Analysis and evaluation of techniques for the extraction of classes in the ontology learning process

This paper analyzes and evaluates, in the context of Ontology learning, some techniques to identify and extract candidate terms to classes of a taxonomy. Besides, this work points out some inconsistencies that may be occurring in the preprocessing of text corpus, and proposes techniques to obtain good terms candidate to classes of a taxonomy.

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.

Addressing Practical Issues Related Tto Nursing Care For International Visitors To Hiroshima

When nine million foreigners visited Japan in 2013, the federal government set a goal to attract an additional two and a half million visitors including medical tourists by 2020. This research investigates the attitudes and concerns of Japanese nurses when they are in a situation dealing with foreign patients. The data were collected from March through September 2010, from 114 nurses at three hospitals, in close proximity to popular tourist destinations in Hiroshima. A questionnaire was developed for this research, named Mari Meter, which included a section to write answers to an open question for the nurses to express their opinions. These responses were examined statistically and by word analysis using Text Mining Studio. Japanese nurses expressed greatest concern about payment options, foreign language skills, and issues of informed consent, when dealing with foreigners. The results confirm that, in order to provide a high quality of patient care, extra preparation and a greater knowledge of international workers and visitors are required by nursing professionals in Japan.


A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network.

BACKGROUND: The nuclear receptors are a large family of eukaryotic transcription factors that constitute major pharmacological targets. They exert their combinatorial control through homotypic heterodimerisation. Elucidation of this dimerisation network is vital in order to understand the complex dynamics and potential cross-talk involved. RESULTS: Phylogeny, protein-protein interactions, protein-DNA interactions and gene expression data have been integrated to provide a comprehensive and up-to-date description of the topology and properties of the nuclear receptor interaction network in humans. We discriminate between DNA-binding and non-DNA-binding dimers, and provide a comprehensive interaction map, that identifies potential cross-talk between the various pathways of nuclear receptors. CONCLUSION: We infer that the topology of this network is hub-based, and much more connected than previously thought. The hub-based topology of the network and the wide tissue expression pattern of NRs create a highly competitive environment for the common heterodimerising partners. Furthermore, a significant number of negative feedback loops is present, with the hub protein SHP [NR0B2] playing a major role. We also compare the evolution, topology and properties of the nuclear receptor network with the hub-based dimerisation network of the bHLH transcription factors in order to identify both unique themes and ubiquitous properties in gene regulation. In terms of methodology, we conclude that such a comprehensive picture can only be assembled by semi-automated text-mining, manual curation and integration of data from various sources.

Bioinformatics-driven identification and examination of candidate genes for non-alcoholic fatty liver disease.

ObjectiveCandidate genes for non-alcoholic fatty liver disease (NAFLD) identified by a bioinformatics approach were examined for variant associations to quantitative traits of NAFLD-related phenotypes.Research Design and MethodsBy integrating public database text mining, trans-organism protein-protein interaction transferal, and information on liver protein expression a protein-protein interaction network was constructed and from this a smaller isolated interactome was identified. Five genes from this interactome were selected for genetic analysis. Twenty-one tag single-nucleotide polymorphisms (SNPs) which captured all common variation in these genes were genotyped in 10,196 Danes, and analyzed for association with NAFLD-related quantitative traits, type 2 diabetes (T2D), central obesity, and WHO-defined metabolic syndrome (MetS).Results273 genes were included in the protein-protein interaction analysis and EHHADH, ECHS1, HADHA, HADHB, and ACADL were selected for further examination. A total of 10 nominal statistical significant associations (P<0.05) to quantitative metabolic traits were identified. Also, the case-control study showed associations between variation in the five genes and T2D, central obesity, and MetS, respectively. Bonferroni adjustments for multiple testing negated all associations.ConclusionsUsing a bioinformatics approach we identified five candidate genes for NAFLD. However, we failed to provide evidence of associations with major effects between SNPs in these five genes and NAFLD-related quantitative traits, T2D, central obesity, and MetS.

