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Daniel Pedro de Jesus Faria. Concluiu o(a) Doutoramento em Doutoramento em Informática, Especialidade Bioinformática em 2012 pelo(a) Universidade de Lisboa Faculdade de Ciências, Doutoramento em Informática em 2012/09/18 pelo(a) Universidade de Lisboa e Licenciatura em Licenciatura em Engenharia Biológica em 2004/10/31 pelo(a) Universidade de Lisboa Instituto Superior Técnico. Publicou 4 artigos em revistas especializadas. Possui 5 livro(s). Atua na(s) área(s) de Ciências Exatas com ênfase em Ciências da Computação e da Informação e Ciências Exatas com ênfase em Ciências da Computação e da Informação com ênfase em Bioinformática. No seu currículo Ciência Vitae os termos mais frequentes na contextualização da produção científica, tecnológica e artístico-cultural são: Ontologias; Modelos de conhecimento; Anotação funcional; Análise de enriquecimento funcional; .
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Identification

Personal identification

Full name
Daniel Pedro de Jesus Faria

Citation names

  • Faria, Daniel

Author identifiers

Ciência ID
F712-80BD-030D
ORCID iD
0000-0003-1511-277X

Knowledge fields

  • Exact Sciences - Computer and Information Sciences
  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Spanish; Castilian Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
French Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2007/01/01 - 2012/09/28
Concluded
 Doutoramento em Informática, Especialidade Bioinformática (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Automated Knowledge Extraction From Protein Sequence" (THESIS/DISSERTATION)
 N/A
2006/06/30
Concluded
 Curso pós-graduado de especialização em Bioinformática (Pós-Graduação)
Universidade de Lisboa Faculdade de Ciências, Portugal
"N/A" (THESIS/DISSERTATION)
 18
2004/10/31
Concluded
 Licenciatura em Engenharia Biológica (Licenciatura)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"N/A" (THESIS/DISSERTATION)
 15
Affiliation

Science

Category
Host institution 		Employer
2022/10/06 - Current Researcher (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2021/02/19 - 2022/10/05 Contracted Researcher (Research) Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2019/09/01 - 2021/01/31 Postdoc (Research) Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2015/06/01 - 2019/08/31 Postdoc (Research) Instituto Gulbenkian de Ciência, Portugal
Instituto Gulbenkian de Ciência, Portugal
2012/10/01 - 2014/10/31 Postdoc (Research) Universidade de Lisboa Faculdade de Ciências, Portugal
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2022/10/06 - Current Assistant Professor (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/02/01 - 2022/06/30 Invited Assistant Professor (University Teacher) Universidade Católica Portuguesa, Portugal
2021/02/01 - 2021/07/31 Invited Assistant Professor (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
Projects

Grant

Designation Funders
2019/09/01 - Current ELIXIR - Data for Life  European Life Sciences Infrastructure for Biological Information
info:eu-repo/grantAgreement/AKA/271642/FI
Post-doc Fellow
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Ongoing
2022/06/01 - 2027/05/31 AgroServ: Integrated SERvices supporting a sustainable AGROecological transition
101058020
Researcher
2020/06/01 - 2020/12/31 VITACOV: Vitamin D-related polymorphisms and vitamin D levels as risk biomarkers of COVID-19 infection severity
613401452
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded
2015/09/01 - 2019/08/31 ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.
info:eu-repo/grantAgreement/EC/H2020/676559/EU
Post-doc Fellow
Instituto Gulbenkian de Ciência, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluded
2012/10/01 - 2014/10/29 SOMER: Semantic Ontology Matching using External Resources
info:eu-repo/grantAgreement/FCT/3599-PPCDT/119119/PT
Post-doc
Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
 Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluded

