BOA (Biomedical Ontology Applications) (Aplicações de Ontologias Biomédicas) aims at researching and developing applications to effectively explore all the information contained in Biomedical Ontologies.
- ProteInOn can be used to find interacting proteins, find assigned GO terms and calculate the functional semantic similarity of proteins and to get the information content and calculate the functional semantic similarity of GO terms
- CMPSim provides a functional similarity measure between chemical compounds and metabolic pathways using ChEBI-based semantic similarity measures
- GRYFUN for the visualization and analysis of GO functional annotation profiles of a given protein sets (or families)
- CESSM provides a tool for the automated evaluation of GO-based semantic similarity measures
BOA API Documentation
These tools may not be working properly since they are not maintained anymore. If you would like to continue using these tools please contact us.
- GRYFUN alpha5 for the visualization, filtering and analysis of GO functional annotation profiles of CAZy protein families
- ProteInOn v1 can be used to find interacting proteins, find assigned GO terms and calculate the functional semantic similarity of proteins and to get the information content and calculate the functional semantic similarity of GO terms
- GOAnnotator for verification of electronic protein annotations using GO terms automatically extracted from literature
- FuSSiMeG provides a functional similarity measure between two proteins using the semantic similarity between the GO terms annotated with the proteins
- WebAPEG provides functional annotations automatically extracted from literature of genes from the Arabidopsis Pollen Expressed Gene database
- BOLOS provides a clustering of the SwissProtKb sequence space. The clusters are characterized by three GO-based parameters (measuring coherence, functional characterization and center representativeness). It is an suitable platform for protein functional analysis
- Mário J. Silva (research advisor)
- Francisco Couto
- André Falcão
- Daniel Faria
- Cátia Pesquita
- Hugo Bastos
- Tiago Grego
- João D Ferreira
Tiago Grego, Francisco Pinto, Francisco Couto, Identifying Chemical Entities based on ChEBI.Proceedings of ICBO 2012.
Francisco Couto, Mário J. Silva 2011: Disjunctive Shared Information between Ontology Concepts: application to Gene Ontology. Journal of Biomedical Semantics.
T. Simões, N. Charro, J. Blonder, Daniel Faria, Francisco Couto, K.C. Chan, T. Waybright, H.J. Isaaq, T.D. Veenstra, D. Penque 2011: Molecular profiling of the human nasal epithelium: A proteomics approach. Journal of Proteomics 75(1), 56-69.
Catia Pesquita, Francisco Couto, Where GO is going and what it means for ontology extension.International Conference on Biomedical Ontologies 2011.
Bruno Tavares, Hugo Bastos, Daniel Faria, Joao D. Ferreira, Tiago Grego, Catia Pesquita, Francisco Couto, The Biomedical Ontology Applications (BOA) framework.Proceedings of ICBO 2011.
João D. Ferreira, Francisco Couto, Generic semantic relatedness measure for biomedical ontologies.Proceedings of ICBO 2011.
Hugo Bastos, Bruno Tavares, Catia Pesquita, Daniel Faria, Francisco Couto: Application of Gene Ontology to Gene Identification. In Silico Tools for Gene Discovery: Methods in Molecular Biology. Springer, 2011.
Hugo Bastos, Francisco Couto, Pedro M. Coutinho, Exploring Gene Ontology relationships in Enzyme Families: An application to Polysaccharide Lyases (as a poster).9th Carbohydrate Bioengineering Meeting p. 67, May, 2011.
Catia Pesquita, Cosmin Stroe, Isabel F. Cruz, Francisco Couto, BLOOMS on AgreementMaker: results for OAEI 2010.ISWC Workshop on Ontology Matching 2010.
N. Charro, B.L. Hood, Daniel Faria, P. Pacheco, P. Azevedo, C. Lopes, A. Almeida, Francisco Couto, T.P. Conrads, D. Penque 2011: Serum proteomics signature of Cystic Fibrosis patients: A complementary 2-DE and LC--MS/MS approach. Journal of Proteomics 74(1), 110-126.
