CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis

<p>Abstract</p> <p>Background</p> <p>The <it>Comparative Data Analysis Ontology (CDAO) </it>is an ontology developed, as part of the EvoInfo and EvoIO groups supported by the National Evolutionary Synthesis Center, to provide semantic descriptions of data and transformations commonly found in the domain of phylogenetic analysis. The core concepts of the ontology enable the description of phylogenetic trees and associated character data matrices.</p> <p>Results</p> <p>Using CDAO as the semantic back-end, we developed a triple-store, named <it>CDAO</it>-<it>Store</it>. CDAO-Store is a RDF-based store of phylogenetic data, including a complete import of TreeBASE. CDAO-Store provides a programmatic interface, in the form of web services, and a web-based front-end, to perform both user-defined as well as domain-specific queries; domain-specific queries include search for nearest common ancestors, minimum spanning clades, filter multiple trees in the store by size, author, taxa, tree identifier, algorithm or method. In addition, CDAO-Store provides a visualization front-end, called <it>CDAO</it>-<it>Explorer</it>, which can be used to view both character data matrices and trees extracted from the CDAO-Store. CDAO-Store provides import capabilities, enabling the addition of new data to the triple-store; files in PHYLIP, MEGA, <monospace>nexml</monospace>, and NEXUS formats can be imported and their CDAO representations added to the triple-store.</p> <p>Conclusions</p> <p>CDAO-Store is made up of a versatile and integrated set of tools to support phylogenetic analysis. To the best of our knowledge, CDAO-Store is the first semantically-aware repository of phylogenetic data with domain-specific querying capabilities. The portal to CDAO-Store is available at <url>http://www.cs.nmsu.edu/~cdaostore</url>.</p

Knowledge-rich Image Gist Understanding Beyond Literal Meaning

We investigate the problem of understanding the message (gist) conveyed by images and their captions as found, for instance, on websites or news articles. To this end, we propose a methodology to capture the meaning of image-caption pairs on the basis of large amounts of machine-readable knowledge that has previously been shown to be highly effective for text understanding. Our method identifies the connotation of objects beyond their denotation: where most approaches to image understanding focus on the denotation of objects, i.e., their literal meaning, our work addresses the identification of connotations, i.e., iconic meanings of objects, to understand the message of images. We view image understanding as the task of representing an image-caption pair on the basis of a wide-coverage vocabulary of concepts such as the one provided by Wikipedia, and cast gist detection as a concept-ranking problem with image-caption pairs as queries. To enable a thorough investigation of the problem of gist understanding, we produce a gold standard of over 300 image-caption pairs and over 8,000 gist annotations covering a wide variety of topics at different levels of abstraction. We use this dataset to experimentally benchmark the contribution of signals from heterogeneous sources, namely image and text. The best result with a Mean Average Precision (MAP) of 0.69 indicate that by combining both dimensions we are able to better understand the meaning of our image-caption pairs than when using language or vision information alone. We test the robustness of our gist detection approach when receiving automatically generated input, i.e., using automatically generated image tags or generated captions, and prove the feasibility of an end-to-end automated process

Automated tagging of environmental data using a novel SKOS formatted environmental thesaurus

There is increasing need to use the widest range of data to address issues of environmental management and change, which is reflected in increasing emphasis from government funding agencies for better management and access to environmental data. Bringing together different environmental datasets to confidently enable integrated analysis requires reference to common standards and definitions, which are frequently lacking in environmental data, due to the broad subject area and lack of metadata. Automatic inclusion within datasets of controlled vocabulary concepts from publicly available standard vocabularies facilitates accurate annotation and promotes efficiency of metadata creation. To this end, we have developed a thesaurus capable of describing environmental chemistry datasets. We demonstrate a novel method for tagging datasets, via insertion of this thesaurus into a Laboratory Information Management System, enabling automated tagging of data, thus promoting semantic interoperability between tagged data resources. Being web available, and formatted using the Simple Knowledge Organisation System (SKOS) semantic standard, this thesaurus is capable of providing links both to and from other relevant thesauri, thus facilitating a linked data approach. Future developments will see extension of the thesaurus by the user community, in terms of both concepts included and links to externally hosted vocabularies. By employing a Linked Open Data approach, we anticipate that Web-based tools will be able to use concepts from the thesaurus to discover and link data to other information sources, including use in national assessment of the extent and condition of environmental resources

