João Almeida

Subject	Enriching information extraction pipelines in clinical decision support systems
Advisor	José Luís Oliveira
Group	Biomedical Informatics and Technologies
Status	Other
Starts	2018/10/01
Ends	2022/01/21
Country	Portugal
Projects	EHDEN
Past projects	EMIF, NETDIAMOND, RD-Connect
Events
Proposals
Personal page

Publications

Books

• João Almeida, Alejandro Rodríguez González, Linlin Shen, Bridget Kane, Agma Traina, Paolo Soda, José Luís Oliveira. 2021 IEEE 34th International Symposium on Computer-Based Medical Systems. IEEE Computer Society Conference Publishing Services, Aveiro, June 2021

Articles in international journals listed in the ISI

• João Almeida, Leonardo Coelho, José Luís Oliveira. BIcenter: A collaborative Web ETL solution based on a reflective software approach. SoftwareX, vol. 16, p. 100892, December 2021
• João Almeida, Luís Bastião Silva, Isabelle Bos, Pieter Jelle Visser, José Luís Oliveira. A methodology for cohort harmonisation in multicentre clinical research. Informatics in Medicine Unlocked, p. 100760, October 2021
• João Almeida, João Figueira Silva, Sérgio Matos, José Luís Oliveira. A two-stage workflow to extract and harmonize drug mentions from clinical notes into observational databases. Journal of Biomedical Informatics, vol. 120, p. 103849, August 2021 [IF 2018: 2.950 (Q2, 33/106)]
• João Almeida, Diogo Pratas, José Luís Oliveira. A semi-automatic methodology for analysing distributed and private biobanks. Computers in Biology and Medicine, vol. 130, p. 104180, January 2021 [IF 2018: 2.895]
• João Figueira Silva, João Almeida, Sérgio Matos. Extraction of Family History Information From Clinical Notes: Deep Learning and Heuristics Approach. JMIR Medical Informatics, vol. 8, no. 12, December 2020 [IF 2020: 2.955 (Q3, 17/30)]
• João Almeida, Armando J. Pinho, José Luís Oliveira, Olga Fajarda, Diogo Pratas. GTO: A toolkit to unify pipelines in genomic and proteomic research. SoftwareX, vol. 12, p. 100535, July 2020
• Tiago Godinho, Rui Lebre, João Almeida, Carlos Costa. ETL Framework for Real-Time Business Intelligence over Medical Imaging Repositories. Journal of Digital Imaging, vol. 32, p. 870-879, October 2019 [IF 2018: 2.572 (Q2, 51/129)]
• João Almeida, Rosa Gini, Giuseppe Roberto, Peter Rijnbeek, José Luís Oliveira. TASKA: A modular task management system to support health research studies. BMC Medical Informatics and Decision Making, vol. 19, no. 1, p. 121, July 2019 [IF 2018: 2.067 (Q3, 15/26)]

Chapters in books

• João Almeida, João Figueira Silva, Alejandro Pazos, Sérgio Matos, José Luís Oliveira. Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information. Biomedical Engineering Systems and Technologies, Xuesong Ye, Filipe Soares, Elisabetta De Maria, Pedro Gómez Vilda, Federico Cabitza, Ana Fred, Hugo Gamboa (Ed.), Springer International Publishing, vol. 1400, p. 521-540, March 2021
• João Almeida, Olga Fajarda, José Luís Oliveira. File Forgery Detection Using a Weighted Rule-Based System. Experimental IR Meets Multilinguality, Multimodality, and Interaction, CLEF 2020. Lecture Notes in Computer Science (Ed.), Springer, Cham, vol. 12260, p. 85-96, September 2020

