Publications
"Generic Semantic Relatedness Measure for Biomedical Ontologies.",
ICBO, vol. 833, 2011.
"MEDCollector: Multisource epidemic data collector",
Transactions on large-scale data-and knowledge-centered systems IV: Springer Berlin Heidelberg, pp. 40–72, 2011.
"Molecular profiling of the human nasal epithelium: A proteomics approach",
Journal of proteomics, vol. 75, no. 1: Elsevier, pp. 56–69, 2011.
"POWER-Politics Ontology for Web Entity Retrieval",
Advanced Information Systems Engineering Workshops: Springer Berlin Heidelberg, pp. 489–500, 2011.
"Serum proteomics signature of Cystic Fibrosis patients: A complementary 2-DE and LC–MS/MS approach",
Journal of proteomics, vol. 74, no. 1: Elsevier, pp. 110–126, 2011.
"Using AgreementMaker to align ontologies for OAEI 2011",
Proceedings of the Sixth International Workshop on Ontology Matching, pp. 114–121, 2011.
"Where GO is Going and What it Means for Ontology Extension.",
ICBO, 2011.
"Where GO is going and what it means for ontology extension",
International Conference on Biomedical Ontology, 2011.
"BLOOMS on AgreementMaker: results for OAEI 2010",
Ontology Matching, pp. 134, 2010.
"Building a digital library for epidemic modelling",
Proceedings of ICDL, pp. 23–27, 2010.
Desenvolvimento de Aplicações Web baseadas em SOA e AJAX,
: DI-FCUL, 2010.
"Epidemic Marketplace: an e-Science Platform for Epidemic Modelling and Analysis",
ERCIM News, 2010.
"Epidemic marketplace: an information management system for epidemiological data",
Information Technology in Bio-and Medical Informatics, ITBAM 2010: Springer Berlin Heidelberg, pp. 31–44, 2010.
"Geographic signatures for semantic retrieval",
Proceedings of the 6th Workshop on Geographic Information Retrieval: ACM, pp. 19, 2010.
"MEDCollector: Multisource epidemic data collector",
Information Technology in Bio-and Medical Informatics, ITBAM 2010: Springer, pp. 16–30, 2010.
"Rescue of F508del-CFTR by RXR motif inactivation triggers proteome modulation associated with the unfolded protein response",
Biochimica et Biophysica Acta (BBA)-Proteins & Proteomics, vol. 1804, no. 4: Elsevier, pp. 856–865, 2010.
"Semantic characterization of hypertrophic cardiomyopathy disease",
Bioinformatics and Biomedicine Workshops (BIBMW), 2010 IEEE International Conference on: IEEE, pp. 432–439, 2010.
"Semantic Similarities in Biomedical Ontologies",
IMIA Yearbook, vol. 5, pp. 84–84, 2010.
"Semantic similarity for automatic classification of chemical compounds",
PLoS computational biology, vol. 6, no. 9: Public Library of Science, pp. e1000937, 2010.
"1: Meta-model Initial Specification",
Catalogue of Relevant Data, Platform Requirements. 30th September, 2009.
"Automated social network epidemic data collector",
INForum informatics symposium. Lisboa, 2009.
"Carbohydrate-Active Enzymes Database: Principles and Classification of Glycosyltransferases",
Bioinformatics for Glycobiology and Glycomics: An Introduction: John Wiley & Sons, Ltd, pp. 89–118, 2009.
"CESSM: collaborative evaluation of semantic similarity measures",
JB2009: Challenges in Bioinformatics, 2009.
Collaborative Evaluation of GO-based Similarity Measures,
: 12th Annual Bio-Ontologies Meeting at ISMB/ECCB 2009, 2009.
Enzyme family coherence assessment: validation and prediction,
: JB'2009-Challenges in Bioinformatics, 2009.
Epiwork D3. 1: Meta-model Initial Specification, Catalogue of Relevant Data, Platform Requirements,
, 2009.
GO where we need it to go: focused automated enrichment of the Gene Ontology. Student Council Symposium,
: Student Council Symposium at ISMB/ECCB 2009, 2009.
"GOclasses: molecular function as viewed by proteins",
The 12th Annual Bio-Ontologies, 2009.
"GREAT: gene regulation evaluation tool",
Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living: Springer Berlin Heidelberg, pp. 930–933, 2009.
Handling self-citations using Google Scholar,
: International Journal of Scientometrics, Informetrics and Bibliometrics, 2009.
"Identification of chemical entities in patent documents",
Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living: Springer, pp. 942–949, 2009.
"Identifying Gene Ontology Areas for Automated Enrichment",
Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living: Springer, pp. 934–941, 2009.
"Measuring coherence between electronic and manual annotations in biological databases",
Proceedings of the 2009 ACM symposium on Applied Computing: ACM, pp. 806–807, 2009.
"Semantic similarity in biomedical ontologies",
PLoS computational biology, vol. 5, no. 7: Public Library of Science, pp. e1000443, 2009.
"ThermInfo: Collecting and Presenting Thermochemical Properties",
methods, vol. 1, pp. 3, 2009.
"Untangling BioOntologies for Mining Biomedical Information",
Handbook of research on text and Web mining technologies: Information Science Reference, 2009.
