Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.

BACKGROUND: Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. RESULTS: The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. CONCLUSION: The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel.

Heterogeenisen palveluverkon kuvaus ja käyttö XML-kielen avulla

Tämän diplomityön tarkoituksena on käydä läpi XML:n tarjoamia mahdollisuuksia heterogeenisen palveluverkon integroinnissa. Työssä kuvataan XML-kielen yleistä teoriaa ja perehdytään etenkin sovellusten välisen kommunikoinnin kannalta tärkeisiin ominaisuuksiin. Samalla käydään läpi sovelluskehitysympäristöjen muuttumista heterogeenisemmiksi ja siitä seurannutta palveluarkkitehtuurien kehittymistä ja kuinka nämä muutokset vaikuttavat XML:n hyväksikäyttöön. Työssä suunniteltiin ja toteutettiin luonnollisen kielen palvelukehitykseen Fuse-palvelualusta. Työssä kuvataan palvelualustan arkkitehtuuri ja siinä tarkastellaan XML:n hyödyntämistä luonnollisen kielen tulkin ja palvelun integroinnissa. Samalla arvioidaan muita XML:n käyttömahdollisuuksia Fuse-palvelualustan parantamiseksi.

Désambiguisation de sens par modèles de contextes et son application à la Recherche d’Information

Il est connu que les problèmes d'ambiguïté de la langue ont un effet néfaste sur les résultats des systèmes de Recherche d'Information (RI). Toutefois, les efforts de recherche visant à intégrer des techniques de Désambiguisation de Sens (DS) à la RI n'ont pas porté fruit. La plupart des études sur le sujet obtiennent effectivement des résultats négatifs ou peu convaincants. De plus, des investigations basées sur l'ajout d'ambiguïté artificielle concluent qu'il faudrait une très haute précision de désambiguation pour arriver à un effet positif. Ce mémoire vise à développer de nouvelles approches plus performantes et efficaces, se concentrant sur l'utilisation de statistiques de cooccurrence afin de construire des modèles de contexte. Ces modèles pourront ensuite servir à effectuer une discrimination de sens entre une requête et les documents d'une collection. Dans ce mémoire à deux parties, nous ferons tout d'abord une investigation de la force de la relation entre un mot et les mots présents dans son contexte, proposant une méthode d'apprentissage du poids d'un mot de contexte en fonction de sa distance du mot modélisé dans le document. Cette méthode repose sur l'idée que des modèles de contextes faits à partir d'échantillons aléatoires de mots en contexte devraient être similaires. Des expériences en anglais et en japonais montrent que la force de relation en fonction de la distance suit généralement une loi de puissance négative. Les poids résultant des expériences sont ensuite utilisés dans la construction de systèmes de DS Bayes Naïfs. Des évaluations de ces systèmes sur les données de l'atelier Semeval en anglais pour la tâche Semeval-2007 English Lexical Sample, puis en japonais pour la tâche Semeval-2010 Japanese WSD, montrent que les systèmes ont des résultats comparables à l'état de l'art, bien qu'ils soient bien plus légers, et ne dépendent pas d'outils ou de ressources linguistiques. La deuxième partie de ce mémoire vise à adapter les méthodes développées à des applications de Recherche d'Information. Ces applications ont la difficulté additionnelle de ne pas pouvoir dépendre de données créées manuellement. Nous proposons donc des modèles de contextes à variables latentes basés sur l'Allocation Dirichlet Latente (LDA). Ceux-ci seront combinés à la méthodes de vraisemblance de requête par modèles de langue. En évaluant le système résultant sur trois collections de la conférence TREC (Text REtrieval Conference), nous observons une amélioration proportionnelle moyenne de 12% du MAP et 23% du GMAP. Les gains se font surtout sur les requêtes difficiles, augmentant la stabilité des résultats. Ces expériences seraient la première application positive de techniques de DS sur des tâches de RI standard.

Design And Development Of A Named Entity Based Question Answering System For Malayalam Language

