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120 results on '"Berlanga, R"'

1. Building conceptual spaces for exploring and linking biomedical resources

Author

Berlanga, R., Jimenez-Ruiz, E., and Nebot, V.

Subjects
Computer Science - Information Retrieval, J.3
Abstract

The establishment of links between data (e.g., patient records) and Web resources (e.g., literature) and the proper visualization of such discovered knowledge is still a challenge in most Life Science domains (e.g., biomedicine). In this paper we present our contribution to the community in the form of an infrastructure to annotate information resources, to discover relationships among them, and to represent and visualize the new discovered knowledge. Furthermore, we have also implemented a Web-based prototype tool which integrates the proposed infrastructure., Comment: in Adrian Paschke, Albert Burger, Andrea Splendiani, M. Scott Marshall, Paolo Romano: Proceedings of the 3rd International Workshop on Semantic Web Applications and Tools for the Life Sciences, Berlin,Germany, December 8-10, 2010

Published
2010

2. The Management and Integration of Biomedical Knowledge: Application in the Health-e-Child Project (Position Paper)

Author

Jimenez-Ruiz, E., Berlanga, R., Sanz, I., McClatchey, R., Danger, R., Manset, D., Paraire, J., and Rios, A.

Subjects
Computer Science - Databases, H.2.4, J.3
Abstract

The Health-e-Child project aims to develop an integrated healthcare platform for European paediatrics. In order to achieve a comprehensive view of childrens health, a complex integration of biomedical data, information, and knowledge is necessary. Ontologies will be used to formally define this domain knowledge and will form the basis for the medical knowledge management system. This paper introduces an innovative methodology for the vertical integration of biomedical knowledge. This approach will be largely clinician-centered and will enable the definition of ontology fragments, connections between them (semantic bridges) and enriched ontology fragments (views). The strategy for the specification and capture of fragments, bridges and views is outlined with preliminary examples demonstrated in the collection of biomedical information from hospital databases, biomedical ontologies, and biomedical public databases., Comment: 6 pages; 2 figures. Proceedings of the 1st International Workshop on Ontology content and evaluation in Enterprise

Published
2006

3. OntoPath: A Language for Retrieving Ontology Fragments

Author

Jiménez-Ruiz, E., Berlanga, R., Nebot, V., Sanz, I., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Meersman, Robert, editor, and Tari, Zahir, editor

Published
2007
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4. Automatic Generation of Semantic Fields for Resource Discovery in the Semantic Web

Author

Navas, I., Sanz, I., Aldana, J. F., Berlanga, R., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Andersen, Kim Viborg, editor, Debenham, John, editor, and Wagner, Roland, editor

Published
2005
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17. Enriching the Human Phenotype Ontology with inferred axioms from textual descriptions

Author

Kudama, S, Berlanga, R, and Jiménez-Ruiz, E

Subjects
QA75, Z665
Abstract

The Human Phenotype Ontology (HP) is a reference vocabulary of human phenotypic abnormalities. HP, apart from the textual information (general definitions, descriptions, synonyms, etc.) of each ontology concept, also provides computer-readable logical definitions (axioms) of terms that will allow human phenotypic abnormalities to be related to entities from anatomy, pathology, bio- chemistry and other areas. In this paper we present a prototype to generate new axiomatic knowledge from the textual descriptions of each HP term. The proto- type (i) detects terms in the textual descriptions and not found in the given logical expressions, (ii) generates pair combinations of those terms, (iii) builds triples after detecting the most probable relation between the pair of terms using a sta- tistical model and, finally, (iv) suggests the most probable triples to the user so she can decide which ones can be added to the original axioms.

Published
2018

19. Assessemnt of NER solutions against the first and second CALBC Silver Standard Corpus

Author

Rebholz-Schuhmann, D, Jimeno Yepes, A, Li, C, Kafkas, S, Lewin, I, Kang, Ning, Corbett, P, Milward, D, Buyko, E, Beisswanger, E, Hornbostel, K, Kouznetsov, A, Witte, R, Laurila, JB, Baker, CJO, Kuo, C-J, Clematide, S, Rinaldi, F, Farkas, R, Mora, G, Hara, K, Furlong, LI, Rautschka, M, Lara Neves, M, Pascual-Montano, A, Wei, Q, Collier, N, Chowdhury, FM, Lavelli, A, Berlanga, R, Morante, R, van Asch, V, Daelemans, W, Luis Marina, J, van Mulligen, Erik, Kors, Jan, Hahn, U, and Medical Informatics

