XML-based Markup Language Research Articles

EnzymeML: seamless data flow and modeling of enzymatic data.

The design of biocatalytic reaction systems is highly complex owing to the dependency of the estimated kinetic parameters on the enzyme, the reaction conditions, and the modeling method. Consequently, reproducibility of enzymatic experiments and reusability of enzymatic data are challenging. We developed the XML-based markup language EnzymeML to enable storage and exchange of enzymatic data such as reaction conditions, the time course of the substrate and the product, kinetic parameters and the kinetic model, thus making enzymatic data findable, accessible, interoperable and reusable (FAIR). The feasibility and usefulness of the EnzymeML toolbox is demonstrated in six scenarios, for which data and metadata of different enzymatic reactions are collected and analyzed. EnzymeML serves as a seamless communication channel between experimental platforms, electronic lab notebooks, tools for modeling of enzyme kinetics, publication platforms and enzymatic reaction databases. EnzymeML is open and transparent, and invites the community to contribute. All documents and codes are freely available at https://enzymeml.org .

Development of XMLbased Markup Language

Development of XMLbased Markup Language

Building a Chatbot for the Department of ECE using Flask

A Chatbot aims to make a conversation between both human and machine. The machine has been embedded with knowledge to identify the sentences and make a decision as the response to a question. The present technical project consists of developing a system for ECE Department enquiry using web based Chatbot. The ECE Department Chatbot has the capacity to make friendly conversations and gives the link for academic syllabus of different years as well. It also gives the faculty details such as their email address and mobile number. Implementation of the ECE Department Chatbot overcomes certain barriers of a website since it correctly understands the user's questions, asks clarifying questions if required and then retrains the system to give the response that the user intends to get. The heart of ChatBot technology lies in Natural Language Processing or NLP. The project uses Artificial Intelligence Mark-up Language (AIML) which is an XML based mark-up language meant to create artificial intelligence applications. AIML makes it possible to create human interfaces while keeping the implementation simple to program, easy to understand and highly maintainable. Along with AIML it uses Flask, which is a web-framework similar to Django, but is more Pythonic. Implementation is done in Python using some of its software libraries.

CODA-ML: context-specific biological knowledge representation for systemic physiology analysis

BackgroundComputational analysis of complex diseases involving multiple organs requires the integration of multiple different models into a unified model. Different models are often constructed in heterogeneous formats. Thus, the integration of the models requires a standard language format that can effectively represent essential biological information. However, the previously introduced formats have limitations that prevent from adequately representing essential biological information, particularly specifications of bio-molecules and biological contexts.ResultsWe defined an XML-based markup language called context-oriented directed association markup language (CODA-ML), which better represents essential biological information. The CODA-ML has two major strengths in designating molecular specifications and biological contexts. It can cover heterogeneous entity types involved in biological events (e.g. gene/protein, compound, cellular function, disease). Molecular types of entities can have molecular specifications which include detailed information of a molecule from isoforms to modifications, enabling high-resolution representation of molecules. In addition, it can distinguish biological events that vary depending on different biological contexts such as cell types or disease conditions. Especially representation of inter-cellular events as well as intra-cellular events is available. These two major strengths can resolve contradictory associations when different models are integrated into one unified model, which improves the accuracy of the model.ConclusionsWith the CODA-ML, diverse models such as signaling pathways, metabolic pathways, and gene regulatory pathways can be represented in a unified language format. Heterogeneous entity types can be covered by the CODA-ML, thus it enables detailed description for the mechanisms of diseases or drugs from multiple perspectives (e.g., molecule, function or disease). The CODA-ML is expected to help integrate different models into one systemic model in an efficient and effective. The unified model can be used to perform computational analysis not only for cancer but also for other complex diseases involving multiple organs beyond a single cell.