This is a Named Entity Based Question Answering System for Malayalam Language. Although a vast amount of information is available today in digital form, no effective information access mechanism exists to provide humans with convenient information access. Information Retrieval and Question Answering systems are the two mechanisms available now for information access. Information systems typically return a long list of documents in response to a user’s query which are to be skimmed by the user to determine whether they contain an answer. But a Question Answering System allows the user to state his/her information need as a natural language question and receives most appropriate answer in a word or a sentence or a paragraph. This system is based on Named Entity Tagging and Question Classification. Document tagging extracts useful information from the documents which will be used in finding the answer to the question. Question Classification extracts useful information from the question to determine the type of the question and the way in which the question is to be answered. Various Machine Learning methods are used to tag the documents. Rule-Based Approach is used for Question Classification. Malayalam belongs to the Dravidian family of languages and is one of the four major languages of this family. It is one of the 22 Scheduled Languages of India with official language status in the state of Kerala. It is spoken by 40 million people. Malayalam is a morphologically rich agglutinative language and relatively of free word order. Also Malayalam has a productive morphology that allows the creation of complex words which are often highly ambiguous. Document tagging tools such as Parts-of-Speech Tagger, Phrase Chunker, Named Entity Tagger, and Compound Word Splitter are developed as a part of this research work. No such tools were available for Malayalam language. Finite State Transducer, High Order Conditional Random Field, Artificial Immunity System Principles, and Support Vector Machines are the techniques used for the design of these document preprocessing tools. This research work describes how the Named Entity is used to represent the documents. Single sentence questions are used to test the system. Overall Precision and Recall obtained are 88.5% and 85.9% respectively. This work can be extended in several directions. The coverage of non-factoid questions can be increased and also it can be extended to include open domain applications. Reference Resolution and Word Sense Disambiguation techniques are suggested as the future enhancements

Scalable real-time crisis mapping and analytics of social media streams for disaster management and breaking news

Real-time geoparsing of social media streams (e.g. Twitter, YouTube, Instagram, Flickr, FourSquare) is providing a new 'virtual sensor' capability to end users such as emergency response agencies (e.g. Tsunami early warning centres, Civil protection authorities) and news agencies (e.g. Deutsche Welle, BBC News). Challenges in this area include scaling up natural language processing (NLP) and information retrieval (IR) approaches to handle real-time traffic volumes, reducing false positives, creating real-time infographic displays useful for effective decision support and providing support for trust and credibility analysis using geosemantics. I will present in this seminar on-going work by the IT Innovation Centre over the last 4 years (TRIDEC and REVEAL FP7 projects) in building such systems, and highlights our research towards improving trustworthy and credible of crisis map displays and real-time analytics for trending topics and influential social networks during major news worthy events.

Asistentes virtuales en plataformas 3.0

Los asistentes virtuales son herramientas inteligentes que ayudan a los usuarios a buscar información en un conglomerado de recursos web. El despliegue natural de los mismos se realiza en las propias páginas web, donde permiten resolver las dudas de los usuarios formuladas en lenguaje natural usando técnicas de Inteligencia Artificial. En este artículo presentamos las características más relevantes del asistente virtual Elvira y su integración en la página web de la Universidad de Granada. De forma paralela a la aparición de los asistentes virtuales, en la última década, los avances tecnológicos han hecho que el acceso a la información se produzca desde diferentes fuentes, trasladando la necesidad de la asistencia artificial a otros ámbitos. En este trabajo, detallamos la ampliación de los despliegues del asistente virtual Elvira sobre dispositivos móviles y redes sociales.

Effects of second language on cognition in English users of L2 Japanese

It is now established that certain cognitive processes such as categorisation are tightly linked to the concepts encoded in language. Recent studies have shown that bilinguals with languages that differ in their concepts may show a shift in their cognition towards the L2 pattern primarily as a function of their L2 proficiency. This research has so far focused predominantly on L2 users who started learning the L2 in childhood or early puberty. The current study asks whether similar effects can be found in adult L2 learners. English speakers of L2 Japanese were given an object classification task involving real physical objects, and an online classification task involving artificial novel objects. Results showed a shift towards the L2 pattern, indicating that some degree of cognitive plasticity exists even when a second language is acquired later in life. These results have implications for theories of L2 acquisition and bilingualism, and contribute towards our understanding of the nature of the relationship between language and cognition in the L2 user’s mind.

SRDigital: proposta de um modelo baseado na linguagem natural e controlada como instrumentos de apoio ao agente computacional do processo de referência

