Combining computational models, semantic annotations, and 1 associated simulation experiments in a graph database PrePrints

Abstract 13 Model repositories such as the BioModels Database or the CellML Model Repository are 14 frequently accessed to retrieve computational models describing biological systems. However, 15 the current designs of these databases limit the types of supported queries, and many data 16 in these repositories cannot easily be accessed. Computational methods for model retrieval 17 cannot be applied. In this paper we present a storage concept that meets this challenge. It 18 grounds on a graph database, reects the models' structure, incorporates semantic annotations 19 and experiment descriptions, and ultimately connects dierent types of model-related data. 20 The connections between heterogeneous model-related data and bio-ontologies enable ecient 21 search via biological facts and grant access to new model features such as network structure. 22 The introduced concept notably improves the access of computational models and associate

Controlled vocabularies and semantics in systems biology

The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the systems biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments

Fireground location understanding by semantic linking of visual objects and building information models

This paper presents an outline for improved localization and situational awareness in fire emergency situations based on semantic technology and computer vision techniques. The novelty of our methodology lies in the semantic linking of video object recognition results from visual and thermal cameras with Building Information Models (BIM). The current limitations and possibilities of certain building information streams in the context of fire safety or fire incident management are addressed in this paper. Furthermore, our data management tools match higher-level semantic metadata descriptors of BIM and deep-learning based visual object recognition and classification networks. Based on these matches, estimations can be generated of camera, objects and event positions in the BIM model, transforming it from a static source of information into a rich, dynamic data provider. Previous work has already investigated the possibilities to link BIM and low-cost point sensors for fireground understanding, but these approaches did not take into account the benefits of video analysis and recent developments in semantics and feature learning research. Finally, the strengths of the proposed approach compared to the state-of-the-art is its (semi -)automatic workflow, generic and modular setup and multi-modal strategy, which allows to automatically create situational awareness, to improve localization and to facilitate the overall fire understanding

Harmonizing semantic annotations for computational models in biology

Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol. Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current annotation practices among the COmputational Modeling in BIology NEtwork community and provide a set of recommendations for building a consensus approach to semantic annotation

Improving reproducibility and reuse of modelling results in the life sciences

Research results are complex and include a variety of heterogeneous data. This entails major computational challenges to (i) to manage simulation studies, (ii) to ensure model exchangeability, stability and validity, and (iii) to foster communication between partners. I describe techniques to improve the reproducibility and reuse of modelling results. First, I introduce a method to characterise differences in computational models. Second, I present approaches to obtain shareable and reproducible research results. Altogether, my methods and tools foster exchange and reuse of modelling results.Die verteilte Entwicklung von komplexen Simulationsstudien birgt eine große Zahl an informationstechnischen Herausforderungen: (i) Modelle müssen verwaltet werden; (ii) Reproduzierbarkeit, Stabilität und Gültigkeit von Ergebnissen muss sichergestellt werden; und (iii) die Kommunikation zwischen Partnern muss verbessert werden. Ich stelle Techniken vor, um die Reproduzierbarkeit und Wiederverwendbarkeit von Modellierungsergebnissen zu verbessern. Meine Implementierungen wurden erfolgreich in internationalen Anwendungen integriert und fördern das Teilen von wissenschaftlichen Ergebnissen

Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should therefore be as reliable and versatile as possible. In this context, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Progresses toward a grid-enabled chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa