XML Syntax Research Articles

Composition of Biochemical Networks using Domain Knowledge

AbstractGraph composition has applications in a variety of practical applications. In drug development, for instance, in order to understand possible drug interactions, one has to merge known networks and examine topological variants arising from such composition. Similarly, the design of sensor nets may use existing network infrastructures, and the superposition of one network on another can help with network design and optimisation. The problem of network composition has not received much attention in algorithm and database research. Here, we work with biological networks encoded in Systems Biology Markup Language (SBML), based on XML syntax. We focus on XML merging and examine the algorithmic and performance challenges we encountered in our work and the possible solutions to the graph merge problem. We show that our XML graph merge solution performs well in practice and improves on the existing toolsets. This leads us into future work directions and the plan of research which will aim to implement graph merging primitives using domain knowledge to perform composition and decomposition on specific graphs in the biological domain.

Composition of Biochemical Networks using Domain Knowledge

Graph composition has applications in a variety of practical applications. In drug development, for instance, in order to understand possible drug interactions, one has to merge known networks and examine topological variants arising from such composition. Similarly, the design of sensor nets may use existing network infrastructures, and the superposition of one network on another can help with network design and optimisation. The problem of network composition has not received much attention in algorithm and database research. Here, we work with biological networks encoded in Systems Biology Markup Language (SBML), based on XML syntax. We focus on XML merging and examine the algorithmic and performance challenges we encountered in our work and the possible solutions to the graph merge problem. We show that our XML graph merge solution performs well in practice and improves on the existing toolsets. This leads us into future work directions and the plan of research which will aim to implement graph merging primitives using domain knowledge to perform composition and decomposition on specific graphs in the biological domain.

NineML – a description language for spiking neuron network modeling: the user layer

With an increasing number of studies related to largescale neuronal network modeling, the International Neuroinformatics Coordinating Facility (INCF) has identified a need for standards and guidelines to ease model sharing and facilitate the replication of results across different simulators. To create such standards, the INCF formed a program on Multiscale Modeling with a goal to develop a common standardized description language for neuronal network models. The first version of the proposed standard - the Network Interchange for Neuroscience Modeling Language (NineML) - is designed for the description of large networks of spiking neurons. NineML consists of two layers: an abstraction layer that provides the core concepts, mathematics and syntax with which model variables and state update rules are explicitly described and a user layer that provides syntax to specify the instantiation and parameterization of a network model in biological terms. Here we describe the details of the user layer from the first draft proposal of NineML. The user layer provides the syntax for specifying the model and parameters to be used to instantiate the key elements of a spiking neuron network. This includes descriptions of individual elements (cells, synapses, inputs) and the constructs for describing the grouping of these entities into networks. In addition the user layer defines the syntax for specifying a range of connectivity patterns. The user layer is intended to be primarily machine-readable and uses XML syntax. It is designed with a focus on ease of parsing, verification, and automatic model construction. This does not prevent advanced users from editing the user layer XML descriptions by hand, but the primary means for creation of these descriptions is expected to be software tools that will convert GUI- or script-based representations of objects and properties into valid XML. NineML aims to provide a tool to explicitly define a spiking neuron network model both conceptually and mathematically in a simulator independent manner. In addition, NineML is designed to be self-consistent and highly flexible, allowing addition of new models and mathematical descriptions without modification of the previous structure and organization of the language. To achieve these goals, the language is being iteratively designed using several representative models with various levels of complexity [1-6] as test cases.

Research on Operation Rules Modeling in Equipment Training System

Modeling for operation rules is essential function requirement in equipment simulation training system based on VR. Aiming at the modeling actuality of present equipment operation rules, which has no systematic, no generality and no formatting expression, layered modeling system framework based on federation is brought forward referencing to the “Federation and Member” concept of HLA. Open modeling method is adopted to modeling equipment operation rules and it can be described with XML syntax structure. Finally, the basic implement principle of equipment operation rules is presented combing with some large tactical communication system equipment. It can provide beneficial reference for constructing similar large scale equipment simulation training system based on VR.

