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Sobre

Sobre

João Correia Lopes é Professor Auxiliar em Engenharia Informática na Universidade do Porto e investigador sénior do INESC TEC.
Formou-se em Engenharia Eletrotécnica e de Computadores na Universidade do Porto em 1984 e obteve doutoramento em Ciência da Computação pela Universidade de Glasgow em 1997.
Tem ensinado cursos de graduação e pós-graduação em bases de dados e aplicações web, engenharia de software e programação, linguagens de anotação e web semântica.
Esteve envolvido em projectos de investigação na área de Preservação a longo prazo, em Arquiteturas orientadas a serviços e em e-Ciência.
Atualmente, os seus principais interesses de investigação são a Gestão de dados de investigação, e-Saúde e as infra-estruturas para e-Ciência.

Tópicos
de interesse
Detalhes

Detalhes

  • Nome

    João Correia Lopes
  • Cargo

    Investigador Sénior
  • Desde

    19 junho 1985
014
Publicações

2024

Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data

Autores
Peres, A; Klein, V; Frankel, B; Lees, W; Polak, P; Meehan, M; Rocha, A; Lopes, JC; Yaari, G;

Publicação
BRIEFINGS IN BIOINFORMATICS

Abstract
Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency, reproducibility, and collaboration in AIRR-seq data analysis, serving as a model for handling and documenting bioinformatics pipelines in other research domains.

2023

Secure, Dynamic and Uncomplicated Licensing of Movies on a Blockchain Infrastructure

Autores
Santos, J; Amorim, I; Ulisses, A; Lopes, JC; Filipe, V;

Publicação
2023 INTERNATIONAL CONFERENCE ON INFORMATION NETWORKING, ICOIN

Abstract
Nowadays, the consumption of media content has been growing rapidly and consistently, driven by an easy access to Video on Demand platforms. In this context, licensing is needed to ensure that filmmakers receive rightful payment for their content and ensure that their rights as content owners are respected. The traditional licensing process, which is heavily dependent on third parties (legal entities) to mediate the transaction, is very long, costly, and complex, which is a barrier to smaller independent filmmakers. The solution proposed in this work, to address this problem, is to create a business-to-business marketplace platform supported by a Blockchain licensing module. This module takes advantage of Blockchain technology to ensure the licensing requirements and to provide a secure, practical and straightforward way to license media in a decentralised paradigm. The result of this work was validated though a prototype, and a global assessment of the system's usability was performed using the System Usability Scale, where it got the best possible grade.

2023

Using Digital Tools to Study the Health of Adults Born Preterm at a Large Scale: e-Cohort Pilot Study

Autores
Lorthe, E; Santos, C; Ornelas, JP; Doetsch, JN; Marques, SCS; Teixeira, R; Santos, AC; Rodrigues, C; Goncalves, G; Sousa, PF; Lopes, JC; Rocha, A; Barros, H;

Publicação
JOURNAL OF MEDICAL INTERNET RESEARCH

Abstract
Background: Preterm birth is a global health concern. Its adverse consequences may persist throughout the life course, exerting a potentially heavy burden on families, health systems, and societies. In high-income countries, the first children who benefited from improved care are now adults entering middle age. However, there is a clear gap in the knowledge regarding the long-term outcomes of individuals born preterm. Objective: This study aimed to assess the feasibility of recruiting and following up an e-cohort of adults born preterm worldwide and provide estimations of participation, characteristics of participants, the acceptability of questions, and the quality of data collected. Methods: We implemented a prospective, open, observational, and international e-cohort pilot study (Health of Adult People Born Preterm-an e-Cohort Pilot Study [HAPP-e]). Inclusion criteria were being an adult (aged =18 years), born preterm (<37 weeks of gestation), having internet access and an email address, and understanding at least 1 of the available languages. A large, multifaceted, and multilingual communication strategy was established. Between December 2019 and June 2021, inclusion and repeated data collection were performed using a secured web platform. We provided descriptive statistics regarding participation in the e-cohort, namely, the number of persons who registered on the platform, signed the consent form, initiated and completed the baseline questionnaire, and initiated and completed the follow-up questionnaire. We also described the main characteristics of the HAPP-e participants and provided an assessment of the quality of the data and the acceptability of sensitive questions. Results: As of December 31, 2020, a total of 1004 persons had registered on the platform, leading to 527 accounts with a confirmed email and 333 signed consent forms. A total of 333 participants initiated the baseline questionnaire. All participants were invited to follow-up, and 35.7% (119/333) consented to participate, of whom 97.5% (116/119) initiated the follow-up questionnaire. Completion rates were very high both at baseline (296/333, 88.9%) and at follow-up (112/116, 96.6%). This sample of adults born preterm in 34 countries covered a wide range of sociodemographic and health characteristics. The gestational age at birth ranged from 23+6 to 36+6 weeks (median 32, IQR 29-35 weeks). Only 2.1% (7/333) of the participants had previously participated in a cohort of individuals born preterm. Women (252/333, 75.7%) and highly educated participants (235/327, 71.9%) were also overrepresented. Good quality data were collected thanks to validation controls implemented on the web platform. The acceptability of potentially sensitive questions was excellent, as very few participants chose the I prefer not to say option when available. Conclusions: Although we identified room for improvement in specific procedures, this pilot study confirmed the great potential for recruiting a large and diverse sample of adults born preterm worldwide, thereby advancing research on adults born preterm.