Published
2011

27. Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

Author

Rebholz-Schuhmann, D. (Dietrich), Jimeno-Yepes, A. (Antonio), Li, C. (Chen), Kafkas, S. (Senay), Lewin, I. (Ian), Kang, N. (Ning), Corbett, P. (Peter), Milward, D. (David), Buyko, E. (Ekaterina), Beisswanger, E. (Elena), Hornbostel, K. (Kerstin), Kouznetsov, A. (Alexandre), Witte, R. (René), Laurila, J.B. (Jonas B), Baker, C.J.O. (Christopher), Kuo, C.-J. (Cheng-Ju), Clematide, S. (Simone), Rinaldi, F. (Fabio), Farkas, R. (Richárd), Móra, G. (György), Hara, K. (Kazuo), Furlong, L.I. (Laura), Rautschka, M. (Michael), Neves, M.L. (Mariana Lara), Pascual-Montano, A. (Alberto), Wei, Q. (Qi), Collier, N. (Nigel), Chowdhury, M.F.M. (Md Faisal Mahbub), Lavelli, A. (Alberto), Berlanga, R. (Rafael), Morante, R. (Roser), Van Asch, V. (Vincent), Daelemans, W. (Walter), Marina, J.L. (José Luís), Van Mulligen, E.M. (Erik M.), Kors, J.A. (Jan), Hahn, U. (Udo), Rebholz-Schuhmann, D. (Dietrich), Jimeno-Yepes, A. (Antonio), Li, C. (Chen), Kafkas, S. (Senay), Lewin, I. (Ian), Kang, N. (Ning), Corbett, P. (Peter), Milward, D. (David), Buyko, E. (Ekaterina), Beisswanger, E. (Elena), Hornbostel, K. (Kerstin), Kouznetsov, A. (Alexandre), Witte, R. (René), Laurila, J.B. (Jonas B), Baker, C.J.O. (Christopher), Kuo, C.-J. (Cheng-Ju), Clematide, S. (Simone), Rinaldi, F. (Fabio), Farkas, R. (Richárd), Móra, G. (György), Hara, K. (Kazuo), Furlong, L.I. (Laura), Rautschka, M. (Michael), Neves, M.L. (Mariana Lara), Pascual-Montano, A. (Alberto), Wei, Q. (Qi), Collier, N. (Nigel), Chowdhury, M.F.M. (Md Faisal Mahbub), Lavelli, A. (Alberto), Berlanga, R. (Rafael), Morante, R. (Roser), Van Asch, V. (Vincent), Daelemans, W. (Walter), Marina, J.L. (José Luís), Van Mulligen, E.M. (Erik M.), Kors, J.A. (Jan), and Hahn, U. (Udo)

Abstract

Background: Competitions in text mining have been used to measure the performance of automatic text processing solutions against a manually annotated gold standard corpus (GSC). The preparation of the GSC is time-consuming and costly and the final corpus consists at the most of a few thousand documents annotated with a limited set of semantic groups. To overcome these shortcomings, the CALBC project partners (PPs) have produced a large-scale annotated biomedical corpus with four different semantic groups through the harmonisation of annotations from automatic text mining solutions, the first version of the Silver Standard Corpus (SSC-I). The four semantic groups are chemical entities and drugs (CHED), genes and proteins (PRGE), diseases and disorders (DISO) and species (SPE). This corpus has been used for the First CALBC Challenge asking the participants to annotate the corpus with their text processing solutions. Results: All four PPs from the CALBC project and in addition, 12 challenge participants (CPs) contributed annotated data sets for an evaluation against the SSC-I. CPs could ignore the training data and deliver the annotations from their genuine annotation system, or could train a machine-learning approach on the provided pre-annotated data. In general, the performances of the annotation solutions were lower for entities from the categories CHED and PRGE in comparison to the identification of entities categorized as DISO and SPE. The best perfo

Published
2011
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28. Aplicación de nuevas técnicas docentes en la asignatura Sistemas Cliente/Servidor

Author

Corchuelo Gil, Rafael, Jiménez Rodríguez, María José, Romero Ternero, María del Carmen, Universidad de Sevilla. Departamento de Lenguajes y Sistemas Informáticos, Universidad de Sevilla. Departamento de Matemática Aplicada I (ETSII), Universidad de Sevilla. Departamento de Tecnología Electrónica, Jiménez Ruiz, E., Llido, D., Berlanga, R., Rajadell, O., Corchuelo Gil, Rafael, Jiménez Rodríguez, María José, Romero Ternero, María del Carmen, Universidad de Sevilla. Departamento de Lenguajes y Sistemas Informáticos, Universidad de Sevilla. Departamento de Matemática Aplicada I (ETSII), Universidad de Sevilla. Departamento de Tecnología Electrónica, Jiménez Ruiz, E., Llido, D., Berlanga, R., and Rajadell, O.