A Unified Approach for Representing Structurally-Complex Models in SBML Level 3

AbstractThe aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3 Core specification. The approach is illustrated with reference to Simile, a modelling environment which appears to have most of the capabilities of the various SBML Level 3 package proposals which deal with model structure. Simile (http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships between them.The note is organised around the 6 packages listed on the SBML Level 3 Proposals web page (http://sbml.org/Community/Wiki/SBML_Level_3_Proposals) which deal with model structure, namely comp, arrays, spatial, geom, dyn and multi. For each one, I consider how the requirements which motivated the package can be handled using Simile's unified approach. Although Simile has a declarative model-representation language (in both Prolog and XML syntax), I use Simile diagrams and equation syntax throughout, since this is more compact and readable than large chunks of XML.The conclusion is that Simile can indeed meet most of the requirements of these various packages, using a generic set of constructs - basically, the multiple-instance submodel, the concept of a relationship (association) between submodels, and array variables. This suggests the possibility of having a single SBML Level 3 extension package similar to the Simile data model, rather than a series of separate packages. Such an approach has a number of potential advantages and disadvantages compared with having the current set of discrete packages: these are discussed in this paper.

A Unified Approach for Representing Structurally-Complex Models in SBML Level 3

The aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3 Core specification. The approach is illustrated with reference to Simile, a modelling environment which appears to have most of the capabilities of the various SBML Level 3 package proposals which deal with model structure. Simile (http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships between them.The note is organised around the 6 packages listed on the SBML Level 3 Proposals web page (http://sbml.org/Community/Wiki/SBML_Level_3_Proposals) which deal with model structure, namely comp, arrays, spatial, geom, dyn and multi. For each one, I consider how the requirements which motivated the package can be handled using Simile's unified approach. Although Simile has a declarative model-representation language (in both Prolog and XML syntax), I use Simile diagrams and equation syntax throughout, since this is more compact and readable than large chunks of XML.The conclusion is that Simile can indeed meet most of the requirements of these various packages, using a generic set of constructs - basically, the multiple-instance submodel, the concept of a relationship (association) between submodels, and array variables. This suggests the possibility of having a single SBML Level 3 extension package similar to the Simile data model, rather than a series of separate packages. Such an approach has a number of potential advantages and disadvantages compared with having the current set of discrete packages: these are discussed in this paper.

The PSI semantic validator: A framework to check MIAPE compliance of proteomics data

The Human Proteome Organization's Proteomics Standards Initiative (PSI) promotes the development of exchange standards to improve data integration and interoperability. PSI specifies the suitable level of detail required when reporting a proteomics experiment (via the Minimum Information About a Proteomics Experiment), and provides extensible markup language (XML) exchange formats and dedicated controlled vocabularies (CVs) that must be combined to generate a standard compliant document. The framework presented here tackles the issue of checking that experimental data reported using a specific format, CVs and public bio-ontologies (e.g. Gene Ontology, NCBI taxonomy) are compliant with the Minimum Information About a Proteomics Experiment recommendations. The semantic validator not only checks the XML syntax but it also enforces rules regarding the use of an ontology class or CV terms by checking that the terms exist in the resource and that they are used in the correct location of a document. Moreover, this framework is extremely fast, even on sizable data files, and flexible, as it can be adapted to any standard by customizing the parameters it requires: an XML Schema Definition, one or more CVs or ontologies, and a mapping file describing in a formal way how the semantic resources and the format are interrelated. As such, the validator provides a general solution to the common problem in data exchange: how to validate the correct usage of a data standard beyond simple XML Schema Definition validation. The framework source code and its various applications can be found at http://psidev.info/validator.