2022

Development of a data classification system for preterm birth cohort studies: the RECAP Preterm project

Autores
Bamber, D; Collins, HE; Powell, C; Goncalves, GC; Johnson, S; Manktelow, B; Ornelas, JP; Lopes, JC; Rocha, A; Draper, ES;

Publicação
BMC MEDICAL RESEARCH METHODOLOGY

Abstract
Background The small sample sizes available within many very preterm (VPT) longitudinal birth cohort studies mean that it is often necessary to combine and harmonise data from individual studies to increase statistical power, especially for studying rare outcomes. Curating and mapping data is a vital first step in the process of data harmonisation. To facilitate data mapping and harmonisation across VPT birth cohort studies, we developed a custom classification system as part of the Research on European Children and Adults born Preterm (RECAP Preterm) project in order to increase the scope and generalisability of research and the evaluation of outcomes across the lifespan for individuals born VPT. Methods The multidisciplinary consortium of expert clinicians and researchers who made up the RECAP Preterm project participated in a four-phase consultation process via email questionnaire to develop a topic-specific classification system. Descriptive analyses were calculated after each questionnaire round to provide pre- and post- ratings to assess levels of agreement with the classification system as it developed. Amendments and refinements were made to the classification system after each round. Results Expert input from 23 clinicians and researchers from the RECAP Preterm project aided development of the classification system's topic content, refining it from 10 modules, 48 themes and 197 domains to 14 modules, 93 themes and 345 domains. Supplementary classifications for target, source, mode and instrument were also developed to capture additional variable-level information. Over 22,000 individual data variables relating to VPT birth outcomes have been mapped to the classification system to date to facilitate data harmonisation. This will continue to increase as retrospective data items are mapped and harmonised variables are created. Conclusions This bespoke preterm birth classification system is a fundamental component of the RECAP Preterm project's web-based interactive platform. It is freely available for use worldwide by those interested in research into the long term impact of VPT birth. It can also be used to inform the development of future cohort studies.

2022

WindsPT e-Science platform for wind measurement campaigns

Autores
Gomes D.F.; Lopes J.C.; Palma J.M.L.M.; Senra F.; Dias S.; Coimbra I.L.;

Publicação
Journal of Physics: Conference Series

Abstract
Experimental field campaigns for collecting wind data, essential for academic research and the wind energy industry, are non-trivial due to the complex equipment and infrastructure required. This paper reports the latest developments of the WindsPT e-Science platform for planning, executing, and disseminating wind measurement campaign data. Existing e-Science platforms have been developed for more generic domains, preventing them from capturing the details and requirements of the field. Additionally, we propose a protocol for transferring large volumes of data from the in-site devices to our platform, ensuring data replication. With an easy-to-use Web interface, WindsPT promotes collaboration between participants, disseminates results among the stakeholders, publishes metadata, uses DOI, and includes metadata that enables machine-to-machine communication. The platform has multiple sections, with maps, images, and documents, where there is information about the location of the stations, positioning of the sensors, operating dates, photos, technical sheets, calibration documents, among others. The WindsPT platform has been used to host the Perdigão 2017 experimental campaign and proved to be a valuable tool during all the phases of this large field experiment. A new version of WindsPT, designed to be FAIR, host multiple campaigns, and include multiple cross-campaign shared features, as full-text search capabilities, is now developed and tested.

Teses
supervisionadas

2023

Advanced tool for aggregation and visualization of atomized data

Autor
Ana Teresa Feliciano da Cruz

Instituição
UP-FEUP

2023

Collaborative web application for real-time monitoring of sport events

Autor
João Diogo Martins Romão

Instituição
UP-FEUP

2022

Reproducible and Privacy-Preserving Analyses for Next-Generation Sequencing Data

Autor
Mark Timothy Vasconcelos Meehan

Instituição
UP-FEUP

2022

Gestão de fluxo de dados para processos de injunção

Autor
Mário André Macedo Ferreira

Instituição
UP-FEUP

2022

Impact of Gamification on Subject Engagement and Data Quality in Health-care Surveys on Mobile Applications

Autor
Raúl Manuel Fidalgo da Silva Teixeira Viana

Instituição
UP-FEUP