Twenty Years of Theological Markup Languages

ThML—the first open, XML-based markup language designed specifically for digital libraries handling theological collections—was first conceived in 1998, sparking a period of development in discipline-specific markup languages for theology that lasted until the early 2000s, when the dominance of the TEI standard led the field to stagnate. Despite the disappearance of the active developer communities behind most of the projects as well as technical improvements in the TEI, however, ThML and other languages developed during that period remain in use by several notable projects. After presenting a brief history of theology-specific markup, this article seeks to understand what its persistence tells us about the discipline-specific needs of biblical and theological studies that are still not being met by the TEI, and offers insights as to the lessons that may be drawn from these projects for the future of theological markup.

OpenCOR: a modular and interoperable approach to computational biology.

Computational biologists have been developing standards and formats for nearly two decades, with the aim of easing the description and exchange of experimental data, mathematical models, simulation experiments, etc. One of those efforts is CellML (cellml.org), an XML-based markup language for the encoding of mathematical models. Early CellML-based environments include COR and OpenCell. However, both of those tools have limitations and were eventually replaced with OpenCOR (opencor.ws). OpenCOR is an open source modeling environment that is supported on Windows, Linux and OS X. It relies on a modular approach, which means that all of its features come in the form of plugins. Those plugins can be used to organize, edit, simulate and analyze models encoded in the CellML format. We start with an introduction to CellML and two of its early adopters, which limitations eventually led to the development of OpenCOR. We then go onto describing the general philosophy behind OpenCOR, as well as describing its openness and its development process. Next, we illustrate various aspects of OpenCOR, such as its user interface and some of the plugins that come bundled with it (e.g., its editing and simulation plugins). Finally, we discuss some of the advantages and limitations of OpenCOR before drawing some concluding remarks.

Semantically linking in silico cancer models.

Multiscale models are commonplace in cancer modeling, where individual models acting on different biological scales are combined within a single, cohesive modeling framework. However, model composition gives rise to challenges in understanding interfaces and interactions between them. Based on specific domain expertise, typically these computational models are developed by separate research groups using different methodologies, programming languages, and parameters. This paper introduces a graph-based model for semantically linking computational cancer models via domain graphs that can help us better understand and explore combinations of models spanning multiple biological scales. We take the data model encoded by TumorML, an XML-based markup language for storing cancer models in online repositories, and transpose its model description elements into a graph-based representation. By taking such an approach, we can link domain models, such as controlled vocabularies, taxonomic schemes, and ontologies, with cancer model descriptions to better understand and explore relationships between models. The union of these graphs creates a connected property graph that links cancer models by categorizations, by computational compatibility, and by semantic interoperability, yielding a framework in which opportunities for exploration and discovery of combinations of models become possible.

Connecting digital cancer model repositories with markup

The cancer research community requires a standardized way of describing mathematical and computational models to enable interoperation between systems, repositories, and between the models themselves. In this paper we describe a new markup language, TumorML, for describing computational models that fall within the domain of cancer. TumorML is an XML-based markup language that wraps existing cancer model implementations with metadata for model curation, parametric interface description, implementation description, and compound model linking. In this paper we first introduce the rationale for a new markup language for computational cancer model description based on our experiences and requirements from the European Commission's 'Transatlantic Tumor Model Repositories' project. The aim of the project is to develop a European-based digital cancer model repository to link and interoperate with a similar established repository based in the United States. TumorML was developed to enable this interoperation between repositories. We introduce the language and describe the main features of the specification and go on to describe a real application of TumorML where a molecular pathway model has been packaged using the new markup language.

Dealing with diversity in computational cancer modeling.

This paper discusses the need for interconnecting computational cancer models from different sources and scales within clinically relevant scenarios to increase the accuracy of the models and speed up their clinical adaptation, validation, and eventual translation. We briefly review current interoperability efforts drawing upon our experiences with the development of in silico models for predictive oncology within a number of European Commission Virtual Physiological Human initiative projects on cancer. A clinically relevant scenario, addressing brain tumor modeling that illustrates the need for coupling models from different sources and levels of complexity, is described. General approaches to enabling interoperability using XML-based markup languages for biological modeling are reviewed, concluding with a discussion on efforts towards developing cancer-specific XML markup to couple multiple component models for predictive in silico oncology.