XML for SAS®programmers

Abstract XML (the eXtensible Markup Language) is an open standard for the definition, transmission, validation and interpretation of data. The standard was developed by the Worldwide Web Consortium (W3C) in order to provide a simple and efficient way to manage self-documenting data files. SAS® software includes a number of useful tools for creating and parsing XML data. These include: (1) the XML libname engine, used to import and export documents in XML format into or from a SAS dataset, optionally using an XMLMap. The new XML92 engine now supports XML Maps on output as well as input; (2) the XML Mapper application is a graphical interface to analyse the structure of an XML document or an XML schema and generate XML syntax for the XMLMap; (3) the ODS MARKUP output destination is used to create XML from SAS output; ODS MARKUP creates but does not read XML documents. This paper will introduce these concepts and present some brief examples of each, including some of the new features available in SAS 9.2.

AN INFERENCE-ENABLED ACCESS CONTROL MODEL FOR RDF ONTOLOGY

Although RDF ontologies are expressed based on XML syntax, existing methods to protect XML documents are not suitable for securing RDF ontologies. The graph style and inference feature of RDF ontologies demands new methods for access control. Driven by this goal, this paper proposes a query-oriented model for RDF ontology access control. The model adopts the concept of ontology view to rewrite user queries. In our approach, ontology views define accessible ontology concepts and instances a user can visit, and enables a controlled inference capability for the user. The design of the views guarantees that the views are free of conflict. Based on that, the paper describes algorithms for rewriting queries according to different views, and provides a system architecture along with an implemented prototype. In the evaluation, the system exhibits a promising result in terms of effectiveness and soundness.

Managing structured data with the extensible markup language (XML)

PurposeThe purpose of this paper is to provide information about the extensible markup language (XML) – its history, function, legacy, and contribution to the world wide web and to the discipline of knowledge management. The knowledge worker will better understand how XML supports the codification aspect of the technology pillar of knowledge management.Design/methodology/approachThe author gives an overview of markup languages, which preceded XML, details XML syntax structure, and discusses techniques for processing XML data. Derivative markup languages which use XML's syntactical structure are listed, and an exercise explaining the process behind generating XML documents from spreadsheets is provided.FindingsXML has served as an integral part of the world wide web for over a decade, and enables internet applications to transform and exchange data in a very efficient manner. The codification of knowledge is germane to the KM process, and XML provides a very capable means for warehousing knowledge that can later be retrieved from knowledge repositories and relational databases. Additionally, XML‐like markup languages such as ebXML (electronic business for XML) help improve the effectiveness and efficiency of knowledge organizations.Originality/valueThe paper hightlights how the management and valuation of knowledge assets are greatly facilitated by the functionality offered by XML, which enables a knowledge worker to store and retrieve knowledge artifacts in the form of structured data.

GlycoCT—a unifying sequence format for carbohydrates

As part of the EUROCarbDB project ( www.eurocarbdb.org) we have carefully analyzed the encoding capabilities of all existing carbohydrate sequence formats and the content of publically available structure databases. We have found that none of the existing structural encoding schemata are capable of coping with the full complexity to be expected for experimentally derived structural carbohydrate sequence data across all taxonomic sources. This gap motivated us to define an encoding scheme for complex carbohydrates, named GlycoCT, to overcome the current limitations. This new format is based on a connection table approach, instead of a linear encoding scheme, to describe the carbohydrate sequences, with a controlled vocabulary to name monosaccharides, adopting IUPAC rules to generate a consistent, machine-readable nomenclature. The format uses a block concept to describe frequently occurring special features of carbohydrate sequences like repeating units. It exists in two variants, a condensed form and a more verbose XML syntax. Sorting rules assure the uniqueness of the condensed form, thus making it suitable as a direct primary key for database applications, which rely on unique identifiers. GlycoCT encompasses the capabilities of the heterogeneous landscape of digital encoding schemata in glycomics and is thus a step forward on the way to a unified and broadly accepted sequence format in glycobioinformatics.

Dual syntax for XML languages

XML is successful as a machine processable data interchange format, but it is often too verbose for human use. For this reason, many XML languages permit an alternative more legible non-XML syntax. XSLT stylesheets are often used to convert from the XML syntax to the alternative syntax; however, such transformations are not reversible since no general tool exists to automatically parse the alternative syntax back into XML. We present XSugar, which makes it possible to manage dual syntax for XML languages. An XSugar specification is built around a context-free grammar that unifies the two syntaxes of a language. Given such a specification, the XSugar tool can translate from alternative syntax to XML and vice versa. Moreover, the tool statically checks that the transformations are reversible and that all XML documents generated from the alternative syntax are valid according to a given XML schema.

Clinical practice guidelines: A case study of combining OWL-S, OWL, and SWRL

As the number of available Web services increases there is a growing demand to realise complex business processes by combining and reusing available Web services. In this context, the Ontology Web Language for Services (OWL-S) can be used to specify semantic types of the input and output data of a Web service and its functionality. This paper uses OWL-S to describe Web services and takes advantage of a XML syntax based on the OWL Web Ontology Language to encode OWL domain ontology fragments and SWRL rule fragments as the inputs and outputs of Web services. The approach presented outlines the use of the OWL’s XML presentation syntax to obtain Web services that provide reasoning support and easily deal with facts and rules. To validate the proposal, the research has focused on Clinical Practice Guidelines (GLs) related to the biomedical field. This paper highlights the benefits and drawbacks found when applying the approach to obtain Web services that are intended to be used in clinical decision-making and rely on GLs. As an example of use, this paper concentrates on a services-based application for diagnosis and clinical management of Diabetic Retinopathy, where the end-users are health professionals who are not familiarized with Semantic Web technologies.

The Italian CBI 2: New corporate banking services to optimise the financial value chain

In recent times, the payments industry has been deeply affected by technological evolution, which has affected every industrial sector: security, integrity, authenticity of transactions, end-to-end, flexibility, integration with corporate systems and automatic reconciliation are words which have been in use for years, and now is the time to shift them into concrete solutions, as expected by the market. Moreover, the need for European Union harmonisation of payment methods, prices and standards has led to the creation of the single euro payments area (SEPA), which represents a major opportunity for multinational enterprises and banks who operate at a cross-border level. The Association for Interbank Corporate Banking (ACBI), thanks to its numbers (over 620,000 corporates connected and most of the Italian banking system), has ridden the wave and is now becoming a real benchmark for the corporate banking community thanks to the launch of a new Internet-based Virtual Private Network, the use of XML syntax, the integration between the financial cycle (payments) and the supply chain (trade relationships and documents, eg e-invoice). The new services cite the maximum alignment with ISO 20022 standards (UNIversal Financial Industry message scheme) providing bank customers with a set of specific Additional Optional Services built over the core scheme of existing services (eg credit transfer), offering new end-to-end functions, such as the trade documents exchange, and financing traditional solutions which have been now converted to electronic, such as the invoice financing request. But how does it work? And what value added do the new mentioned functions generate for companies? This paper explains in detail all these topics, by describing the experience of the ACBI, the critical factor of success, lessons learned and the value that the model could have in other countries and zones, given the widespread impact on the Italian market.

Ontology Aided Modeling of Organic Reaction Mechanisms with Flexible and Fragment Based XML Markup Procedures

The mechanism models for primary organic reactions encoding the structural fragments undergoing substitution, addition, elimination, and rearrangements are developed. In the proposed models, each and every structural component of mechanistic pathways is represented with flexible and fragment based markup technique in XML syntax. A significant feature of the system is the encoding of the electron movements along with the other components like charges, partial charges, half bonded species, lone pair electrons, free radicals, reaction arrows, etc. needed for a complete representation of reaction mechanism. The rendering of reaction schemes described with the proposed methodology is achieved with a concise XML extension language interoperating with the structure markup. The reaction scheme is visualized as 2D graphics in a browser by converting them into SVG documents enabling the desired layouts normally perceived by the chemists conventionally. An automatic representation of the complex patterns of the reaction mechanism is achieved by reusing the knowledge in chemical ontologies and developing artificial intelligence components in terms of axioms.

