Extracting kinetic information from literature with KineticRE

To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The approach proposed integrates the development of a novel plug-in over the text mining framework @Note2. In the end, the pipeline developed was validated with a case study on Kluyveromyces lactis, spanning the analysis and results of 20 full text documents.

Apoio à decisão na análise inteligente de reclamações

Dissertação de mestrado integrado em Engenharia e Gestão de Sistemas de Informação

Automatic distinction of Fernando Pessoas’ heteronyms

Text Mining has opened a vast array of possibilities concerning automatic information retrieval from large amounts of text documents. A variety of themes and types of documents can be easily analyzed. More complex features such as those used in Forensic Linguistics can gather deeper understanding from the documents, making possible performing di cult tasks such as author identi cation. In this work we explore the capabilities of simpler Text Mining approaches to author identification of unstructured documents, in particular the ability to distinguish poetic works from two of Fernando Pessoas' heteronyms: Alvaro de Campos and Ricardo Reis. Several processing options were tested and accuracies of 97% were reached, which encourage further developments.

BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines

The Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsef

Enhancing text classification to improve information filtering

Text classification, information filtering, semi-supervised learning, quality control

Formulierung von Nutzerpräferenzen in Multimedia-Retrieval-Systemen

Multimedia, retrieval, multimedia-retrieval-system, multimedia query languages, weighting, preferences

Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development.

Identification of Research Portfolio for the Development of Filtration Equipment

This piece of work which is Identification of Research Portfolio for Development of Filtration Equipment aims at presenting a novel approach to identify promising research topics in the field of design and development of filtration equipment and processes. The projected approach consists of identifying technological problems often encountered in filtration processes. The sources of information for the problem retrieval were patent documents and scientific papers that discussed filtration equipments and processes. The problem identification method adopted in this work focussed on the semantic nature of a sentence in order to generate series of subject-action-object structures. This was achieved with software called Knowledgist. List of problems often encountered in filtration processes that have been mentioned in patent documents and scientific papers were generated. These problems were carefully studied and categorized. Suggestions were made on the various classes of these problems that need further investigation in order to propose a research portfolio. The uses and importance of other methods of information retrieval were also highlighted in this work.

Text Classification and Indexing in IP Networks

Internet on elektronisen postin perusrakenne ja ollut tärkeä tiedonlähde akateemisille käyttäjille jo pitkään. Siitä on tullut merkittävä tietolähde kaupallisille yrityksille niiden pyrkiessä pitämään yhteyttä asiakkaisiinsa ja seuraamaan kilpailijoitansa. WWW:n kasvu sekä määrällisesti että sen moninaisuus on luonut kasvavan kysynnän kehittyneille tiedonhallintapalveluille. Tällaisia palveluja ovet ryhmittely ja luokittelu, tiedon löytäminen ja suodattaminen sekä lähteiden käytön personointi ja seuranta. Vaikka WWW:stä saatavan tieteellisen ja kaupallisesti arvokkaan tiedon määrä on huomattavasti kasvanut viime vuosina sen etsiminen ja löytyminen on edelleen tavanomaisen Internet hakukoneen varassa. Tietojen hakuun kohdistuvien kasvavien ja muuttuvien tarpeiden tyydyttämisestä on tullut monimutkainen tehtävä Internet hakukoneille. Luokittelu ja indeksointi ovat merkittävä osa luotettavan ja täsmällisen tiedon etsimisessä ja löytämisessä. Tämä diplomityö esittelee luokittelussa ja indeksoinnissa käytettävät yleisimmät menetelmät ja niitä käyttäviä sovelluksia ja projekteja, joissa tiedon hakuun liittyvät ongelmat on pyritty ratkaisemaan.

Identification of the Emerging Issues in Recycled Fiber Processing

The objectives of this research work “Identification of the Emerging Issues in Recycled Fiber processing” are discovering of emerging research issues and presenting of new approaches to identify promising research themes in recovered paper application and production. The projected approach consists of identifying technological problems often encountered in wastepaper preparation processes and also improving the quality of recovered paper and increasing its proportion in the composition of paper and board. The source of information for the problem retrieval is scientific publications in which waste paper application and production were discussed. The study has exploited several research methods to understand the changes related to utilization of recovered paper. The all assembled data was carefully studied and categorized by applying software called RefViz and CiteSpace. Suggestions were made on the various classes of these problems that need further investigation in order to propose an emerging research trends in recovered paper.

Biomedical Event Extraction with Machine Learning

Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.

Dual retrieval in conceptual information systems

Conceptual Information Systems provide a multi-dimensional conceptually structured view on data stored in relational databases. On restricting the expressiveness of the retrieval language, they allow the visualization of sets of realted queries in conceptual hierarchies, hence supporting the search of something one does not have a precise description, but only a vague idea of. Information Retrieval is considered as the process of finding specific objects (documents etc.) out of a large set of objects which fit to some description. In some data analysis and knowledge discovery applications, the dual task is of interest: The analyst needs to determine, for a subset of objects, a description for this subset. In this paper we discuss how Conceptual Information Systems can be extended to support also the second task.