Contract

Designation Funders
2021/03/01 - 2024/02/29 Data sciEnce Tools for Epidemiologic surveillance using multiple sourCes of daTa - Improved flu/COVID-19 tracking and detection of new outbreaks
DSAIPA/DS/0133/2020
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2007/01/01 - 2010/12/31 PREVISÃO DE FUNÇÃO DE PROTEINAS POR MÉTODOS DE APRENDIZAGEM AUTOMÁTICA
SFRH/BD/29797/2006
Universidade de Lisboa Faculdade de Ciências, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book
  1. Dragisic, Z.; Ivanova, V.; Lambrix, P.; Faria, D.; Jiménez-Ruiz, E.; Pesquita, C.. User validation in ontology alignment. 2016.
    10.1007/978-3-319-46523-4_13
  2. Pesquita, C.; Faria, D.; Santos, E.; Neefs, J.-M.; Couto, F.M.. Towards visualizing the alignment of large biomedical ontologies. 2014.
    10.1007/978-3-319-08590-6_10
  3. Faria, D.; Jiménez-Ruiz, E.; Pesquita, C.; Santos, E.; Couto, F.M.. Towards annotating potential incoherences in bioportal mappings. 2014.
  4. Pesquita, C.; Faria, D.; Stroe, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. What's in a 'nym'? Synonyms in biomedical ontology matching. 2013.
    10.1007/978-3-642-41335-3_33
Conference paper
  1. Faria, D.; Pesquita, C.; Tervo, T.; Couto, F.M.; Cruz, I.F.. "AML and AMLC results for OAEI 2019". 2019.
  2. Algergawy, A.; Faria, D.; Ferrara, A.; Fundulaki, I.; Harrow, I.; Hertling, S.; Jiménez-Ruiz, E.; et al. "Results of the ontology alignment evaluation initiative 2019". 2019.
  3. Jiménez-Ruiz, E.; Saveta, T.; Zamazal, O.; Hertling, S.; Röder, M.; Fundulaki, I.; Ngomo, A.-C.N.; et al. "Introducing the HOBBIT platform into the Ontology Alignment Evaluation campaign". 2018.
  4. Algergawy, A.; Cheatham, M.; Faria, D.; Ferrara, A.; Fundulaki, I.; Harrow, I.; Hertling, S.; et al. "Results of the ontology alignment evaluation initiative 2018". 2018.
  5. Faria, D.; Pesquita, C.; Balasubramani, B.S.; Tervo, T.; Carriço, D.; Garrilha, R.; Couto, F.M.; Cruz, I.F.. "Results of AML participation in OAEI2018". 2018.
  6. Cardoso, J.; Bakhshandeh, M.; Faria, D.; Pesquita, C.; Borbinha, J.. "Ontology-based approach for heterogeneity analysis of EA models". Paper presented in International Conference on Business Process Management, 2017.
    10.1007/978-3-319-58457-7_10
  7. Achichi, M.; Cheatham, M.; Dragisic, Z.; Euzenat, J.; Faria, D.; Ferrara, A.; Flouris, G.; et al. "Results of the ontology alignment evaluation initiative 2017?". 2017.
  8. Faria, D.; Balasubramani, B.S.; Shivaprabhu, V.R.; Mott, I.; Pesquita, C.; Couto, F.M.; Cruz, I.F.. "Results of AML in OAEI 2017". 2017.
  9. Achichi, M.; Cheatham, M.; Dragisic, Z.; Euzenat, J.; Faria, D.; Ferrara, A.; Flouris, G.; et al. "Results of the Ontology Alignment Evaluation Initiative 2016". 2016.
  10. Faria, D.; Pesquita, C.; Balasubramani, B.S.; Martins, C.; Cardoso, J.; Curado, H.; Couto, F.M.; Cruz, I.F.. "OAEI 2016 results of AML". 2016.
  11. Martins, C.; Faria, D.; Pesquita, C.. "Visualization and editing of biomedical ontology alignments in AgreementMakerLight". 2015.
  12. Cheatham, M.; Dragisic, Z.; Euzenat, J.; Faria, D.; Ferrara, A.; Flouris, G.; Fundulaki, I.; et al. "Results of the ontology alignment evaluation initiative 2015". 2015.
  13. Faria, D.; Martins, C.; Nanavaty, A.; Oliveira, D.; Balasubramani, B.S.; Taheri, A.; Pesquita, C.; Couto, F.M.; Cruz, I.F.. "AML results for OAEI 2015". 2015.
  14. Faria, D.; Martins, C.; Nanavaty, A.; Taheri, A.; Pesquita, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. "Agreementmakerlight results for OAEI 2014". 2014.
  15. Pesquita, C.; Cheatham, M.; Faria, D.; Barros, J.; Santos, E.; Couto, F.M.. "Building reference alignments for compound matching of multiple ontologies using OBO cross-products". 2014.
  16. Faria, D.; Pesquita, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. "AgreementMakerLight 2.0: Towards efficient large-scale ontology matching". 2014.
  17. Dragisic, Z.; Eckert, K.; Euzenat, J.; Faria, D.; Ferrara, A.; Granada, R.; Ivanova, V.; et al. "Results of the ontology alignment evaluation initiative 2014". 2014.
  18. Faria, D.; Pesquita, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. "AgreementMakerLight results for OAEI 2013". 2013.
  19. Pesquita, C.; Faria, D.; Santos, E.; Couto, F.M.. "To repair or not to repair: Reconciling correctness and coherence in ontology reference alignments". 2013.
  20. Tavares, B.; Bastos, H.P.; Faria, D.; Ferreira, J.D.; Grego, T.; Pesquita, C.; Couto, F.M.. "The biomedical ontology applications (BOA) framework". 2011.
Journal article
  1. "Vitamin D-related polymorphisms and vitamin D levels as risk biomarkers of COVID-19 disease severity". Scientific Reports 11 1 (2021): http://dx.doi.org/10.1038/s41598-021-99952-z.
    10.1038/s41598-021-99952-z
  2. "CorkOakDB—The Cork Oak Genome Database Portal". Database 2020 (2020): http://dx.doi.org/10.1093/database/baaa114.
    10.1093/database/baaa114
  3. Evangelia A. Papoutsoglou; Daniel Faria; Daniel Arend; Elizabeth Arnaud; Ioannis N. Athanasiadis; Inês Chaves; Frederik Coppens; et al. "Enabling reusability of plant phenomic datasets with MIAPPE 1.1". New Phytologist 227 1 (2020): 260-273. https://doi.org/10.1111/nph.16544.
    10.1111/nph.16544
  4. Faria, Daniel. "User validation in ontology alignment: functional assessment and impact". The Knowledge Engineering Review (2019): http://dx.doi.org/10.1017/s0269888919000080.
    10.1017/s0269888919000080
  5. Daniel Faria; Catia Pesquita; Isabela Mott; Catarina Martins; Francisco M. Couto; Isabel F. Cruz. "Tackling the challenges of matching biomedical ontologies". Journal of Biomedical Semantics 9 1 (2018): https://doi.org/10.1186/s13326-017-0170-9.
    10.1186/s13326-017-0170-9
  6. Santos, E.; Faria, D.; Pesquita, C.; Couto, F.M.. "Ontology alignment repair through modularization and confidence-based heuristics". PLoS ONE 10 12 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84957588757&partnerID=MN8TOARS.
    10.1371/journal.pone.0144807
  7. Faria, D.; Pesquita, C.; Santos, E.; Cruz, I.F.; Couto, F.M.. "Automatic background knowledge selection for matching biomedical ontologies". PLoS ONE 9 11 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84915758310&partnerID=MN8TOARS.
    10.1371/journal.pone.0111226
  8. Faria, D.; Pesquita, C.; Santos, E.; Palmonari, M.; Cruz, I.F.; Couto, F.M.. "The AgreementMakerLight ontology matching system". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 8185 LNCS (2013): 527-541. http://www.scopus.com/inward/record.url?eid=2-s2.0-84886730657&partnerID=MN8TOARS.
    10.1007/978-3-642-41030-7_38
  9. Faria, D.; Schlicker, A.; Pesquita, C.; Bastos, H.; FerreiraAntó, A.E.N.; Albrecht, M.; Falcão, A.O.. "Mining GO annotations for improving annotation consistency". PLoS ONE 7 7 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84864674779&partnerID=MN8TOARS.
    10.1371/journal.pone.0040519
  10. Charro, N.; Hood, B.L.; Faria, D.; Pacheco, P.; Azevedo, P.; Lopes, C.; de Almeida, A.B.; et al. "Serum proteomics signature of Cystic Fibrosis patients: A complementary 2-DE and LC-MS/MS approach". Journal of Proteomics 74 1 (2011): 110-126. http://www.scopus.com/inward/record.url?eid=2-s2.0-78649872123&partnerID=MN8TOARS.
    10.1016/j.jprot.2010.10.001
  11. Bastos, H.P.; Tavares, B.; Pesquita, C.; Faria, D.; Couto, F.M.. "Application of gene ontology to gene identification". Methods in Molecular Biology 760 (2011): 141-157. http://www.scopus.com/inward/record.url?eid=2-s2.0-79960906222&partnerID=MN8TOARS.
    10.1007/978-1-61779-176-5_9
  12. Simões, T.; Charro, N.; Blonder, J.; Faria, D.; Couto, F.M.; Chan, K.C.; Waybright, T.; et al. "Molecular profiling of the human nasal epithelium: A proteomics approach". Journal of Proteomics 75 1 (2011): 56-69. http://www.scopus.com/inward/record.url?eid=2-s2.0-84858721493&partnerID=MN8TOARS.
    10.1016/j.jprot.2011.05.012
  13. Pesquita, C.; Faria, D.; Couto, F.M.. "Measuring coherence between electronic and manual annotations in biological databases". Proceedings of the ACM Symposium on Applied Computing (2009): 806-807. http://www.scopus.com/inward/record.url?eid=2-s2.0-72949093556&partnerID=MN8TOARS.
    10.1145/1529282.1529452
  14. Taylor, I.W.; Linding, R.; Warde-Farley, D.; Liu, Y.; Pesquita, C.; Faria, D.; Bull, S.; et al. "Dynamic modularity in protein interaction networks predicts breast cancer outcome". Nature Biotechnology 27 2 (2009): 199-204. http://www.scopus.com/inward/record.url?eid=2-s2.0-59849125136&partnerID=MN8TOARS.
    10.1038/nbt.1522
  15. Pesquita, C.; Faria, D.; Falcão, A.O.; Lord, P.; Couto, F.M.. "Semantic similarity in biomedical ontologies". PLoS Computational Biology 5 7 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-68249087607&partnerID=MN8TOARS.
    10.1371/journal.pcbi.1000443
  16. Faria, D.; Ferreira, A.E.N.; Falcão, A.O.. "Enzyme classification with peptide programs: A comparative study". BMC Bioinformatics 10 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-68949098339&partnerID=MN8TOARS.
    10.1186/1471-2105-10-231
  17. Pesquita, C.; Faria, D.; Bastos, H.; Ferreira, A.E.N.; Falcão, A.O.; Couto, F.M.. "Metrics for GO based protein semantic similarity: A systematic evaluation". BMC Bioinformatics 9 SUPPL. 5 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-47149083877&partnerID=MN8TOARS.
    10.1186/1471-2105-9-S5-S4
  18. Bastos, H.P.; Pesquita, C.; Faria, D.; Falcão, A.O.. "BOLOS: BLAST & ontology linked-hOmologue stars". Proceedings of the ACM Symposium on Applied Computing (2008): 1278-1281. http://www.scopus.com/inward/record.url?eid=2-s2.0-56749095713&partnerID=MN8TOARS.
    10.1145/1363686.1363982
  19. Falcao, A.O.; Faria, D.; Ferreira, A.. "Peptide programs: Applying fragment programs to protein classification". International Conference on Information and Knowledge Management, Proceedings (2008): 37-44. http://www.scopus.com/inward/record.url?eid=2-s2.0-68949093215&partnerID=MN8TOARS.
    10.1145/1458449.1458459

Other

Other output
  1. RDMkit. Web portal with guidelines and good data management practices for enabling FAIR data by design. 2021. https://rdmkit.elixir-europe.org/.
  2. CorkOakDB. Genome portal for Quercus suber. 2020. http://www.corkoakdb.org/.
Standard or policy
  1. MIAPPE: Minimal Information About Plant Phenotyping Experiments. 2019. https://www.miappe.org/.
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2021/02/01 - Current Distributed Knowledge Graphs for Biomedical Explainable Artificial Intelligence
Co-supervisor
Universidade de Lisboa Faculdade de Ciências, Portugal
2016/09/01 - 2022/07/31 Addressing Research Data Management with Semantic Technology
Co-supervisor
Universidade de Lisboa Instituto Superior Técnico, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2019/07/17 Computational approaches to virtual screening in human central nervous system therapeutic targets
(Thesis) Arguer
 Samina Kausar (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal

Committee member

Activity description
Role 		Institution / Organization
2014/01/01 - Current Organizing committee of the annual Ontology Alignment Evaluation Initiative
Member

Conference scientific committee

Conference name Conference host
2016/01/01 - Current Extended Semantic Web Conference (ESWC)
2015/03/01 - Current Ontology Matching Workshop