A courseware to script animated pedagogical agents in instructional material for elementary students in English education

Animated agents are virtual characters who demonstrate facial expressions, gestures, movements, and speech to facilitate students’ engagement in the learning environment. Our research developed a courseware that supports a XML-based markup language and an authoring tool for teachers to script animated pedagogical agents in teaching materials. The design of the markup language refers to Mayer's segmenting principle that is efficient for assisting a teacher to edit teaching contents into a set of segments and further organize the segments in a given lesson in class. This paper details a case study of applying the proposed courseware for elementary students in English education, and further investigates how the instructional materials scripted using the courseware affect the learning achievement of students. Two groups of participants from an elementary school in Taiwan enrolled in this experiment. The experimental group used animated agent-based instructional materials in their English classroom, whereas the control group participated in a traditional curriculum. Post-test results revealed that the experimental group outperformed the control group. Our experiment demonstrated that the developed courseware provides an opportunity for scripting animated pedagogical agents as appropriate instructional tools in a computer-assisted language learning environment to foster elementary students’ English learning.

Scripting Animated Conversational Agents in an Internet Multi-Agent Advertising System

This study is aimed to develop an agent-based Internet advertising system. This system allows consumers actively announce requirements. Therefore, advertisers are easier to find and analyze potential consumers for designing appropriate advertisements. Furthermore, the designed Internet advertising system supports a XML-based interactive drama markup language (IDML) for advertisers to edit animated conversational agents in advertisements for expressively interacting with consumers. IDML proposed in our previous study integrates the concept of interactive drama to support branching narrations that enables the audience to affect an animated agent’s behaviors and also enables an animated agent to present a variety of dialogues. We also developed the advertising system attached to an Internet e-novel community. The empirical statistics collected from the e-novel community shows that this example system is helpful for novelists to design interactive advertisements to attract potential readers.

Software Reconfiguration Based on Service Model-Driven Architecture over Cloud Computing

Cloud computing is changing the way enterprises develop and deploy information systems. With the rapid development and successful implementations of the model-driven architecure(MDA) and service-oriented architecture (SOA), clouding computing has become the focus of researches. This paper describes the design and implementation of a service template markup language (STML) and its integrated development tools, which provide a comprehensive solution to the reconfiguration of applications over cloud computing platforms. In the paper, we first analyze and point out the limitations of current software reconfiguration approaches, then propose a framework for a SMDA-based approach to software reconfiguration in a PaaS platform, next present a series of PaaS service models and an XML-based service template markup language, finally conclude by an example showing the practicability of the tools.

WEB-BASED PERSONAL DIGITAL PHOTO COLLECTIONS: MULTIMODAL RETRIEVAL

When personal photo collections get large retrieval of specific photos or sets of photos becomes difficult mainly due to the fairly primitive means by which they are organised. Commercial photo handling systems help but often have only elementary searching features. In this paper, we describe an interactive web-based photo retrieval system that enables personal digital photo users to accomplish photo browsing by using multimodal interaction. This system not only enables users to use mouse click input modalities but also speech input modality to browse their personal digital photos in the World Wide Web (WWW) environment. The prototype system and it architecture utilise web technology which was built using web programming scripting (JavaScript, XHTML, ASP, XML based mark-up language) and image database in order to achieve its objective. All prototype programs and data files including the user’s photo repository, profiles, dialogues, grammars, prompt, and retrieval engine are stored and located in the web server. Our approach also consists of human-computer speech dialogue based on photo browsing of image content by four main categories (Who? What? When? and Where?). Our user study with 20 digital photo users showed that the participants reacted positively to their experience with the system interactions.

