Knowledge Rich Natural Language Queries over Structured Biological Databases

Increasingly, keyword, natural language and NoSQL queries are being used for information retrieval from traditional as well as non-traditional databases such as web, document, image, GIS, legal, and health databases. While their popularity are undeniable for obvious reasons, their engineering is far from simple. In most part, semantics and intent preserving mapping of a well understood natural language query expressed over a structured database schema to a structured query language is still a difficult task, and research to tame the complexity is intense. In this paper, we propose a multi-level knowledge-based middleware to facilitate such mappings that separate the conceptual level from the physical level. We augment these multi-level abstractions with a concept reasoner and a query strategy engine to dynamically link arbitrary natural language querying to well defined structured queries. We demonstrate the feasibility of our approach by presenting a Datalog based prototype system, called BioSmart, that can compute responses to arbitrary natural language queries over arbitrary databases once a syntactic classification of the natural language query is made

Synchronic Curation for Assessing Reuse and Integration Fitness of Multiple Data Collections

Data driven applications often require using data integrated from different, large, and continuously updated collections. Each of these collections may present gaps, overlapping data, have conflicting information, or complement each other. Thus, a curation need is to continuously assess if data from multiple collections are fit for integration and reuse. To assess different large data collections at the same time, we present the Synchronic Curation (SC) framework. SC involves processing steps to map the different collections to a unifying data model that represents research problems in a scientific area. The data model, which includes the collections' provenance and a data dictionary, is implemented in a graph database where collections are continuously ingested and can be queried. SC has a collection analysis and comparison module to track updates, and to identify gaps, changes, and irregularities within and across collections. Assessment results can be accessed interactively through a web-based interactive graph. In this paper we introduce SC as an interdisciplinary enterprise, and illustrate its capabilities through its implementation in ASTRIAGraph, a space sustainability knowledge system

Structure-based knowledge acquisition from electronic lab notebooks for research data provenance documentation

BACKGROUND: Electronic Laboratory Notebooks (ELNs) are used to document experiments and investigations in the wet-lab. Protocols in ELNs contain a detailed description of the conducted steps including the necessary information to understand the procedure and the raised research data as well as to reproduce the research investigation. The purpose of this study is to investigate whether such ELN protocols can be used to create semantic documentation of the provenance of research data by the use of ontologies and linked data methodologies. METHODS: Based on an ELN protocol of a biomedical wet-lab experiment, a retrospective provenance model of the raised research data describing the details of the experiment in a machine-interpretable way is manually engineered. Furthermore, an automated approach for knowledge acquisition from ELN protocols is derived from these results. This structure-based approach exploits the structure in the experiment’s description such as headings, tables, and links, to translate the ELN protocol into a semantic knowledge representation. To satisfy the Findable, Accessible, Interoperable, and Reuseable (FAIR) guiding principles, a ready-to-publish bundle is created that contains the research data together with their semantic documentation. RESULTS: While the manual modelling efforts serve as proof of concept by employing one protocol, the automated structure-based approach demonstrates the potential generalisation with seven ELN protocols. For each of those protocols, a ready-to-publish bundle is created and, by employing the SPARQL query language, it is illustrated that questions about the processes and the obtained research data can be answered. CONCLUSIONS: The semantic documentation of research data obtained from the ELN protocols allows for the representation of the retrospective provenance of research data in a machine-interpretable way. Research Object Crate (RO-Crate) bundles including these models enable researchers to easily share the research data including the corresponding documentation, but also to search and relate the experiment to each other

Machine Understandable Contracts with Deep Learning

This research investigates the automatic translation of contracts to computer understandable rules trough Natural Language Processing. The most challenging aspect, which is studied throughout this paper, is to understand the meaning of the contract and express it into a structured format. This problem can be reduced to the Named Entity Recognition and Rule Extraction tasks, the latter handles the extraction of terms and conditions. These two problems are difficult, but deep learning models can tackle them. We think that this paper is the first work to approach Rule Extraction with deep learning. This method is data-hungry, so the research also introduces data sets for these two tasks. Additionally, it contributes to the literature by introducing Law-Bert, a model based on BERT which is pre-trained on unlabelled contracts. The results obtained on Named Entity Recognition and Rule Extraction show that pre-training on contracts has a positive effect on performance for the downstream tasks

Multi Agent Systems in Logistics: A Literature and State-of-the-art Review

Based on a literature survey, we aim to answer our main question: “How should we plan and execute logistics in supply chains that aim to meet today’s requirements, and how can we support such planning and execution using IT?†Today’s requirements in supply chains include inter-organizational collaboration and more responsive and tailored supply to meet specific demand. Enterprise systems fall short in meeting these requirements The focus of planning and execution systems should move towards an inter-enterprise and event-driven mode. Inter-organizational systems may support planning going from supporting information exchange and henceforth enable synchronized planning within the organizations towards the capability to do network planning based on available information throughout the network. We provide a framework for planning systems, constituting a rich landscape of possible configurations, where the centralized and fully decentralized approaches are two extremes. We define and discuss agent based systems and in particular multi agent systems (MAS). We emphasize the issue of the role of MAS coordination architectures, and then explain that transportation is, next to production, an important domain in which MAS can and actually are applied. However, implementation is not widespread and some implementation issues are explored. In this manner, we conclude that planning problems in transportation have characteristics that comply with the specific capabilities of agent systems. In particular, these systems are capable to deal with inter-organizational and event-driven planning settings, hence meeting today’s requirements in supply chain planning and execution.supply chain;MAS;multi agent systems