Separation of the Control Plane and Forwarding Plane in Next-Generation Routers

Ever since the Internet appeared, network elements, such as routers, have been enhanced with much functionality. They tend to increasingly integrate more services, such as support and security mechanisms, which ensure Quality of Service. Similarly, processor performance continues to increase rapidly. Thus, these two types of evolution trigger the concept of separating the Control plane and the Forwarding plane in network elements.This study addresses the separation of the control plane and the forwarding plane in Next-Generation Routers. XML syntax is used to model, on the one hand, the suitable elements of the control plane and the forwarding plane. Implementation and prototyping results indicate that this syntax type for modeling provides a flexible platform, which is truly able to manage the heterogeneity of the material implementing the Forwarding Plane.

Representing organizational memory for computer-aided utilization

Organizational memory (OM) is the means by which knowledge from the past is brought to bear on present activities. For effective use of OM, it must be represented in a machine-understandable form, so that man, machine, and OM can work in concert to perform business activities such as problem solving, decision making, workflow management, and organizational learning. To this end, we have developed a knowledge representation scheme that uses a trio of logic, ontology, and computation as knowledge representation constructs, Topic Maps in XML syntax (XTM) and related software tools as the representation technology, and three distinct but closely related ontologies (information, enterprise, and domain ontology) as the operationalized knowledge objects. Based on this knowledge representation scheme, we propose an OM architecture along with a feasible and practical methodology for representing OM to facilitate computer-aided utilization. The methodology has been applied to a laboratory experiment for a provider of knowledge-intensive services dubbed ‘Taiwan's Dun & Bradstreet.’ A field interview indicates that top management endorses the OM architecture and developers confirm the feasibility of the methodology.

Representing digital assets usingMPEG-21 Digital Item Declaration

Various XML-based approaches aimed at representing compound digital assets have emerged over the last several years. Approaches that are of specific relevance to the digital library community include the Metadata Encoding and Transmission Standard (METS), the IMS Content Packaging XML Binding, and the XML Formatted Data Units (XFDU) developed by CCSDS Panel 2. The MPEG-21 Digital Item Declaration (MPEG-21 DID) is another standard specifying the representation of digital assets in XML that, so far, has received little attention in the digital library community. This article gives a brief insight into the MPEG-21 standardization effort, highlights the major characteristics of the MPEG-21 DID Abstract Model, and describes the MPEG-21 Digital Item Declaration Language (MPEG-21 DIDL), an XML syntax for the representation of digital assets based on the MPEG-21 DID Abstract Model. Also, it briefly demonstrates the potential relevance of MPEG-21 DID to the digital library community by describing its use in the aDORe repository environment at the Research Library of the Los Alamos National Laboratory (LANL) for the representation of digital assets.

Semantics and Extensions of WS-Agreement

When having repeated interactions with a service provider, a service consumer might desire guarantees on the delivery of the service. These guarantees involve both functional and non-functional properties of the offered service over a number of invocations. When the guarantee terms are explicitly defined in a document, we talk about a service level agreement.WS-Agreement is an industry driven emerging protocol for the specification of agreements in the context of Web Services. If, on the one hand, WS-Agreement defines the XML syntax for the language and protocol, on the other hand, it gives only a vague textual overview of the intended meaning. We fill this gap by providing a formal definition of an agreement and analyzing the possible evolutions of agreements and their terms over an execution. As a result we identify a number of extensions which involve the initial negotiation, the monitoring of running agreements, and the possibility of renegotiating agreements in executions. We evaluate the proposed approach through experimentation.

Named graphs

The Semantic Web consists of many RDF graphs nameable by URIs. This paper extends the syntax and semantics of RDF to cover such named graphs. This enables RDF statements that describe graphs, which is beneficial in many Semantic Web application areas. Named graphs are given an abstract syntax, a formal semantics, an XML syntax, and a syntax based on N3. SPARQL is a query language applicable to named graphs. A specific application area discussed in detail is that of describing provenance information. This paper provides a formally defined framework suited to being a foundation for the Semantic Web trust layer.