology is the single one which talks about semantics and thus supports the decision support system. This paper proposes an OBDMR model for railway systems to integrate the information at the knowledge level. The paper has used railML (version 2.2) as a data resource as railML covers all the aspects of the railway system. railML (Railway Mark-up Language) is an open, XML-based data exchange format for data interoperability of railway application. The proposed ontology adds the semantics to the given data and even allows to infer new information from current data which XML cannot do. OBDMR is capable of taking decisions by automated reasoning using software agents. A generic model proposed in this paper satiates the standards and specifications of most countries’ railway systems. A use-case for Indian Railways is discussed with some examples.

GRID-system Based on European EGI Standards for Large-scale Calculations Using the Original Accelerated Method of Quantum Chemistry

Based on the analysis of modern tools for creating GRID-type information systems that are part of the European EGI “standard” – UMD repository (including new versions of Globus Toolkit, ARC, dCache, etc.), the applying of GRID systems for computational chemistry is briefly discussed. The GRID system created by the authors combines two clusters with Linux CentOS 7 and is based on software from UMD-4. The relevance and effectiveness of batch processing systems (we use Torque 4.2.10) in quantum chemical calculations is increased for mass calculations of docking complexes (including for drug modeling problems), for which an improved semiempirical method with more efficient approximations was proposed, implemented in the Fortran-95 LSSDOCK software package. For such calculations, new approximation methods have been developed, including for DFT functionals, and their software implementation is carried out. Converters of calculation results by LSSDOCK into a natural for GRID XML-based format CML version 3 are developed. Using the CML format based on dCache software, a single tree of a virtual GRID filesystem distributed between heterogeneous nodes is used to store the results of LSSDOCK calculations.

Framework for energy efficiency optimization of industrial systems based on the Control Layer Model

Abstract In the context of sustainable manufacturing, the energy efficient operation of industrial systems is of major interest. This paper presents a modular framework for practical research about energy efficiency optimization of complex technical systems. Whereas many approaches focus on stand-alone machines or processes, this approach is concerned with energy-related coupling of several entities. Using a method for energy-related key performance indicators, the overall efficiency is deduced from all subsystems. A given topology is modeled in an XML-based format, inspired by AutomationML. The framework gives the opportunity to analyze and compare optimization algorithms. First experiments with two optimization algorithms were applied to a simulated cooling system.

A tool written in Scala for preparation and analysis in MD simulation and 3D-RISM calculation of biomolecules.

Researchers studying biomolecules require easy-to-use, customizable tools allowing them to effectively use other molecular science packages written for molecular dynamics (MD), quantum chemistry, statistical mechanics, and molecular graphics. This paper presents a Scala tool for the computational science of biomolecules (STCSB) developed in Scala, which allows users to prepare and run MD simulations, as well as perform three-dimensional reference interaction site model (3D-RISM) calculations of biomolecules. Features of the STCSB include the following: (1) a cross-platform application running on a Java virtual machine; (2) handling hierarchical XML-based data formats such as the protein data bank markup language (PDBML); (3) prepared application programming interfaces (APIs) with both character user interface (CUI) and graphical user interface (GUI) options; (4) prepared APIs for molecular graphics; and (5) a scalable source code based on the Model-View-Controller (MVC) architectural pattern.

Smart factory: Jdf and XJdf

In this paper, the relation between “Industry 4.0” and the metadata formats JDF/XJDF is discussed. While “Industry 4.0” is a term for a certain method of production in general, the XML-based data formats JDF/XJDF are commonly considered being technologies for implementing Industry 4.0 production in the graphic arts industry. The paper shows that the original architecture behind JDF, however, is more compat-ible with Industry 4.0 that the new XJDF format. For this purpose, some important features of these two data formats are outlined.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).

The creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given simulation experiment, (i) which models to use; (ii) which modifications to apply to models before simulation; (iii) which simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1) implemented support for the encoding of basic time course simulations. SED-ML L1V2 added support for more complex types of simulations, specifically repeated tasks and chained simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a simulation experiment.

A PROPOSAL FOR GENERALIZATION OF 3D MODELS

Abstract. In recent years, 3D models have been created of many cities around the world. Most of the 3D city models have been introduced as completely graphic or geometric models, and the semantic and topographic aspects of the models have been neglected. In order to use 3D city models beyond the task, a generalization is necessary. CityGML is an open data model and XML-based format for the storage and exchange of virtual 3D city models. Level of Details (LoD) which is an important concept for 3D modelling, can be defined as outlined degree or prior representation of real-world objects. The paper aim is first describes some requirements of 3D model generalization, then presents problems and approaches that have been developed in recent years. In conclude the paper will be a summary and outlook on problems and future work.

A Tool to Graphically Edit CP-Nets

Conditional preference networks (CP-nets) are a mathematical formalism for compactly representing preferences over combinatorial domains. The software package presented allows editing of CP-nets through a graphical interface, loads and saves to an XML-based file format, and detects properties of the currently loaded CP-net.