Pós-graduação em Ciência da Informação - FFC

BIOMEDICAL LANGUAGE UNDERSTANDING AND EXTRACTION (BLUE-TEXT): A MINIMAL SYNTACTIC, SEMANTIC METHOD

Clinical text understanding (CTU) is of interest to health informatics because critical clinical information frequently represented as unconstrained text in electronic health records are extensively used by human experts to guide clinical practice, decision making, and to document delivery of care, but are largely unusable by information systems for queries and computations. Recent initiatives advocating for translational research call for generation of technologies that can integrate structured clinical data with unstructured data, provide a unified interface to all data, and contextualize clinical information for reuse in multidisciplinary and collaborative environment envisioned by CTSA program. This implies that technologies for the processing and interpretation of clinical text should be evaluated not only in terms of their validity and reliability in their intended environment, but also in light of their interoperability, and ability to support information integration and contextualization in a distributed and dynamic environment. This vision adds a new layer of information representation requirements that needs to be accounted for when conceptualizing implementation or acquisition of clinical text processing tools and technologies for multidisciplinary research. On the other hand, electronic health records frequently contain unconstrained clinical text with high variability in use of terms and documentation practices, and without commitmentto grammatical or syntactic structure of the language (e.g. Triage notes, physician and nurse notes, chief complaints, etc). This hinders performance of natural language processing technologies which typically rely heavily on the syntax of language and grammatical structure of the text. This document introduces our method to transform unconstrained clinical text found in electronic health information systems to a formal (computationally understandable) representation that is suitable for querying, integration, contextualization and reuse, and is resilient to the grammatical and syntactic irregularities of the clinical text. We present our design rationale, method, and results of evaluation in processing chief complaints and triage notes from 8 different emergency departments in Houston Texas. At the end, we will discuss significance of our contribution in enabling use of clinical text in a practical bio-surveillance setting.

Sistema de recomendación semántico para la movilidad en el entorno AFRICA BUILD Portal

La Gestión de Recursos Humanos a través de Internet es un problema latente y presente actualmente en cualquier sitio web dedicado a la búsqueda de empleo. Este problema también está presente en AFRICA BUILD Portal. AFRICA BUILD Portal es una emergente red socio-profesional nacida con el ánimo de crear comunidades virtuales que fomenten la educación e investigación en el área de la salud en países africanos. Uno de los métodos para fomentar la educación e investigación es mediante la movilidad de estudiantes e investigadores entre instituciones, apareciendo así, el citado problema de la gestión de recursos humanos. Por tanto, este trabajo se centra en solventar el problema de la gestión de recursos humanos en el entorno específico de AFRICA BUILD Portal. Para solventar este problema, el objetivo es desarrollar un sistema de recomendación que ayude en la gestión de recursos humanos en lo que concierne a la selección de las mejores ofertas y demandas de movilidad. Caracterizando al sistema de recomendación como un sistema semántico el cual ofrecerá las recomendaciones basándose en las reglas y restricciones impuestas por el dominio. La aproximación propuesta se basa en seguir el enfoque de los sistemas de Matchmaking semánticos. Siguiendo este enfoque, por un lado, se ha empleado un razonador de lógica descriptiva que ofrece inferencias útiles en el cálculo de las recomendaciones y por otro lado, herramientas de procesamiento de lenguaje natural para dar soporte al proceso de recomendación. Finalmente para la integración del sistema de recomendación con AFRICA BUILD Portal se han empleado diversas tecnologías web. Los resultados del sistema basados en la comparación de recomendaciones creadas por el sistema y por usuarios reales han mostrado un funcionamiento y rendimiento aceptable. Empleando medidas de evaluación de sistemas de recuperación de información se ha obtenido una precisión media del sistema de un 52%, cifra satisfactoria tratándose de un sistema semántico. Pudiendo concluir que con la solución implementada se ha construido un sistema estable y modular posibilitando: por un lado, una fácil evolución que debería ir encaminada a lograr un rendimiento mayor, incrementando su precisión y por otro lado, dejando abiertas nuevas vías de crecimiento orientadas a la explotación del potencial de AFRICA BUILD Portal mediante la Web 3.0. ---ABSTRACT---The Human Resource Management through Internet is currently a latent problem shown in any employment website. This problem has also appeared in AFRICA BUILD Portal. AFRICA BUILD Portal is an emerging socio-professional network with the objective of creating virtual communities to foster the capacity for health research and education in African countries. One way to foster this capacity of research and education is through the mobility of students and researches between institutions, thus appearing the Human Resource Management problem. Therefore, this dissertation focuses on solving the Human Resource Management problem in the specific environment of AFRICA BUILD Portal. To solve this problem, the objective is to develop a recommender system which assists the management of Human Resources with respect to the selection of the best mobility supplies and demands. The recommender system is a semantic system which will provide the recommendations according to the domain rules and restrictions. The proposed approach is based on semantic matchmaking solutions. So, this approach on the one hand uses a Description Logics reasoning engine which provides useful inferences to the recommendation process and on the other hand uses Natural Language Processing techniques to support the recommendation process. Finally, Web technologies are used in order to integrate the recommendation system into AFRICA BUILD Portal. The results of evaluating the system are based on the comparison between recommendations created by the system and by real users. These results have shown an acceptable behavior and performance. The average precision of the system has been obtained by evaluation measures for information retrieval systems, so the average precision of the system is at 52% which may be considered as a satisfactory result taking into account that the system is a semantic system. To conclude, it could be stated that the implemented system is stable and modular. This fact on the one hand allows an easy evolution that should aim to achieve a higher performance by increasing its average precision and on the other hand keeps open new ways to increase the functionality of the system oriented to exploit the potential of AFRICA BUILD Portal through Web 3.0.