LBD LOCAL: un sistema para la recuperación de documentos con referencias geográficas

Tanto los Sistemas de Información Geográfica como la Recuperación de Información han sido campos de investigación muy importantes en las últimas décadas. Recientemente, un nuevo campo de investigación llamado Recuperación de Información Geográfica ha surgido fruto de la confluencia de estos dos campos. El objetivo principal de este campo es definir estructuras de indexación y técnicas para almacenar y recuperar documentos de manera eficiente empleando tanto las referencias textuales como las referencias geográficas contenidas en el texto. En este artículo presentamos la arquitectura de un sistema para recuperación de información geográfica y definimos el flujo de trabajo para la extracción de las referencias geográficas de los documentos. Presentamos además una nueva estructura de indexación que combina un índice invertido, un índice espacial y una ontología. Esta estructura mejora las capacidades de consulta de otras propuestas

Full text library resources 2010-11

Finding journal articles from full text sources such as IEEEXplore, ACM and LNCS (Lecture Noters in Computer Science)

Information sources selection methodology for recommender systems based on intrinsic characteristics and trust measure

El treball desenvolupat en aquesta tesi presenta un profund estudi i proveïx solucions innovadores en el camp dels sistemes recomanadors. Els mètodes que usen aquests sistemes per a realitzar les recomanacions, mètodes com el Filtrat Basat en Continguts (FBC), el Filtrat Col·laboratiu (FC) i el Filtrat Basat en Coneixement (FBC), requereixen informació dels usuaris per a predir les preferències per certs productes. Aquesta informació pot ser demogràfica (Gènere, edat, adreça, etc), o avaluacions donades sobre algun producte que van comprar en el passat o informació sobre els seus interessos. Existeixen dues formes d'obtenir aquesta informació: els usuaris ofereixen explícitament aquesta informació o el sistema pot adquirir la informació implícita disponible en les transaccions o historial de recerca dels usuaris. Per exemple, el sistema recomanador de pel·lícules MovieLens (http://movielens.umn.edu/login) demana als usuaris que avaluïn almenys 15 pel·lícules dintre d'una escala de * a * * * * * (horrible, ...., ha de ser vista). El sistema genera recomanacions sobre la base d'aquestes avaluacions. Quan els usuaris no estan registrat en el sistema i aquest no té informació d'ells, alguns sistemes realitzen les recomanacions tenint en compte l'historial de navegació. Amazon.com (http://www.amazon.com) realitza les recomanacions tenint en compte les recerques que un usuari a fet o recomana el producte més venut. No obstant això, aquests sistemes pateixen de certa falta d'informació. Aquest problema és generalment resolt amb l'adquisició d'informació addicional, se li pregunta als usuaris sobre els seus interessos o es cerca aquesta informació en fonts addicionals. La solució proposada en aquesta tesi és buscar aquesta informació en diverses fonts, específicament aquelles que contenen informació implícita sobre les preferències dels usuaris. Aquestes fonts poden ser estructurades com les bases de dades amb informació de compres o poden ser no estructurades com les pàgines web on els usuaris deixen la seva opinió sobre algun producte que van comprar o posseïxen. Nosaltres trobem tres problemes fonamentals per a aconseguir aquest objectiu: 1 . La identificació de fonts amb informació idònia per als sistemes recomanadors. 2 . La definició de criteris que permetin la comparança i selecció de les fonts més idònies. 3 . La recuperació d'informació de fonts no estructurades. En aquest sentit, en la tesi proposada s'ha desenvolupat: 1 . Una metodologia que permet la identificació i selecció de les fonts més idònies. Criteris basats en les característiques de les fonts i una mesura de confiança han estat utilitzats per a resoldre el problema de la identificació i selecció de les fonts. 2 . Un mecanisme per a recuperar la informació no estructurada dels usuaris disponible en la web. Tècniques de Text Mining i ontologies s'han utilitzat per a extreure informació i estructurar-la apropiadament perquè la utilitzin els recomanadors. Les contribucions del treball desenvolupat en aquesta tesi doctoral són: 1. Definició d'un conjunt de característiques per a classificar fonts rellevants per als sistemes recomanadors 2. Desenvolupament d'una mesura de rellevància de les fonts calculada sobre la base de les característiques definides 3. Aplicació d'una mesura de confiança per a obtenir les fonts més fiables. La confiança es definida des de la perspectiva de millora de la recomanació, una font fiable és aquella que permet millorar les recomanacions. 4. Desenvolupament d'un algorisme per a seleccionar, des d'un conjunt de fonts possibles, les més rellevants i fiable utilitzant les mitjanes esmentades en els punts previs. 5. Definició d'una ontologia per a estructurar la informació sobre les preferències dels usuaris que estan disponibles en Internet. 6. Creació d'un procés de mapatge que extreu automàticament informació de les preferències dels usuaris disponibles en la web i posa aquesta informació dintre de l'ontologia. Aquestes contribucions permeten aconseguir dos objectius importants: 1 . Millorament de les recomanacions usant fonts d'informació alternatives que sigui rellevants i fiables. 2 . Obtenir informació implícita dels usuaris disponible en Internet.