Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models. The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.

Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene regulation etc., SBML can also be used to encode any kinetic model. SBML offers mechanisms to describe biological components by means of compartments and reacting species, as well as their dynamic behaviour, using reactions, events and arbitrary mathematical rules. SBML also offers all the housekeeping structures needed to ensure an unambiguous understanding of quantitative descriptions.

This is Release 1 of the specification for SBML Level 2 Version 4, describing the structures of the language and the rules used to build a valid model. SBML XML Schema and other related documents and software are also available from the SBML project web site, "http://sbml.org/":http://sbml.org/

SBML models and MathSBML

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

Enhancing the EAST-ADL error model with HiP-HOPS semantics

EAST-ADL is a domain-specific modelling language for the engineering of automotive embedded systems. The language has abstractions that enable engineers to capture a variety of information about design in the course of the lifecycle — from requirements to detailed design of hardware and software architectures. The specification of the EAST-ADL language includes an error model extension which documents language structures that allow potential failures of design elements to be specified locally. The effects of these failures are then later assessed in the context of the architecture design. To provide this type of useful assessment, a language and a specification are not enough; a compiler-like tool that can read and operate on a system specification together with its error model is needed. In this paper we integrate the error model of EAST-ADL with the precise semantics of HiP-HOPS — a state-of-the-art tool that enables dependability analysis and optimization of design models. We present the integration concept between EAST-ADL structure and HiP-HOPS error propagation logic and its transformation into the HiP-HOPS model. Source and destination models are represented using the corresponding XML formats. The connection of these two models at tool level enables practical EAST-ADL designs of embedded automotive systems to be analysed in terms of dependability, i.e. safety, reliability and availability. In addition, the information encoded in the error model can be re-used across different contexts of application with the associated benefits for cost reduction, simplification, and rationalisation of dependability assessments in complex engineering designs

Scalable XQuery type matching

XML Schema awareness has been an integral part of the XQuery language since its early design stages. Matching XML data against XML types is the main operation that backs up XQuery type expressions, such as typeswitch, instance of, or certain XPath operators. This interaction is particularly vital in data-centric XQuery applications, where data come with detailed type information from an XML Schema document. So far there has been little work on the optimization of those operations. This work presents an efficient implementation of the runtime aspects of XML Schema support. We propose type ranks as a novel and uniform way to implement all facets of type matching in the W3C XQuery Recommendation. As a concise encoding of the type hierarchy defined by an XML Schema document, type ranks minimize the cost of checking the runtime type of XQuery singleton items. By aggregating type ranks, we leverage the grouping capabilities of modern DBMS implementations to efficiently execute type matching on XQuery sequences. In addition, we improve the complexity bounds incurring with typeswitch expressions over existing approaches. Experiments on an off-the-shelf database system demonstrate the potential of our approach

Hierarchical Event Descriptors (HED): Semi-Structured Tagging for Real-World Events in Large-Scale EEG.

Real-world brain imaging by EEG requires accurate annotation of complex subject-environment interactions in event-rich tasks and paradigms. This paper describes the evolution of the Hierarchical Event Descriptor (HED) system for systematically describing both laboratory and real-world events. HED version 2, first described here, provides the semantic capability of describing a variety of subject and environmental states. HED descriptions can include stimulus presentation events on screen or in virtual worlds, experimental or spontaneous events occurring in the real world environment, and events experienced via one or multiple sensory modalities. Furthermore, HED 2 can distinguish between the mere presence of an object and its actual (or putative) perception by a subject. Although the HED framework has implicit ontological and linked data representations, the user-interface for HED annotation is more intuitive than traditional ontological annotation. We believe that hiding the formal representations allows for a more user-friendly interface, making consistent, detailed tagging of experimental, and real-world events possible for research users. HED is extensible while retaining the advantages of having an enforced common core vocabulary. We have developed a collection of tools to support HED tag assignment and validation; these are available at hedtags.org. A plug-in for EEGLAB (sccn.ucsd.edu/eeglab), CTAGGER, is also available to speed the process of tagging existing studies

Validation of Modern JSON Schema: Formalization and Complexity

JSON Schema is the de-facto standard schema language for JSON data. The language went through many minor revisions, but the most recent versions of the language added two novel features, dynamic references and annotation-dependent validation, that change the evaluation model. Modern JSON Schema is the name used to indicate all versions from Draft 2019-09, which are characterized by these new features, while Classical JSON Schema is used to indicate the previous versions. These new "modern" features make the schema language quite difficult to understand, and have generated many discussions about the correct interpretation of their official specifications; for this reason we undertook the task of their formalization. During this process, we also analyzed the complexity of data validation in Modern JSON Schema, with the idea of confirming the PTIME complexity of Classical JSON Schema validation, and we were surprised to discover a completely different truth: data validation, that is expected to be an extremely efficient process, acquires, with Modern JSON Schema features, a PSPACE complexity. In this paper, we give the first formal description of Modern JSON Schema, which we consider a central contribution of the work that we present here. We then prove that its data validation problem is PSPACE-complete. We prove that the origin of the problem lies in dynamic references, and not in annotation-dependent validation. We study the schema and data complexities, showing that the problem is PSPACE-complete with respect to the schema size even with a fixed instance, but is in PTIME when the schema is fixed and only the instance size is allowed to vary. Finally, we run experiments that show that there are families of schemas where the difference in asymptotic complexity between dynamic and static references is extremely visible, even with small schemas

A platform designed with lexicographical data in mind

UIDB/03213/2020 UIDP/03213/2020LeXmart is an open-source web platform used to support the lexicographer’s work through editing, control, validation, management, and publication of lexical resources. This tool was specifically developed to facilitate the compilation of general monolingual dictionaries in which data is encoded according to the Text Encoding Initiative (TEI) schema (chapter 9). Here, we will describe the challenges of adapting LeXmart to deal with TEI Lex-0 and distinct types of lexical resources, namely Dicionário da Língua Portuguesa (DLP) and Vocabulário Ortográfico da Língua Portuguesa, lexicographic works from Academia das Ciências Lisboa, and Dicionário Aberto, the retro-digitised version of the Cândido de Figueiredo dictionary. This article describes the steps taken to update the LeXmart platform to deal with the TEI Lex-0 schema and describe the challenges on properly encoding these three projects while allowing the lexicographical team to work continuously. This work builds on automatic operations performed on top of the original resources. It also includes the changes made to the editor to make it capable of dealing with the encoding updates and the new types of resources.publishersversionpublishe

Semi-supervised prediction of protein interaction sentences exploiting semantically encoded metrics

Protein-protein interaction (PPI) identification is an integral component of many biomedical research and database curation tools. Automation of this task through classification is one of the key goals of text mining (TM). However, labelled PPI corpora required to train classifiers are generally small. In order to overcome this sparsity in the training data, we propose a novel method of integrating corpora that do not contain relevance judgements. Our approach uses a semantic language model to gather word similarity from a large unlabelled corpus. This additional information is integrated into the sentence classification process using kernel transformations and has a re-weighting effect on the training features that leads to an 8% improvement in F-score over the baseline results. Furthermore, we discover that some words which are generally considered indicative of interactions are actually neutralised by this process

NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata

In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input–output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML