17 documents found, page 1 of 2
Use social media knowledge for exploring the portuguese wine industry: followin...
Pérez-Rodríguez, Gael; Baptista, João Pedro; Igrejas, Gilberto; Fdez-Riverola, Florentino; Lourenço, AnáliaThis work presents an exploratory study that retrieves, processes, and analyses Twitter data to gain insights about the relevance and perceptions of the wine industry in the Douro Portuguese region (including Porto and Douro wines), as well as other regions in the country. The main techniques and algorithms used in our work belong to the families of natural language processing and machine learning, and the prac...
Application of agent-based modelling to simulate ribosome translation
Pérez-Rodríguez, Gael; Magalhães, Beatriz T.; Azevedo, Nuno F.; Lourenço, AnáliaTranslation is a key process in the cell that encompasses the formation of proteins. However, how the translation mechanisms are affected by physiological changes is yet to be determined. Saccharomyces cerevisiae is one of the most used microorganisms to express recombinant proteins, showing great industrial/commercial value. Modelling the translation process in this yeast can thus bring forward novel insights ...
Using Twitter to understand the human bowel disease community: exploratory anal...
Pérez-Pérez, Martín; Pérez-Rodríguez, Gael; Fdez-Riverola, Florentino; Lourenço, AnáliaBackground: Nowadays, the use of social media is part of daily life, with more and more people, including governments and health organizations, using at least one platform regularly. Social media enables users to interact among large groups of people that share the same interests and suffer the same afflictions. Notably, these channels promote the ability to find and share information about health and medical c...
Next generation community assessment of biomedical entity recognition web serve...
Pérez-Pérez, Martin; Pérez-Rodríguez, Gael; Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Valencia, Alfonso; Krallinger, Martin; Lourenço, AnáliaShared tasks and community challenges represent key instruments to promote research, collaboration and determine the state of the art of biomedical and chemical text mining technologies. Traditionally, such tasks relied on the comparison of automatically generated results against a so-called Gold Standard dataset of manually labelled textual data, regardless of efficiency and robustness of the underlying implem...
Application of agent-based modelling to assess single-molecule transport across...
Maia, Paulo; Pérez-Rodríguez, Gael; Pérez-Pérez, Martín; Fdez-Riverola, Florentino; Lourenço, Anália; Azevedo, Nuno F.Motivation Single cells often show stochastic behaviour and variations in the physiological state of individual cells affect the behaviour observed in cell populations. This may be partially explained by variations in the concentration and spatial location of molecules within and in the vicinity of each cell. Methods This paper introduces an agent-based model that represents single-molecule transport through th...
Online visibility of software-related web sites: The case of biomedical text mi...
Pérez-Rodríguez, Gael; Pérez-Pérez, Martín; Fdez-Riverola, Florentino; Lourenço, AnáliaInternet, in general, and the WWW, in particular, have become an immediate, practical means of introducing software tools and resources, and most importantly, a key vehicle to attract the attention of the potential users. In this scenario, content organization as well as different development practices may affect the online visibility of the target resource. Therefore, the careful selection, organization and pr...
Agent-based model of diffusion of N-acyl homoserine lactones in a multicellular...
Pérez-Rodríguez, Gael; Dias, Sónia; Pérez-Pérez, Martín; Fdez-Riverola, Florentino; Azevedo, Nuno Filipe Ribeiro Pinto OliveiraExperimental incapacity to track microbemicrobe interactions in structures like biofilms, and the complexity inherent to the mathematical modelling of those interactions, raises the need for feasible, alternative modelling approaches. This work proposes an agent-based representation of the diffusion of N-acyl homoserine lactones (AHL) in a multicellular environment formed by Pseudomonas aeruginosa and Candida a...
Evaluation of chemical and gene/protein entity recognition systems at BioCreati...
Pérez-Pérez, Martin; Rabal, Obdulia; Pérez-Rodríguez, Gael; Vazquez, Miguel; Fdez-Riverola, Florentino; Oyarzabal, Julen; Valencia, AlfonsoThis paper presents the results of the BioCreative V.5 offline tasks related to the evaluation of the performance as well as assess progress made by strategies used for the automatic recognition of mentions of chemical names and gene in running text of medicinal chemistry patent abstracts. A total of 21 teams submitted results for at least one of these tasks. The CEMP (chemical entity mention in patents) task e...
Benchmarking biomedical text mining web servers at BioCreative V.5: the technic...
Pérez-Pérez, Martin; Pérez-Rodríguez, Gael; Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Valencia, Alfonso; Krallinger, Martin; Lourenço, AnáliaThe TIPS track consisted in a novel experimental task under the umbrella of the BioCreative text mining challenges with the aim to, for the first time ever, carry out a text mining challenge with particular focus on the continuous assessment of technical aspects of text annotation web servers, specifically of biomedical online named entity recognition systems. A total of 13 teams registered annotation servers, ...
Collaborative relation annotation and quality analysis in Markyt environment
Pérez-Pérez, Martín; Pérez-Rodríguez, Gael; Fdez-Riverola, Florentino; Lourenço, AnáliaText mining is showing potential to help in biomedical knowledge integration and discovery at various levels. However, results depend largely on the specifics of the knowledge problem and, in particular, on the ability to produce high-quality benchmarking corpora that may support the training and evaluation of automatic prediction systems. Annotation tools enabling the flexible and customizable production of su...