Articles in conference proceedings

• Tiago Almeida, Rui Antunes, João Figueira Silva, João Almeida, Sérgio Matos. Chemical detection and indexing in PubMed full text articles using deep learning and rule-based methods. Proceedings of the BioCreative VII Challenge Evaluation Workshop, Online event, p. 119-123, November 2021
• João Figueira Silva, Tiago Almeida, Rui Antunes, João Almeida, Sérgio Matos. Drug mention recognition in Twitter posts using a deep learning approach. Proceedings of the BioCreative VII Challenge Evaluation Workshop, Online event, p. 210-213, November 2021
• Mariana Sequeira, João Almeida, José Luís Oliveira. A Comprehensive Analysis on Retrieval and Visualisation Platforms about Rare Diseases. IEEE 34th International Symposium on Computer-Based Medical Systems (CBMS), Aveiro, Portugal, June 2021
• João Almeida, Eriksson Monteiro, José Luís Oliveira. An Architecture to Define Cohorts over Medical Imaging Datasets. IEEE 34th International Symposium on Computer-Based Medical Systems (CBMS), Aveiro, Portugal, June 2021
• João Almeida, João Figueira Silva, Sérgio Matos, José Luís Oliveira. A Recommender System to Help Refining Clinical Research Studies. 31st Medical Informatics Europe conference, Studies in health technology and informatics, May 2021
• João Almeida, Eriksson Monteiro, Luís Bastião Silva, Alejandro Pazos Sierra, José Luís Oliveira. A Recommender System to Help Discovering Cohorts in Rare Diseases. IEEE 33rd International Symposium on Computer-Based Medical Systems (CBMS), Rochester, MN, USA, p. 25-28, July 2020
• João Almeida, José Luís Oliveira. Multi-language Concept Normalisation of Clinical Cohorts. IEEE 33rd International Symposium on Computer-Based Medical Systems (CBMS), Rochester, MN, USA, p. 261-264, July 2020
• João Almeida, Eriksson Monteiro, Luís Bastião Silva, Alejandro Pazos, José Luís Oliveira. A Recommender System based on Cohorts' Similarity. 30th Medical Informatics Europe conference, MIE 2020, Studies in health technology and informatics, vol. 270, p. 1183-1184, April 2020
• João Figueira Silva, Rui Antunes, João Almeida, Sérgio Matos. Clinical concept normalization on medical records using word embeddings and heuristics. 30th Medical Informatics Europe conference, MIE 2020, Studies in health technology and informatics, vol. 270, p. 93-97, April 2020
• João Almeida, Sérgio Matos. Rule-based extraction of family history information from clinical notes. The 35th ACM/SIGAPP Symposium On Applied Computing, Online event, p. 670–675, March 2020
• João Almeida, Pedro Freire, Olga Fajarda, José Luís Oliveira. A Computational Platform for Heart Failure Cases Research. Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, Malta, vol. 5, p. 601-608, February 2020
• João Almeida, João Figueira Silva, Alejandro Sierra, Sérgio Matos, José Luís Oliveira. Enhancing Decision-making Systems with Relevant Patient Information by Leveraging Clinical Notes. Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, vol. 5, p. 254-262, February 2020
• João Almeida, Pedro Freire, Olga Fajarda, José Luís Oliveira. A Weighted Rule-Based Model for File Forgery Detection: UA. PT Bioinformatics at ImageCLEF 2019. CLEF 2019 Working Notes, September 2019
• João Almeida, José Luís Oliveira. GenericCDSS - A Generic Clinical Decision Support System. 2019 IEEE 32st International Symposium on Computer-Based Medical Systems (CBMS), Cordoba, Spain, June 2019
• João Almeida, Olga Fajarda, Arnaldo Pereira, José Luís Oliveira. Strategies to Access Patient Clinical Data from Distributed Databases. Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies, Prague, Czech Republic, vol. 5, p. 466-473, February 2019
• João Almeida, Tiago Godinho, Luís Bastião Silva, Carlos Costa, José Luís Oliveira. Services Orchestration and Workflow Management in Distributed Medical Imaging Environments. 2018 IEEE 31st International Symposium on Computer-Based Medical Systems (CBMS), Karlstad, Sweden, p. 170-175, June 2018
• João Almeida, Joana Guimarães, José Luís Oliveira. Simplifying the digitization of clinical protocols for diabetes management. 2018 IEEE 31st International Symposium on Computer-Based Medical Systems (CBMS, Karlstad, Sweden, p. 176-181, June 2018
• João Almeida, Ricardo Ribeiro, José Luís Oliveira. A modular workflow management framework. Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies HEALTHINF, Funchal, Madeira, Portugal, vol. 5, p. 414-421, January 2018

Masters thesis

• João Almeida. Software solution management for clinical protocol. Masters Thesis, Departamento de Electrónica e Telecomunicações e Informática, Campus Universitário Santiago, Aveiro, Portugal, July 2018