Using the SpineML toolchain to simulate an integrated brain and biomechanical model of the oculomotor system

Event Abstract Back to Event Using the SpineML toolchain to simulate an integrated brain and biomechanical model of the oculomotor system Sebastian S. James1*, Alexander Cope2, Alexander Blenkinsop1, Chris Papapaulou3, Konstantinos Moustakas3, Sean Anderson4 and Kevin Gurney1 1 The University of Sheffield, Psychology, United Kingdom 2 The University of Sheffield, Computer Science, United Kingdom 3 The University of Patras, Electrical and Computer Engineering, Greece 4 The University of Sheffield, Automatic Control Systems Engineering, United Kingdom SpineML is a declarative XML-based format for the description of neural network models. It is based on the INCF NineML format[1]. SpineCreator[2] is an editor for the SpineML format which allows a researcher to define and lay out a model graphically, rather than using coded instructions. In addition to defining the model components and network, SpineCreator allows the definition of “experiments”, which declare how the model should be executed; inputs, outputs to log, model lesions and model property changes are all defined in the SpineML experiment. SpineML_2_BRAHMS[3] is one of several simulation backends for a SpineML model (others are SpineML_2_GeNN[4] & Damson[5]). SpineML_2_BRAHMS makes use of the BRAHMS[6,7] middleware to simulate the model on conventional CPUs and high performance computer systems. SpineML_2_BRAHMS is a set of scripts which first converts the SpineML declaration of a model's neuron components into C++, and the model's network into a BRAHMS system definition. SpineML_2_BRAHMS then compiles the C++ representation of the components and executes the system using BRAHMS. Collectively, this set of software is referred to as the SpineML toolchain. We will demonstrate several ways to work with a pure SpineML model, including the use of the SpineCreator editor, direct modification of the SpineML XML code and programmatic modification of the model using Jupyter[8] notebooks. We will discuss the use of revision control systems, such as git[9], to manage changes to a model. A common workflow is to modify the model using SpineCreator, push changes (with comments) to a git repository, then pull the updated SpineML model description onto an HPC system for execution using SpineML_2_BRAHMS. Existing rate-coded and spiking models of basal ganglia from our research group will be used as examples. One challenge, which we have been working on within the EU-funded NoTremor project, is how to integrate brain and neuro-muscular models to enable the combined model to demonstrate physical behaviour. Here, we make use of features in BRAHMS which permit the integration of a biomechanical eye within the SpineML toolchain. This allows brain and brainstem SpineML models to drive the motoneuron activations which control the eye's movement. The eye's rotational state is fed back into the brain model making a closed-loop system. This large model, which contains retina, cortex, superior colliculus, basal ganglia and brainstem oculomotor populations, forms an good example of the utility of using a graphical model editor. It also provides a platform to discuss multi-scale modelling in which a portion of the model may be replaced with a more detailed implementation to compare behaviours.

BioC viewer: a web-based tool for displaying and merging annotations in BioC

BioC is an XML-based format designed to provide interoperability for text mining tools and manual curation results. A challenge of BioC as a standard format is to align annotations from multiple systems. Ideally, this should not be a major problem if users follow guidelines given by BioC key files. Nevertheless, the misalignment between text and annotations happens quite often because different systems tend to use different software development environments, e.g. ASCII vs. Unicode. We first implemented the BioC Viewer to assist BioGRID curators as a part of the BioCreative V BioC track (Collaborative Biocurator Assistant Task). For the BioC track, the BioC Viewer helped curate protein-protein interaction and genetic interaction pairs appearing in full-text articles. Here, we describe the BioC Viewer itself as well as improvements made to the BioC Viewer since the BioCreative V Workshop to address the misalignment issue of BioC annotations. While uploading BioC files, a BioC merge process is offered when there are files from the same full-text article. If there is a mismatch between an annotated offset and text, the BioC Viewer adjusts the offset to correctly align with the text. The BioC Viewer has a user-friendly interface, where most operations can be performed within a few mouse clicks. The feedback from BioGRID curators has been positive for the web interface, particularly for its usability and learnability.Database URL: http://viewer.bioqrator.org

Remote access to EAC-CPF context and authority records for metadata indexing: a solution based on open information retrieval standards

This paper describes the implementation of a profile of the Search/Retrieve URL protocol for searching EAC-CPF repositories. This implementation gives archivists access to remote repositories of context and authority records when writing finding aids. This implementation of SRU is a key component in an open, distributed work environment where archivists can locate authority records and reuse them as access points. The possibility of combining and linking EAC-CPF records with descriptive metadata records (based on EAD or in any other XML-based format) leverages the investments made in the development of EAC-CPF repositories and supports innovative, distributed archival information services.

The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module.

The size of digital data is ever increasing and is expected to grow to 40,000 EB by 2020, yet the estimated global information storage capacity in 2011 is <300 EB, indicating that most of the data are transient. DNA, as a very stable nano-molecule, is an ideal massive storage device for long-term data archive. The two most notable illustrations are from Church et al. and Goldman et al., whose approaches are well-optimized for most sequencing platforms – short synthesized DNA fragments without homopolymer. Here, we suggested improvements on error handling methodology that could enable the integration of DNA-based computational process, e.g., algorithms based on self-assembly of DNA. As a proof of concept, a picture of size 438 bytes was encoded to DNA with low-density parity-check error-correction code. We salvaged a significant portion of sequencing reads with mutations generated during DNA synthesis and sequencing and successfully reconstructed the entire picture. A modular-based programing framework – DNAcodec with an eXtensible Markup Language-based data format was also introduced. Our experiments demonstrated the practicability of long DNA message recovery with high error tolerance, which opens the field to biocomputing and synthetic biology.