Knowledge Organization and Terminology: application to Cork

This PhD thesis aims to prove the relevance of texts within the conceptual strand of terminological work. Our methodology serves to demonstrate how linguists can infer knowledge information from texts and subsequently systematise it, either through semiformal or formal representations. We mainly focus on the terminological analysis of specialised corpora resorting to semi-automatic tools for text analysis to systematise lexical-semantic relationships observed in specialised discourse context and subsequent modelling of the underlying conceptual system. The ultimate goal of this methodology is to propose a typology that can help lexicographers to write definitions. Based on the double dimension of Terminology, we hypothesise that text and logic modelling do not go hand in hand since the latter does not directly relate to the former. We highlight that knowledge and language are crucial for knowledge systematisation, albeit keeping in mind that they pertain to different levels of analysis, for they are not isomorphic. To meet our goals, we resorted to specialised texts produced within the industry of cork. These texts provide us with a test bed made of knowledge-rich data which enable us to demonstrate our deductive mechanisms employing the Aristotelian formula: X=Y+DC through the linguistic and conceptual analysis of the semi-automatically extracted textual data. To explore the corpus, we resorted to text mining strategies where regular expressions play a central role. The final goal of this study is to create a terminological resource for the cork industry, where two types of resources interlink, namely the CorkCorpus and the OntoCork. TermCork is a project that stems from the organisation of knowledge in the specialised field of cork. For that purpose, a terminological knowledge database is being developed to feed an e-dictionary. This e-dictionary is designed as a multilingual and multimodal product, where several resources, namely linguistic and conceptual ones are paired. OntoCork is a micro domain-ontology where the concepts are enriched with natural language definitions and complemented with images, either annotated with metainformation or enriched with hyperlinks to additional information, such as a lexicographic resource. This type of e-dictionary embodies what we consider a useful terminological tool in the current digital information society: accounting for its main features, along with an electronic format that can be integrated into the Semantic Web due to its interoperability data format. This aspect emphasises its contribution to reduce ambiguity as much as possible and to increase effective communication between experts of the domain, future experts, and language professionals.Cette thèse vise à prouver la pertinence des textes dans le volet conceptuel du travail terminologique. Notre méthodologie sert à démontrer comment les linguistes peuvent déduire des informations de connaissance à partir de textes et les systématiser par la suite, soit à travers des représentations semi-formelles ou formelles. Nous nous concentrons principalement sur l'analyse terminologique de corpus spécialisé faisant appel à des outils semi-automatiques d'analyse de texte pour systématiser les relations lexico-sémantiques observées dans un contexte de discours spécialisé et la modélisation ultérieure du système conceptuel sous-jacent. L’objectif de cette méthodologie est de proposer une typologie qui peut aider les lexicographes à rédiger des définitions. Sur la base de la double dimension de la terminologie, nous émettons l'hypothèse que la modélisation textuelle et logique ne va pas de pair puisque cette dernière n'est pas directement liée à la première. Nous soulignons que la connaissance et le langage sont essentiels pour la systématisation des connaissances, tout en gardant à l'esprit qu'ils appartiennent à différents niveaux d'analyse, car ils ne sont pas isomorphes. Pour atteindre nos objectifs, nous avons eu recours à des textes spécialisés produits dans l'industrie du liège. Ces textes nous fournissent un banc d'essai constitué de données riches en connaissances qui nous permettent de démontrer nos mécanismes déductifs utilisant la formule aristotélicienne : X = Y + DC à travers l'analyse linguistique et conceptuelle des données textuelles extraites semi-automatiquement. Pour l'exploitation du corpus, nous avons recours à des stratégies de text mining où les expressions régulières jouent un rôle central. Le but de cette étude est de créer une ressource terminologique pour l'industrie du liège, où deux types de ressources sont liés, à savoir le CorkCorpus et l'OntoCork. TermCork est un projet qui découle de l'organisation des connaissances dans le domaine spécialisé du liège. À cette fin, une base de données de connaissances terminologiques est en cours de développement pour alimenter un dictionnaire électronique. Cet edictionnaire est conçu comme un produit multilingue et multimodal, où plusieurs ressources, à savoir linguistiques et conceptuelles, sont jumelées. OntoCork est une micro-ontologie de domaine où les concepts sont enrichis de définitions de langage naturel et complétés par des images, annotées avec des méta-informations ou enrichies d'hyperliens vers des informations supplémentaires. Ce type de dictionnaire électronique désigne ce que nous considérons comme un outil terminologique utile dans la société de l'information numérique actuelle : la prise en compte de ses principales caractéristiques, ainsi qu'un format électronique qui peut être intégré dans le Web sémantique en raison de son format de données d'interopérabilité. Cet aspect met l'accent sur sa contribution à réduire autant que possible l'ambiguïté et à accroître l'efficacité de la communication entre les experts du domaine, les futurs experts et les professionnels de la langue