HepML, an XML-based format for describing simulated data in high energy physics

In this paper we describe a HepML format and a corresponding C++ library developed for keeping complete description of parton level events in a unified and flexible form. HepML tags contain enough information to understand what kind of physics the simulated events describe and how the events have been prepared. A HepML block can be included into event files in the LHEF format. The structure of the HepML block is described by means of several XML Schemas. The Schemas define necessary information for the HepML block and how this information should be located within the block. The library libhepml is a C++ library intended for parsing and serialization of HepML tags, and representing the HepML block in computer memory. The library is an API for external software. For example, Matrix Element Monte Carlo event generators can use the library for preparing and writing a header of an LHEF file in the form of HepML tags. In turn, Showering and Hadronization event generators can parse the HepML header and get the information in the form of C++ classes. libhepml can be used in C++, C, and Fortran programs. All necessary parts of HepML have been prepared and we present the project to the HEP community. Program summary Program title: libhepml Catalogue identifier: AEGL_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEGL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPLv3 No. of lines in distributed program, including test data, etc.: 138 866 No. of bytes in distributed program, including test data, etc.: 613 122 Distribution format: tar.gz Programming language: C++, C Computer: PCs and workstations Operating system: Scientific Linux CERN 4/5, Ubuntu 9.10 RAM: 1 073 741 824 bytes (1 Gb) Classification: 6.2, 11.1, 11.2 External routines: Xerces XML library ( http://xerces.apache.org/xerces-c/), Expat XML Parser ( http://expat.sourceforge.net/) Nature of problem: Monte Carlo simulation in high energy physics is divided into several stages. Various programs exist for these stages. In this article we are interested in interfacing different Monte Carlo event generators via data files, in particular, Matrix Element (ME) generators and Showering and Hadronization (SH) generators. There is a widely accepted format for data files for such interfaces – Les Houches Event Format (LHEF). Although information kept in an LHEF file is enough for proper working of SH generators, it is insufficient for understanding how events in the LHEF file have been prepared and which physical model has been applied. In this paper we propose an extension of the format for keeping additional information available in generators. We propose to add a new information block, marked up with XML tags, to the LHEF file. This block describes events in the file in more detail. In particular, it stores information about a physical model, kinematical cuts, generator, etc. This helps to make LHEF files self-documented. Certainly, HepML can be applied in more general context, not in LHEF files only. Solution method: In order to overcome drawbacks of the original LHEF accord we propose to add a new information block of HepML tags. HepML is an XML-based markup language. We designed several XML Schemas for all tags in the language. Any HepML document should follow rules of the Schemas. The language is equipped with a library for operation with HepML tags and documents. This C++ library, called libhepml, consists of classes for HepML objects, which represent a HepML document in computer memory, parsing classes, serializating classes, and some auxiliary classes. Restrictions: The software is adapted for solving problems, described in the article. There are no additional restrictions. Running time: Tests have been done on a computer with Intel(R) Core(TM)2 Solo, 1.4 GHz. Parsing of a HepML file: 6 ms (size of the HepML files is 12.5 Kb) Writing of a HepML block to file: 14 ms (file size 12.5 Kb) Merging of two HepML blocks and writing to file: 18 ms (file size – 25.0 Kb).

Enhancing semantic web and ontologies for e-tourism

The semantic web provides improved information access founded on the development of machine processing. E-tourism is a good applicant for semantic web because it is based on information on the internet, in sense of marketing and transaction portal. E-tourism/e-travel software is personalised inclusive for creating instantly online reservation/booking. Therefore, the success of the semantic web depends strongly on the production of ontologies. Ontologies can assist organisation, browsing, searching, and more intelligent access to information and services available online. The ideas proposed in this paper are mainly interested in the new promises afforded by ontologies in the area of knowledge management convenient to the tourism industry. The examples of ontologies description in XML-based markup language are also presented with some clarifications. The summary of useful available tourism/travel related ontologies are presented also in this paper.