Verification of Uncurated Protein Annotations,
: Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration, IGI Global Publishing, 2009.
"The Biomedical Ontology Applications (BOA) framework",
evaluation, vol. 9, no. S5, pp. S4, 2008.
Biomedical research line of LASIGE,
, 2008.
"Identifying bioentity recognition errors of rule-based text-mining systems",
Digital Information Management, 2008. ICDIM 2008. Third International Conference on: IEEE, pp. 733–738, 2008.
"Metrics for GO based protein semantic similarity: a systematic evaluation",
BMC bioinformatics, vol. 9, no. Suppl 5: BioMed Central Ltd, pp. S4, 2008.
Untangling BioOntologies for Mining Biomedical Information,
: Handbook of Research on Text and Web Mining Technologies, IGI Global Publishing, 2008.
"Evaluating gobased semantic similarity measures",
Proc. 10th Annual Bio-Ontologies Meeting, vol. 2007, pp. 37–40, 2007.
"Evaluating go-based semantic similarity measures",
Proc. 10th Annual Bio-Ontologies Meeting, vol. 37, no. 40, pp. 38, 2007.
"Evaluating GO-based Semantic Similarity Measures. ISMB/ECCB 2007 SIG Meeting Program Materials",
International Society for Computational Biology, 2007.
"Filtering bioentity recognition errors in bioliterature using a case-based approach",
BioLINK SIG, ISMB/ECCB, 2007.
"Measuring semantic similarity between Gene Ontology terms",
Data & knowledge engineering, vol. 61, no. 1: Elsevier, pp. 137–152, 2007.
Proteinon: A web tool for protein semantic similarity,
: Department of Informatics, University of Lisbon, 2007.
Semantic Similarity Match for Data Quality,
: Department of Informatics, University of Lisbon, 2007.
"Advanced Data Mining Techonologies in Bioinformatics, chapter Mining the BioLiterature: towards automatic annotation of genes and proteins",
Idea Group Inc, 2006.
"GOAnnotator: linking protein GO annotations to evidence text",
Journal of Biomedical Discovery and Collaboration, vol. 1, no. 1: BioMed Central Ltd, pp. 19, 2006.
"Mining BioLiterature: Toward Automatic",
Advanced Data Mining Technologies in Bioinformatics: IGI Global, pp. 283, 2006.
Mining the BioLiterature: towards automatic annotation of genes and proteins,
: Advanced Data Mining Technologies in Bioinformatics, Idea Group IncIdea Group Inc, 2006.
ReBIL: Relating Biological Information through Literature,
: Tese de Doutoramento, Faculdade de Ciências, Departamento de Informática, Universidade de Lisboa, 2006.
"Validating associations in biological databases",
Proceedings of the 15th ACM international conference on Information and knowledge management: ACM, pp. 142–151, 2006.
"Approximate point set match for partial protein structure alignment",
Proceedings of Bioinformatics: Knowledge Discovery in Biology (BKDB2005). Facultade Ciencias Lisboa da Universidade de Lisboa, pp. 53–57, 2005.
Bioinformatics: Knowledge Discovery in Biology,
: Bioinformatics: Knowledge Discovery in Biology-Workshop Proceedings, 2005.
"Facts from text–Is text mining ready to deliver?",
PLoS Biology, vol. 3, no. 2: Public Library of Science, pp. e65, 2005.
"Finding genomic ontology terms in text using evidence content",
BMC bioinformatics, vol. 6, no. Suppl 1: BioMed Central Ltd, pp. S21, 2005.
"Literature based functional annotation of genes",
BKDB2005-Bioinformatics: Knowledge Discovery in Biology, 2005.
"Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors",
Proceedings of the 14th ACM international conference on Information and knowledge management: ACM, pp. 343–344, 2005.
Validation of Automated Protein Annotation,
: Department of Informatics, University of Lisbon, 2005.
"Classifying biological articles using web resources",
Proceedings of the 2004 ACM symposium on Applied computing: ACM, pp. 111–115, 2004.
Classifying biomedical articles using web resources,
: 19th ACM Symposium on Applied Computing (SAC), 2004.
"Figo: Finding go terms in unstructured text",
Proc. of BioCreative Workshop, 2004.
"FIGO: findings GO terms in unStructured text",
Proc. of BioCreative Workshop, 2004.
Bioinformática-Exploração da Informação,
: centroatlantico. pt magazine, 2003.
Classifying Biomedical Articles using Web Resources: application to KDD Cup 02,
: Department of Informatics, University of Lisbon, 2003.
"Curating extracted information through the correlation between structure and function",
third meeting of the special interest group on Text Data Mining: Citeseer, 2003.
DI–FCUL TR–03–29,
, 2003.
Implementation of a functional semantic similarity measure between gene-products,
: Department of Informatics, University of Lisbon, 2003.
"Improving information extraction through biological correlation",
Data Mining and Text Mining for Bioinformatics, pp. 8, 2003.
"ProFAL: PROtein Functional Annotation through Literature.",
JISBD, pp. 747–756, 2003.
"Rebil: Relating biological information through literature",
Intelligent Systems for Molecular Biology, 2003.