MorphoCluster: Efficient Annotation of Plankton Images by Clustering

In this work, we present MorphoCluster, a software tool for data-driven, fast, and accurate annotation of large image data sets. While already having surpassed the annotation rate of human experts, volume and complexity of marine data will continue to increase in the coming years. Still, this data requires interpretation. MorphoCluster augments the human ability to discover patterns and perform object classification in large amounts of data by embedding unsupervised clustering in an interactive process. By aggregating similar images into clusters, our novel approach to image annotation increases consistency, multiplies the throughput of an annotator, and allows experts to adapt the granularity of their sorting scheme to the structure in the data. By sorting a set of 1.2 M objects into 280 data-driven classes in 71 h (16 k objects per hour), with 90% of these classes having a precision of 0.889 or higher. This shows that MorphoCluster is at the same time fast, accurate, and consistent; provides a fine-grained and data-driven classification; and enables novelty detection

Implementing OBDA for an end-user query answering service on an educational ontology

In the age where productivity of society is no longer defined by the amount of information generated, but from the quality and assertiveness that a set of data may potentially hold, the right questions to do depends on the semantic awareness capability that an information system could evolve into. To address this challenge, in the last decade, exhaustive research has been done in the Ontology Based Data Access (OBDA) paradigm. A conspectus of the most promising technologies with data integration capabilities and the foundations where they rely are documented in this memory as a point of reference for choosing tools that supports the incorporation of a conceptual model under a OBDA method. The present study provides a practical approach for implementing an ontology based data access service, to educational context users of a Learning Analytics initiative, by means of allowing them to formulate intuitive enquiries with a familiar domain terminology on top of a Learning Management System. The ontology used was completely transformed to semantic linked data standards and some data mappings for testing were included. Semantic Linked Data technologies exposed in this document may exert modernization to environments in which object oriented and relational paradigms may propagate heterogeneous and contradictory requirements. Finally, to validate the implementation, a set of queries were constructed emulating the most relevant dynamics of the model regarding the dataset nature

New perspectives on cohesion and coherence: Implications for translation

The contributions to this volume investigate relations of cohesion and coherence as well as instantiations of discourse phenomena and their interaction with information structure in multilingual contexts. Some contributions concentrate on procedures to analyze cohesion and coherence from a corpus-linguistic perspective. Others have a particular focus on textual cohesion in parallel corpora that include both originals and translated texts. Additionally, the papers in the volume discuss the nature of cohesion and coherence with implications for human and machine translation.The contributors are experts on discourse phenomena and textuality who address these issues from an empirical perspective. The chapters in this volume are grounded in the latest research making this book useful to both experts of discourse studies and computational linguistics, as well as advanced students with an interest in these disciplines. We hope that this volume will serve as a catalyst to other researchers and will facilitate further advances in the development of cost-effective annotation procedures, the application of statistical techniques for the analysis of linguistic phenomena and the elaboration of new methods for data interpretation in multilingual corpus linguistics and machine translation

New perspectives on cohesion and coherence: Implications for translation

The contributions to this volume investigate relations of cohesion and coherence as well as instantiations of discourse phenomena and their interaction with information structure in multilingual contexts. Some contributions concentrate on procedures to analyze cohesion and coherence from a corpus-linguistic perspective. Others have a particular focus on textual cohesion in parallel corpora that include both originals and translated texts. Additionally, the papers in the volume discuss the nature of cohesion and coherence with implications for human and machine translation.The contributors are experts on discourse phenomena and textuality who address these issues from an empirical perspective. The chapters in this volume are grounded in the latest research making this book useful to both experts of discourse studies and computational linguistics, as well as advanced students with an interest in these disciplines. We hope that this volume will serve as a catalyst to other researchers and will facilitate further advances in the development of cost-effective annotation procedures, the application of statistical techniques for the analysis of linguistic phenomena and the elaboration of new methods for data interpretation in multilingual corpus linguistics and machine translation