BOA

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BOA (Biomedical Ontology Applications) (Aplicações de Ontologias Biomédicas) aims at researching and developing applications to effectively explore all the information contained in Biomedical Ontologies.


Tutorials


Web Tools


  • 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


BOA API Documentation


Legacy Tools

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
Research Team

Publications


Document | BibTeX source
Tiago Grego, Francisco Pinto, Francisco Couto, Identifying Chemical Entities based on ChEBI.Proceedings of ICBO 2012.

DOI | | BibTeX source
Francisco Couto, Mário J. Silva 2011: Disjunctive Shared Information between Ontology Concepts: application to Gene Ontology. Journal of Biomedical Semantics.

| BibTeX source
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.

Document | BibTeX source
Catia Pesquita, Francisco Couto, Where GO is going and what it means for ontology extension.International Conference on Biomedical Ontologies 2011.

Document | BibTeX source
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.

Document | BibTeX source
João D. Ferreira, Francisco Couto, Generic semantic relatedness measure for biomedical ontologies.Proceedings of ICBO 2011.

Document | BibTeX source
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.

Document | BibTeX source
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.

BibTeX source
Catia Pesquita, Cosmin Stroe, Isabel F. Cruz, Francisco Couto, BLOOMS on AgreementMaker: results for OAEI 2010.ISWC Workshop on Ontology Matching 2010.

BibTeX source
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.

| BibTeX source
João D. Ferreira, Francisco Couto 2010: Semantic Similarity for Automatic Classification of Chemical Compounds. PLoS Computational Biology 9(6), e1000937.

BibTeX source
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.

Document | BibTeX source
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.

| BibTeX source
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.

BibTeX source
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.

Poster | BibTeX source
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.

Document | BibTeX source
Catia Pesquita, Delphine Pessoa, Daniel Faria, Francisco Couto, CESSM : Collaborative Evaluation of Semantic Similarity Measures.JB2009: Challenges in Bioinformatics November, 2009.

DOI | | BibTeX source
Catia Pesquita, Daniel Faria, Andre O Falcao, Philip Lord, Francisco Couto 2009: Semantic Similarity in Biomedical Ontologies. PLoS Computational Biology.

Document | BibTeX source
Catia Pesquita, Tiago Grego, Francisco Couto 2009: Identifying Gene Ontology Areas for Automated Enrichment. Lecture Notes in Computer Science (5518), 934-941.

Document | BibTeX source
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.

Poster | BibTeX source
Catia Pesquita, Francisco Couto, Mario Silva, Automated Enrichment of BioOntologies.First Portuguese Forum on Computational Biology (as a poster) IGC, 2008.

DOI | | BibTeX source
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.

| Document | BibTeX source
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.

Document | BibTeX source
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.

Poster | BibTeX source
Daniel Faria, Catia Pesquita, Francisco Couto, Andre O. Falcao, ProteinOn: Web Tool for Protein Semantic Similarity.Poster at ISMB/ECCB 2007 July, 2007.

| Document | BibTeX source
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.

| Document | Presentation | BibTeX source
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.

| Document | BibTeX source
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.


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