A comparative study of open domain and opinion question answering systems for factual and opinionated queries

The development of the Web 2.0 led to the birth of new textual genres such as blogs, reviews or forum entries. The increasing number of such texts and the highly diverse topics they discuss make blogs a rich source for analysis. This paper presents a comparative study on open domain and opinion QA systems. A collection of opinion and mixed fact-opinion questions in English is defined and two Question Answering systems are employed to retrieve the answers to these queries. The first one is generic, while the second is specific for emotions. We comparatively evaluate and analyze the systems’ results, concluding that opinion Question Answering requires the use of specific resources and methods.

An authoring tool for decision support systems in context questions of ecological knowledge

Decision support systems (DSS) support business or organizational decision-making activities, which require the access to information that is internally stored in databases or data warehouses, and externally in the Web accessed by Information Retrieval (IR) or Question Answering (QA) systems. Graphical interfaces to query these sources of information ease to constrain dynamically query formulation based on user selections, but they present a lack of flexibility in query formulation, since the expressivity power is reduced to the user interface design. Natural language interfaces (NLI) are expected as the optimal solution. However, especially for non-expert users, a real natural communication is the most difficult to realize effectively. In this paper, we propose an NLI that improves the interaction between the user and the DSS by means of referencing previous questions or their answers (i.e. anaphora such as the pronoun reference in “What traits are affected by them?”), or by eliding parts of the question (i.e. ellipsis such as “And to glume colour?” after the question “Tell me the QTLs related to awn colour in wheat”). Moreover, in order to overcome one of the main problems of NLIs about the difficulty to adapt an NLI to a new domain, our proposal is based on ontologies that are obtained semi-automatically from a framework that allows the integration of internal and external, structured and unstructured information. Therefore, our proposal can interface with databases, data warehouses, QA and IR systems. Because of the high NL ambiguity of the resolution process, our proposal is presented as an authoring tool that helps the user to query efficiently in natural language. Finally, our proposal is tested on a DSS case scenario about Biotechnology and Agriculture, whose knowledge base is the CEREALAB database as internal structured data, and the Web (e.g. PubMed) as external unstructured information.

Scaling up question-answering to linked data

Linked Data semantic sources, in particular DBpedia, can be used to answer many user queries. PowerAqua is an open multi-ontology Question Answering (QA) system for the Semantic Web (SW). However, the emergence of Linked Data, characterized by its openness, heterogeneity and scale, introduces a new dimension to the Semantic Web scenario, in which exploiting the relevant information to extract answers for Natural Language (NL) user queries is a major challenge. In this paper we discuss the issues and lessons learned from our experience of integrating PowerAqua as a front-end for DBpedia and a subset of Linked Data sources. As such, we go one step beyond the state of the art on end-users interfaces for Linked Data by introducing mapping and fusion techniques needed to translate a user query by means of multiple sources. Our first informal experiments probe whether, in fact, it is feasible to obtain answers to user queries by composing information across semantic sources and Linked Data, even in its current form, where the strength of Linked Data is more a by-product of its size than its quality. We believe our experiences can be extrapolated to a variety of end-user applications that wish to scale, open up, exploit and re-use what possibly is the greatest wealth of data about everything in the history of Artificial Intelligence. © 2010 Springer-Verlag.

AquaLog : an ontology-driven question answering system for organizational semantic intranets

The semantic web vision is one in which rich, ontology-based semantic markup will become widely available. The availability of semantic markup on the web opens the way to novel, sophisticated forms of question answering. AquaLog is a portable question-answering system which takes queries expressed in natural language and an ontology as input, and returns answers drawn from one or more knowledge bases (KBs). We say that AquaLog is portable because the configuration time required to customize the system for a particular ontology is negligible. AquaLog presents an elegant solution in which different strategies are combined together in a novel way. It makes use of the GATE NLP platform, string metric algorithms, WordNet and a novel ontology-based relation similarity service to make sense of user queries with respect to the target KB. Moreover it also includes a learning component, which ensures that the performance of the system improves over the time, in response to the particular community jargon used by end users.

The usability of semantic search tools:a review

The goal of semantic search is to improve on traditional search methods by exploiting the semantic metadata. In this paper, we argue that supporting iterative and exploratory search modes is important to the usability of all search systems. We also identify the types of semantic queries the users need to make, the issues concerning the search environment and the problems that are intrinsic to semantic search in particular. We then review the four modes of user interaction in existing semantic search systems, namely keyword-based, form-based, view-based and natural language-based systems. Future development should focus on multimodal search systems, which exploit the advantages of more than one mode of interaction, and on developing the search systems that can search heterogeneous semantic metadata on the open semantic Web.