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

Complexity, BioComplexity, the Connectionist Conjecture and Ontology of Complexity\ud

This paper develops and integrates major ideas and concepts on complexity and biocomplexity - the connectionist conjecture, universal ontology of complexity, irreducible complexity of totality & inherent randomness, perpetual evolution of information, emergence of criticality and equivalence of symmetry & complexity. This paper introduces the Connectionist Conjecture which states that the one and only representation of Totality is the connectionist one i.e. in terms of nodes and edges. This paper also introduces an idea of Universal Ontology of Complexity and develops concepts in that direction. The paper also develops ideas and concepts on the perpetual evolution of information, irreducibility and computability of totality, all in the context of the Connectionist Conjecture. The paper indicates that the control and communication are the prime functionals that are responsible for the symmetry and complexity of complex phenomenon. The paper takes the stand that the phenomenon of life (including its evolution) is probably the nearest to what we can describe with the term “complexity”. The paper also assumes that signaling and communication within the living world and of the living world with the environment creates the connectionist structure of the biocomplexity. With life and its evolution as the substrate, the paper develops ideas towards the ontology of complexity. The paper introduces new complexity theoretic interpretations of fundamental biomolecular parameters. The paper also develops ideas on the methodology to determine the complexity of “true” complex phenomena.\u

Foreword

The aim of this Workshop is to focus on building and evaluating resources used to facilitate biomedical text mining, including their design, update, delivery, quality assessment, evaluation and dissemination. Key resources of interest are lexical and knowledge repositories (controlled vocabularies, terminologies, thesauri, ontologies) and annotated corpora, including both task-specific resources and repositories reengineered from biomedical or general language resources. Of particular interest is the process of building annotated resources, including designing guidelines and annotation schemas (aiming at both syntactic and semantic interoperability) and relying on language engineering standards. Challenging aspects are updates and evolution management of resources, as well as their documentation, dissemination and evaluation

The role of ontologies in biological and biomedical research: a functional perspective.

Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.This is the final version of the article. It first appeared from Oxford University Press via http://dx.doi.org/10.1093/bib/bbv01

A Similarity Based Approach for Chemical Category Classification

This report aims to describe the main outcomes of an IHCP Exploratory Research Project carried out during 2005 by the European Chemicals Bureau (Computational Toxicology Action). The original aim of this project was to develop a computational method to facilitate the classification of chemicals into similarity-based chemical categories, which would be both useful for building (Q)SAR models (research application) and for defining chemical category proposals (regulatory application).JRC.I-Institute for Health and Consumer Protection (Ispra