Are the World AIDS Conferences guilty of gender bias? Evidence from trends in the monitoring of WAC scientific discourse from 1989 to 2012

Background : The issue of gender is acknowledged as a key issue for the AIDS epidemic. World AIDS Conferences (WAC) have constituted a major discursive space for the epidemic. We sought to establish the balance regarding gender in the AIDS scientific discourse by following its development in the published proceedings of WAC. Fifteen successive WAC 1989-2012 served to establish a "barometer" of scientific interest in heterosexual and homo/bisexual men and women throughout the epidemic. It was hypothesised that, as in other domains of Sexual and Reproductive Health, heterosexual men would be "forgotten" partners. Method : Abstracts from each conference were entered in electronic form into an Access database. Queries were created to generate five categories of interest and to monitor their annual frequency. All abstract titles including the term "men" or "women" were identified. Collections of synonyms were systematically and iteratively developed in order to classify further abstracts according to whether they included terms referring to "homo/bisexual" or "heterosexual". Reference to "Mother to Child Transmission" (MTCT) was also flagged. Results : The category including "men", but without additional reference to "homo-bisexuel" (i.e. referring to men in general and/or to heterosexual men) consistently appears four times less often than the equivalent category for women. Excluding abstracts on women and MTCT has little impact on this difference. Abstracts including reference to both "men" and "homo-bisexual" emerge as the secondmost frequent category; presence of the equivalent category for women is minimal. Conclusion : The hypothesised absence of heterosexual men in the AIDS discourse was confirmed. Although the relative presence of homo-bisexual men and women as a focal subject may be explained by epidemiological data, this is not so in the case of heterosexual men and women. This imbalance has consequences for HIV prevention.

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.

Biblio-MetReS: A bibliometric network reconstruction application and server

Background: Reconstruction of genes and/or protein networks from automated analysis of the literature is one of the current targets of text mining in biomedical research. Some user-friendly tools already perform this analysis on precompiled databases of abstracts of scientific papers. Other tools allow expert users to elaborate and analyze the full content of a corpus of scientific documents. However, to our knowledge, no user friendly tool that simultaneously analyzes the latest set of scientific documents available on line and reconstructs the set of genes referenced in those documents is available. Results: This article presents such a tool, Biblio-MetReS, and compares its functioning and results to those of other user-friendly applications (iHOP, STRING) that are widely used. Under similar conditions, Biblio-MetReS creates networks that are comparable to those of other user friendly tools. Furthermore, analysis of full text documents provides more complete reconstructions than those that result from using only the abstract of the document. Conclusions: Literature-based automated network reconstruction is still far from providing complete reconstructions of molecular networks. However, its value as an auxiliary tool is high and it will increase as standards for reporting biological entities and relationships become more widely accepted and enforced. Biblio- MetReS is an application that can be downloaded from http://metres.udl.cat/. It provides an easy to use environment for researchers to reconstruct their networks of interest from an always up to date set of scientific documents.

Informed recommender: basing recommendations on consumer product reviews

Recommender systems attempt to predict items in which a user might be interested, given some information about the user's and items' profiles. Most existing recommender systems use content-based or collaborative filtering methods or hybrid methods that combine both techniques (see the sidebar for more details). We created Informed Recommender to address the problem of using consumer opinion about products, expressed online in free-form text, to generate product recommendations. Informed recommender uses prioritized consumer product reviews to make recommendations. Using text-mining techniques, it maps each piece of each review comment automatically into an ontology

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.