João D. Ferreira, Francisco Couto 2010: Semantic Similarity for Automatic Classification of Chemical Compounds. PLoS Computational Biology 9(6), e1000937.
Patricia Gomes-Alves, Francisco Couto, Catia Pesquita, AV Coelho, Deborah Penque 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 4(1804), 856-865.
Daniel Faria, Catia Pesquita, Francisco Couto, Andre O Falcao, GOclasses: molecular function as viewed by proteins.BioOntologies SIG at ISMB/ECCB - 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) July, 2009.
Tiago Grego, João D. Ferreira, Catia Pesquita, Hugo Bastos, Diogo Vila Viçosa, João Freire, Francisco Couto, Chemical and Metabolic Pathway Semantic Similarity Technical Report. TR 2010-01. University of Lisbon, Faculty of Sciences, LASIGE, March 2010.
Catia Pesquita, Francisco Couto, Taking GO where we need it to go: focused automated enrichment of the Gene Ontology.Student Council Symposium at ISMB/ECCB 2009. Stockholm, Sweden 2009.
Catia Pesquita, Delphine Pessoa, Daniel Faria, Francisco Couto, Collaborative Evaluation of GO-based Similarity Measures.The 12th Annual Bio-Ontologies Meeting at ISMB/ECCB 2009 2009.
Catia Pesquita, Delphine Pessoa, Daniel Faria, Francisco Couto, CESSM : Collaborative Evaluation of Semantic Similarity Measures.JB2009: Challenges in Bioinformatics November, 2009.
Catia Pesquita, Daniel Faria, Andre O Falcao, Philip Lord, Francisco Couto 2009: Semantic Similarity in Biomedical Ontologies. PLoS Computational Biology.
Catia Pesquita, Tiago Grego, Francisco Couto 2009: Identifying Gene Ontology Areas for Automated Enrichment. Lecture Notes in Computer Science (5518), 934-941.
Catia Pesquita, Daniel Faria, Rui Lopes, Francisco Couto, Measuring coherence between electronic and manual annotations in biological databases.SAC '09: Proceedings of the 2009 ACM Symposium on Applied Computing 2009. ACM.
Catia Pesquita, Francisco Couto, Mario Silva, Automated Enrichment of BioOntologies.First Portuguese Forum on Computational Biology (as a poster) IGC, 2008.
Catia Pesquita, Daniel Faria, Hugo Bastos, António Ferreira, Andre O Falcao, Francisco Couto 2008: Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics Suppl 5(9), S4.
Catia Pesquita, Daniel Faria, Tiago Grego, Francisco Couto, Mário J. Silva: Untangling BioOntologies for Mining Biomedical Information. in: Handbook of Research on Text and Web Mining Technologies. Idea Group Inc. 2008.
Catia Pesquita, Daniel Faria, Hugo Bastos, Andre O. Falcao, Francisco Couto, Evaluating GO-based Semantic Similarity Measures.BioOntologies SIG at ISMB/ECCB - 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) July, 2007.
Daniel Faria, Catia Pesquita, Francisco Couto, Andre O. Falcao, ProteinOn: Web Tool for Protein Semantic Similarity.Poster at ISMB/ECCB 2007 July, 2007.
Daniel Faria, Catia Pesquita, Francisco Couto, Andre O. Falcao, ProteInOn: A Web Tool for Protein Semantic Similarity Technical Report. TR 07-6. DI FCUL, March 2007.
Francisco Couto, Mário J. Silva, Pedro Coutinho, Semantic Similarity over the Gene Ontology: Family Correlation and Selecting Disjunctive Ancestors.ACM CIKM - Conference in Information and Knowledge Management October, 2005.
Francisco Couto, Mário J. Silva, Implementation of a Functional Semantic Similarity Measure between Gene-Products Technical Report. DI/FCUL TR 3-29. FCUL, November 2003.