Abstract

En este trabajo mostramos nuestras experiencias en la aplicación de metodologías de aprendizaje cooperativo y basado en proyectos en la asignatura Sistemas Cliente/Servidor en los cursos académicos 2008/2009 y 2009/2010.

Published
2011

29. Aplicación de nuevas técnicas docentes en la asignatura Sistemas Cliente/Servidor

Author

Jimenez-Ruiz, E., Llido, D., Berlanga, R., Rajadell, O., Jimenez-Ruiz, E., Llido, D., Berlanga, R., and Rajadell, O.

Abstract

En este trabajo mostramos nuestras experiencias en la aplicación de metodologías de aprendizaje cooperativo y basado en proyectos en la asignatura Sistemas Cliente/Servidor en los cursos académicos 2008/2009 y 2009/2010., SUMMARY: In this work we present our teaching experience in the aplication of cooperative and project-based learning methodologies within the subject Client/Server Systems in the academic years 2008/2009 and 2009/2010., Peer Reviewed

Published
2011

31. Assessment of disease named entity recognition on a corpus of annotated sentences

Author

Jimeno, A, Jimenez-Ruiz, E, Lee, V, Gaudan, S, Berlanga, R, Rebholz-Schuhmann, D, Jimeno, A, Jimenez-Ruiz, E, Lee, V, Gaudan, S, Berlanga, R, and Rebholz-Schuhmann, D

Abstract

BACKGROUND: In recent years, the recognition of semantic types from the biomedical scientific literature has been focused on named entities like protein and gene names (PGNs) and gene ontology terms (GO terms). Other semantic types like diseases have not received the same level of attention. Different solutions have been proposed to identify disease named entities in the scientific literature. While matching the terminology with language patterns suffers from low recall (e.g., Whatizit) other solutions make use of morpho-syntactic features to better cover the full scope of terminological variability (e.g., MetaMap). Currently, MetaMap that is provided from the National Library of Medicine (NLM) is the state of the art solution for the annotation of concepts from UMLS (Unified Medical Language System) in the literature. Nonetheless, its performance has not yet been assessed on an annotated corpus. In addition, little effort has been invested so far to generate an annotated dataset that links disease entities in text to disease entries in a database, thesaurus or ontology and that could serve as a gold standard to benchmark text mining solutions. RESULTS: As part of our research work, we have taken a corpus that has been delivered in the past for the identification of associations of genes to diseases based on the UMLS Metathesaurus and we have reprocessed and re-annotated the corpus. We have gathered annotations for disease entities from two curators, analyzed their disagreement (0.51 in the kappa-statistic) and composed a single annotated corpus for public use. Thereafter, three solutions for disease named entity recognition including MetaMap have been applied to the corpus to automatically annotate it with UMLS Metathesaurus concepts. The resulting annotations have been benchmarked to compare their performance. CONCLUSIONS: The annotated corpus is publicly available at ftp://ftp.ebi.ac.uk/pub/software/textmining/corpora/diseases and can serve as a benchmark to othe

Published
2008

32. Effect of maternal smoking on offspring growth

Author

Vio-Del Rio, Fernando, García, Carola, Salazar-Rodríguez, Gabriela, Ahumada, M., Berlanga, R., and Seron-Ferre, M.

Abstract

Background: Maternal smoking negatively affects bir th weight, breast milk volume and growth at one month of age. Aim: To study the effect of maternal smoking on the growth of three month old infants. Subjects and methods: Ten smoking and 10 non smoking mothers with one month old children, under exclusive breast feeding, were selected for the study. Urinary cotinine levels in the mothers and children were measured to assess smoking. Two months later; children were reassessed. Results: Smoking mothers consumed a mean of 6.5 cigarettes/day. Compared to non smokers, urinary continine levels were higher in these mothers (60 +/- 22 and 1428 +/- 716 ng/ml respectively, P < 0.002) and their offspring (21 +/- 20 and 156 +/- 101 ng/ml respectively p < 0.001). Compared with smokers, at three months of age, children of non smoking mothers had a higher average weight (5829 +/- 498 and 6325 +/- 427 g, P < 0.02). Conclusions: Measurement of urinary continue levels is a reliable and objective measure of maternal smoking and nicotine transfer to the offspring. It also allows the assessment of passive smoking. Maternal smoking adversely affects child growth at three months of age.

