Hugo Costa

University of Minho · Institute for Biotechnology and Bioengineering - Centre of Biological Engineering

The construction of repositories with curated information about gene essentiality for organisms of interest in Biotechnology is a very relevant task, mainly in the design of cell factories for the enhanced production of added-value products. However, it requires retrieval and extraction of relevant information from literature, leading to high costs...

Background and objective: The volume of biomedical literature has been increasing in the last years. Patent documents have also followed this trend, being important sources of biomedical knowledge, technical details and curated data, which are put together along the granting process. The field of Biomedical text mining (BioTM) has been creating sol...

Biomedical literature is composed of an ever increasing number of publications in natural language. Patents are a relevant fraction of those, being important sources of information due to all the curated data from the granting process. However, their unstructured data turns the search of information a challenging task. To surpass that, Biomedical t...

Biomedical text mining (BTM) aims to create methods for searching and structuring knowledge extracted from biomedical literature. Named entity recognition (NER), a BTM task, seeks to identify mentions to biological entities in texts. Dictionaries, regular expressions, natural language processing and machine learning (ML) algorithms are used in this...

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 devel...

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 devel...

Transcriptional Regulatory Networks (TRNs) are powerful tool for representing several interactions that occur within a cell. Recent studies have provided information to help researchers in the tasks of building and understanding these networks. One of the major sources of information to build TRNs is biomedical literature. However, due to the rapid...

Systems biology has fostered interest in the use of kinetic models to better understand the dynamic behavior of metabolic networks in a wide variety of conditions. Unfortunately, in most cases, data available in different databases are not sufficient for the development of such models, since a significant part of the relevant information is still s...

Bringing biologists and text miners closer together is a major aim towards the general usage of literature mining tools. Our contribution to this aim is an end-user tool for the extraction of problem-specific biologically relevant relations. Development efforts are being focused on easy-to-use text mining workflows including commonly available enti...