Scalable statistical learning for relation prediction on structured data

Relation prediction seeks to predict unknown but potentially true relations by revealing missing relations in available data, by predicting future events based on historical data, and by making predicted relations retrievable by query. The approach developed in this thesis can be used for a wide variety of purposes, including to predict likely new friends on social networks, attractive points of interest for an individual visiting an unfamiliar city, and associations between genes and particular diseases. In recent years, relation prediction has attracted significant interest in both research and application domains, partially due to the increasing volume of published structured data and background knowledge. In the Linked Open Data initiative of the Semantic Web, for instance, entities are uniquely identified such that the published information can be integrated into applications and services, and the rapid increase in the availability of such structured data creates excellent opportunities as well as challenges for relation prediction. This thesis focuses on the prediction of potential relations by exploiting regularities in data using statistical relational learning algorithms and applying these methods to relational knowledge bases, in particular in Linked Open Data in particular. We review representative statistical relational learning approaches, e.g., Inductive Logic Programming and Probabilistic Relational Models. While logic-based reasoning can infer and include new relations via deduction by using ontologies, machine learning can be exploited to predict new relations (with some degree of certainty) via induction, purely based on the data. Because the application of machine learning approaches to relation prediction usually requires handling large datasets, we also discuss the scalability of machine learning as a solution to relation prediction, as well as the significant challenge posed by incomplete relational data (such as social network data, which is often much more extensive for some users than others). The main contribution of this thesis is to develop a learning framework called the Statistical Unit Node Set (SUNS) and to propose a multivariate prediction approach used in the framework. We argue that multivariate prediction approaches are most suitable for dealing with large, sparse data matrices. According to the characteristics and intended application of the data, the approach can be extended in different ways. We discuss and test two extensions of the approach--kernelization and a probabilistic method of handling complex n-ary relationships--in empirical studies based on real-world data sets. Additionally, this thesis contributes to the field of relation prediction by applying the SUNS framework to various domains. We focus on three applications: 1. In social network analysis, we present a combined approach of inductive and deductive reasoning for recommending movies to users. 2. In the life sciences, we address the disease gene prioritization problem. 3. In the recommendation system, we describe and investigate the back-end of a mobile app called BOTTARI, which provides personalized location-based recommendations of restaurants.Die Beziehungsvorhersage strebt an, unbekannte aber potenziell wahre Beziehungen vorherzusagen, indem fehlende Relationen in verfügbaren Daten aufgedeckt, zukünftige Ereignisse auf der Grundlage historischer Daten prognostiziert und vorhergesagte Relationen durch Anfragen abrufbar gemacht werden. Der in dieser Arbeit entwickelte Ansatz lässt sich für eine Vielzahl von Zwecken einschließlich der Vorhersage wahrscheinlicher neuer Freunde in sozialen Netzen, der Empfehlung attraktiver Sehenswürdigkeiten für Touristen in fremden Städten und der Priorisierung möglicher Assoziationen zwischen Genen und bestimmten Krankheiten, verwenden. In den letzten Jahren hat die Beziehungsvorhersage sowohl in Forschungs- als auch in Anwendungsbereichen eine enorme Aufmerksamkeit erregt, aufgrund des Zuwachses veröffentlichter strukturierter Daten und von Hintergrundwissen. In der Linked Open Data-Initiative des Semantischen Web werden beispielsweise Entitäten eindeutig identifiziert, sodass die veröffentlichten Informationen in Anwendungen und Dienste integriert werden können. Diese rapide Erhöhung der Verfügbarkeit strukturierter Daten bietet hervorragende Gelegenheiten sowie Herausforderungen für die Beziehungsvorhersage. Diese Arbeit fokussiert sich auf die Vorhersage potenzieller Beziehungen durch Ausnutzung von Regelmäßigkeiten in Daten unter der Verwendung statistischer relationaler Lernalgorithmen und durch Einsatz dieser Methoden in relationale Wissensbasen, insbesondere in den Linked Open Daten. Wir geben einen Überblick über repräsentative statistische relationale Lernansätze, z.B. die Induktive Logikprogrammierung und Probabilistische Relationale Modelle. Während das logikbasierte Reasoning neue Beziehungen unter der Nutzung von Ontologien ableiten und diese einbeziehen kann, kann maschinelles Lernen neue Beziehungen (mit gewisser Wahrscheinlichkeit) durch Induktion ausschließlich auf der Basis der vorliegenden Daten vorhersagen. Da die Verarbeitung von massiven Datenmengen in der Regel erforderlich ist, wenn maschinelle Lernmethoden in die Beziehungsvorhersage eingesetzt werden, diskutieren wir auch die Skalierbarkeit des maschinellen Lernens sowie die erhebliche Herausforderung, die sich aus unvollständigen relationalen Daten ergibt (z. B. Daten aus sozialen Netzen, die oft für manche Benutzer wesentlich umfangreicher sind als für Anderen). Der Hauptbeitrag der vorliegenden Arbeit besteht darin, ein Lernframework namens Statistical Unit Node Set (SUNS) zu entwickeln und einen im Framework angewendeten multivariaten Prädiktionsansatz einzubringen. Wir argumentieren, dass multivariate Vorhersageansätze am besten für die Bearbeitung von großen und dünnbesetzten Datenmatrizen geeignet sind. Je nach den Eigenschaften und der beabsichtigten Anwendung der Daten kann der Ansatz auf verschiedene Weise erweitert werden. In empirischen Studien werden zwei Erweiterungen des Ansatzes--ein kernelisierter Ansatz sowie ein probabilistischer Ansatz zur Behandlung komplexer n-stelliger Beziehungen-- diskutiert und auf realen Datensätzen untersucht. Ein weiterer Beitrag dieser Arbeit ist die Anwendung des SUNS Frameworks auf verschiedene Bereiche. Wir konzentrieren uns auf drei Anwendungen: 1. In der Analyse sozialer Netze stellen wir einen kombinierten Ansatz von induktivem und deduktivem Reasoning vor, um Benutzern Filme zu empfehlen. 2. In den Biowissenschaften befassen wir uns mit dem Problem der Priorisierung von Krankheitsgenen. 3. In den Empfehlungssystemen beschreiben und untersuchen wir das Backend einer mobilen App "BOTTARI", das personalisierte ortsbezogene Empfehlungen von Restaurants bietet