Published
1998

34. Determinación de elementos micronutrientes y tóxicos en alimentos de la población infantil de Lima metropolitana: Parte I: determinación mediante análisis por activación neutrónica instrumental de Ca, Cl, K, Mg y N a en muestras de leche y preparaciones de leche con cereal, consumidos por la población infantil en edad de destete

Author

Bedregal, Patricia, Berlanga, R., Zavaleta, N., Montoya, Eduardo, and Díaz, Alfredo

Subjects
Leche, Alimentos, Análisis por activación neutrónica, Dieta, Reactor RP-10, Niños
Abstract

The contents of Ca, Cl, K, Mg and Na, in milk and milk with cereal, consumed by the peruvian children were determined by short irradiation INNA using RP-10 reactor, with a thermal flux of 10 13 ncm-2 s-1, and a pneumatical system. The comparative mcthod with solutions of primary standards of each element determined was used. The IAEA-A11-milk powder, IAEA-H4-Animal muscle and IAEA-V10-Hay powder, reference materials were periodically analyzed, together with the samples, in order to check the quality of analytical results. Organismo Internacional de Energía Atómica. Consejo Nacional de Ciencia y Tecnología. Instituto de Investigaciones Nutricionales. Instituto Peruano de Energía Nuclear

Published
1993

43. OntoPath: A Language for Retrieving Ontology Fragments.

Author

Hutchison, David, Kanade, Takeo, Kittler, Josef, Kleinberg, Jon M., Mattern, Friedemann, Mitchell, John C., Naor, Moni, Nierstrasz, Oscar, Pandu Rangan, C., Steffen, Bernhard, Sudan, Madhu, Terzopoulos, Demetri, Tygar, Doug, Vardi, Moshe Y., Weikum, Gerhard, Meersman, Robert, Tari, Zahir, Jiménez-Ruiz, E., Berlanga, R., and Nebot, V.

Abstract

In this work we introduce a novel retrieval language, named OntoPath, for specifying and retrieving relevant ontology fragments. This language is intended to extract customized self-standing ontologies from very large, general-purpose ones. Through OntoPath, users can specify the desired detail level in the concept taxonomies as well as the properties between concepts that are required by the target applications. The syntax and aims of OntoPath resemble XPath's in that they are simple enough to be handled by non-expert users and they are designed to be included in other XML-based applications (e.g. transformations sheets, semantic annotation of web services, etc.). OntoPath has been implemented on the top of the graph-based database G, for which a Protégé OWL plug-in has been designed to access and retrieve ontology fragments. [ABSTRACT FROM AUTHOR]

Published
2007
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45. The Management and Integration of Biomedical Knowledge: Application in the Health-e-Child Project (Position Paper).

Author

Meersman, Robert, Tari, Zahir, Herrero, Pilar, Jimenez-Ruiz, E., Berlanga, R., Sanz, I., McClatchey, R., Danger, R., Manset, D., Paraire, J., and Rios, A.

Abstract

The Health-e-Child project aims to develop an integrated healthcare platform for European paediatrics. In order to achieve a comprehensive view of children's health, a complex integration of biomedical data, information, and knowledge is necessary. Ontologies will be used to formally define this domain knowledge and will form the basis for the medical knowledge management system. This paper introduces an innovative methodology for the vertical integration of biomedical knowledge. This approach will be largely clinician-centered and will enable the definition of ontology fragments, connections between them (semantic bridges) and enriched ontology fragments (views). The strategy for the specification and capture of fragments, bridges and views is outlined with preliminary examples demonstrated in the collection of biomedical information from hospital databases, biomedical ontologies, and biomedical public databases. Keywords: Vertical Knowledge Integration, Approximate Queries, Ontology Views, Semantic Bridges. [ABSTRACT FROM AUTHOR]

Published
2006
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46. Automatic Generation of Semantic Fields for Resource Discovery in the Semantic Web.

Author

Andersen, Kim Viborg, Debenham, John, Wagner, Roland, Navas, I., Sanz, I., Aldana, J. F., and Berlanga, R.

Abstract

In this paper we present and evaluate two approaches for the generation of Semantic Fields, which are used as a tool for resource discovery in the Semantic Web. We mainly concern ourselves with semantic networks that describe their interests and resources by means of ontologies. Semantic Fields are intended to help users to locate these resources by specifying a brief description (also as an ontology). We propose two ways to automatically build Semantic Fields. The first one is used in the KREIOS approach, which is based on the pre-computation of distances between all the ontology pairs. The second one is based on a fast incremental clustering algorithm, which groups together similar ontologies as they are published. These groups constitute a pre-computed set of Semantic Fields. Keywords: Resource discovery, similarity of ontologies, query distribution. [ABSTRACT FROM AUTHOR]

Published
2005
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