Minimization of the experimental workload for the prediction of pollutants propagation in rivers. Mathematical modelling and knowledge re-use

The present thesis in focused on the minimization of experimental efforts for the prediction of pollutant propagation in rivers by mathematical modelling and knowledge re-use. Mathematical modelling is based on the well known advection-dispersion equation, while the knowledge re-use approach employs the methods of case based reasoning, graphical analysis and text mining. The thesis contribution to the pollutant transport research field consists of: (1) analytical and numerical models for pollutant transport prediction; (2) two novel techniques which enable the use of variable parameters along rivers in analytical models; (3) models for the estimation of pollutant transport characteristic parameters (velocity, dispersion coefficient and nutrient transformation rates) as functions of water flow, channel characteristics and/or seasonality; (4) the graphical analysis method to be used for the identification of pollution sources along rivers; (5) a case based reasoning tool for the identification of crucial information related to the pollutant transport modelling; (6) and the application of a software tool for the reuse of information during pollutants transport modelling research. These support tools are applicable in the water quality research field and in practice as well, as they can be involved in multiple activities. The models are capable of predicting pollutant propagation along rivers in case of both ordinary pollution and accidents. They can also be applied for other similar rivers in modelling of pollutant transport in rivers with low availability of experimental data concerning concentration. This is because models for parameter estimation developed in the present thesis enable the calculation of transport characteristic parameters as functions of river hydraulic parameters and/or seasonality. The similarity between rivers is assessed using case based reasoning tools, and additional necessary information can be identified by using the software for the information reuse. Such systems represent support for users and open up possibilities for new modelling methods, monitoring facilities and for better river water quality management tools. They are useful also for the estimation of environmental impact of possible technological changes and can be applied in the pre-design stage or/and in the practical use of processes as well.

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.

Managing open access workflows at the University of St Andrews: challenges and Pathfinder solutions

Presentation of Janet Aucock, at the FinELib Consortium Seminar (Aineistopäivä), April 16, 2015 in Helsinki.

Le repérage automatique des entités nommées dans la langue arabe : vers la création d'un système à base de règles

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Étude comparative du vocabulaire de description de la danse dans les archives et du vocabulaire de représentation de la danse dans la littérature

Notre recherche s’insère dans la mouvance des humanités numériques; nous y faisons dialoguer les arts et les sciences de l’information. Depuis quelques décennies, la danse est un sujet d’études et de recherche à part entière. Il devient donc nécessaire de mieux décrire la danse dans les archives, sachant que la description en amont influe grandement sur l’accès en aval. Les méthodes d’extraction automatique de connaissances nous semblent offrir de nouvelles possibilités. L’objectif de notre recherche est de contribuer au développement d’outils de gestion de l’information dans les archives de la danse en comparant un vocabulaire de description de la danse dans les archives et un vocabulaire de représentation de la danse dans la littérature, recueilli grâce à des méthodes d’extraction automatique de connaissances, pour en distinguer une possible complémentarité, particulièrement en ce qui a trait au vocabulaire de l’expérience esthétique. D’abord, nous analysons un vocabulaire de description de la danse dans les archives. Nous décrivons certains outils de description des archives de la danse et nous analysons le thésaurus de descripteurs Collier. Nous constatons que le vocabulaire de description de la danse dans les archives ne semble pas prendre en compte l’expérience esthétique. Ensuite, nous analysons un vocabulaire de représentation de la danse dans la littérature. Un vocabulaire structuré de l’expérience esthétique de la danse moderne est ainsi extrait d’un corpus de textes de l’écrivain français Stéphane Mallarmé et analysé. Puis nous comparons les deux vocabulaires afin d'en distinguer la complémentarité quant à la description de l’expérience esthétique. Nous formulons une première suggestion d’amélioration de certains thésaurus employés dans les archives de la danse : un thésaurus au vocabulaire essentiellement factuel, comme le thésaurus de descripteurs Collier, peut être enrichi de termes à propos de l’expérience esthétique. Le vocabulaire de représentation de la danse dans la littérature est jusqu’à un certain point complémentaire au vocabulaire de description de l’expérience esthétique de la danse dans les archives. Nous menons ainsi une première expérimentation qui justifie en partie la pertinence de certaines méthodes d’extraction de connaissances dans le développement et la maintenance de ressources documentaires pour le domaine des arts d’interprétation tels que la danse.