Towards a repository for scientific theory: development of a technical framework and prototype based on TheoryML

This paper proposes a markup language based on XML for the domain of scientific theory, called Theory Markup Language (TheoryML). We argue that this markup language allows structured representations of theories; has the potential to make the search for and analysis of relevant theory more effective. In the first part of the paper, the role of theory and its basic elements are discussed. This paper presents the foundations of TheoryML, the key elements of the current version and discusses recent changes, challenges and future developments. The paper further addresses the development of a prototype repository and tools that are used to capture and analyse information about scientific theories using TheoryML. Finally, issues beyond the technical definition of the markup language are addressed; including issues that are relevant for making a theory repository based on TheoryML documents a useful resource for researchers in management and other disciplines. The specification of this XML-based markup language is an essential step towards the larger goal of creating a repository for scientific theory. While the effort is initially focused on theories frequently used in management research, the framework is designed with the intention to also serve researchers in other scientific disciplines.

An XML-centred approach to creating object-oriented supply chain simulation models

We propose an eXtensible Markup Language (XML)-centred approach to object-oriented simulation modelling of supply chains. Our approach is fundamentally different from previous work in that it uses XML to describe the supply chain itself, as opposed to using XML to store the simulation model. We define a system that includes an XML-based markup language and a 'simulator' that contains a library of fundamental supply chain simulation classes and a simulation 'model mapper'. The simulator processes the supply chain description document and generates an object-oriented simulation model using the class library. We detail working reference implementations of the markup language (Supply Chain Modelling Language (SCML)) and the simulator (Simulator for Integrated Supply Chain Operations (SISCO)).

An evaluation dataset for the toponym resolution task

Toponym resolution is the task of linking place name instances in a text with spatial footprints, given the context in which they occur. Whereas a lot of work on the evaluation of temporal resolution is ongoing (e.g. [Setzer, A., & Gaizauskas, R. (2000). On the importance of annotating temporal event–event relations in text. In LREC 2000 Workshop on annotation standards for temporal information in natural language, Vol. 3 (pp. 1281–1286). Athens, Greece]), to date no reference resource is available to evaluate competing algorithms for toponym resolution. It is thus argued that a shareable, reusable evaluation resource is necessary. To this end, a new proposal for the markup of toponyms in text corpora with their referents and an associated tool data methodology are presented: the Toponym Resolution Markup Language (TRML) is an XML-based markup language, and TAME, the toponym annotation markup editor, is a tool that implements it. A novel evaluation resource is described which comprises a large-scale reference gazetteer server and a human-annotated news corpus in which toponyms are associated with latitude/longitude coordinates of the location they refer to. The reliability of the annotation task is established by determining inter-annotator agreement of the human annotators.

A MODEL-BASED APPROACH FOR USEWARE DEVELOPMENT

The development of human-machine interfaces today is being challenged by the increasing number of interaction devices and multimodality. Developing for multiple devices but yet keeping consistency is unavoidable. Also integrating the future users in the whole development process is important for the final acceptability. Hence the development process is complex. This paper suggests a model-based approach. Aspects of the user interface should be defined in different models of different abstraction levels. This also requires a simple and domain based description language. For this purpose, a XML-based markup language called useML is also introduced. useML defines a simple syntax for the description of a platform-independent and task-oriented use model. Platform-specific interfaces and prototypes can be easily derived from the use model.

Semantic-based access to environmental reports using topic maps

Environmental reporting is an essential component of an organisation's communication with its stakeholders. In order to automate environmental reporting of organisations, the discussion focuses today on structuring and standardising environmental reports using the eXtensible Markup Language (XML). The development of XML-based environmental reporting is embedded in the process towards shaping an XML-based Environmental Markup Language (EML). Extending the XML-based approach, we use the new international topic maps standard to describe the complex structure and the context (metadata) of environmental reporting.