ReBIL

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ReBIL (Relating Biological Information through Literature) (Relacionamento de Informação Biológica através da Literatura) aimed at providing text-mining tools for biological literature that avoid the complex issues of creating rules and patterns encompassing all possible cases and training sets that are too specific to be extended to new domains.

This work fits under our research on text-mining of biomedical information and its integration within the knowledge discovery process in systems biology.


Contents

Web Tools


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  • 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.
  • CALIMACO is a retrieval system and a repository of full-text (bio)articles.
  • WebProFAL(mockup) for retrieval of documents related to a protein, automatic GO annotation from the documents, and validation of the annotations using family correlation.
  • CAZy is a database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. CAZy is using a system developed by ReBIL for retrieving information from scientific literature.

Contributions


  • WeBTC (Web Biological Text Classification) is a novel method for text classification on biomedical literature, involving the use of information extracted from related web resources.
  • FiGO (Finding Genomic Ontology) is a novel unsupervised method for identifying biological properties organized in a genomic ontology in unstructured text using the information content of each word present in the nomenclature of the ontology.
  • CAC (Correlate the Annotations' Components) is a novel method for discarding misannotations identified by automated systems using curated annotations with similar structure and function.
  • GraSM (Graph-based Similarity Measure) is a novel similarity measure that incorporates the semantic richness of a graph into a semantic similarity measure, instead of just using an ontology as a tree-like hierarchy.
  • ProFAL (bioProducts Functional Annotation through Literature) is a system for automatic annotation of biological databases using the previous methods.

Research Team


Funding


Acção Integrada CRUP 2004 Luso-Francesa Nº F-10/04

Acção Integrada CRUP 2005 Luso-Francesa Nº F-27/05

Publications


DOI | BibTeX source
P.M. Coutinho, C. Rancurel, M. Stam, T. Bernard, Francisco Couto, E.G.J. Danchin, B. Henrissat: Carbohydrate-Active Enzymes Database: Principles and Classification of Glycosyltransferases. in: Bioinformatics for Glycobiology and Glycomics. Wiley. 2009.

| Document | BibTeX source
Francisco Couto, Mário Silva, Vivian Lee, Emily Dimmer, Evelyn Camon, Rolf Apweiler, Harald Kirsch, Dietrich Rebholz-Schuhmann: Verification of Uncurated Protein Annotations. in: Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration. Idea Group Inc. 2008.

DOI | | BibTeX source
Francisco Couto, Mário J. Silva, V. Lee, E. Dimmer, E. Camon, R. Apweiler, H. Kirsch, D. Rebholz-Schuhmann 2006: GOAnnotator: linking electronic protein GO annotation to evidence text. Journal of Biomedical Discovery and Collaboration 1(19), -.

DOI | | Document | BibTeX source
Francisco Couto, Mário J. Silva, Pedro M. Coutinho, Validating Associations in Biological Databases.Proceedings of the 2006 ACM CIKM International Conference on Information and Knowledge Management, Arlington, Virginia, USA, November 6-11, 2006 November, 2006.

| Document | BibTeX source
Francisco Couto, Mário J. Silva: Advanced Data Mining Technologies in Bioinformatics. XV Mining the BioLiterature: towards automatic annotation of genes and proteins. in: Idea Group Inc. 2006. ISBN: 1-59140-863-6.

| Document | Presentation | BibTeX source
Francisco Couto, ReBIL: Relating Biological Information through Literature PhD Thesis. DI/FCUL, January 2006.

| Document | BibTeX source
Francisco Couto, Mário J. Silva, V. Lee, E. Dimmer, E. Camon, R. Apweiler, H. Kirsch, D. Rebholz-Schuhmann, GOAnnotator: linking electronic protein GO annotation to evidence text Technical Report. DI/FCUL TR 5-25. FCUL, December 2005.

| Document | BibTeX source
Francisco Couto, Mário J. Silva, Pedro M. Coutinho, Validation of Automated Protein Annotation Technical Report. TR 5-24. FCUL, November 2005.

| Document | Presentation | BibTeX source
Pooja Jain, Francisco Couto, Mário J. Silva, Jorg D. Becker, Literature Based Functional Annotation of Genes.BKDB2005 - Bioinformatics: Knowledge Discovery in Biology June, 2005.

DOI | Document | BibTeX source
Francisco Couto, Mário J. Silva, Pedro Coutinho 2005: Finding Genomic Ontology Terms in Text using Evidence Content. BMC Bioinformatics Journal S1(6), S21.

DOI | Document | BibTeX source
D. Rebholz-Schuhmann, H. Kirsch, Francisco Couto 2005: Facts from text: Is Text Mining ready to deliver? PLoS Biology Journal 2(3), e65.

| Presentation | BibTeX source
Pooja Jain, Gene Function Prediction by Mining Biomedical Literature Master Thesis, University of Lisbon, Faculty of Sciences, June 2004. Also available as Technical Report DI/FCUL TR 4-12

| Document | Presentation | BibTeX source
Francisco Couto, Mário J. Silva, FiGO: Finding GO terms in unstructured text.Critical Assessment of Information Extraction systems in Biology (BioCreative) Granada, Spain, March, 2004.

DOI | | Document | Presentation | BibTeX source
Francisco Couto, Bruno Martins, Mário J. Silva, Classifying Biological Articles using Web Resources.19th ACM Symposium on Applied Computing (SAC), Bioinformatics Track, Nicosia, Cyprus March, 2004.

| Document | BibTeX source
Francisco Couto, Pooja Jain, Mário J. Silva, ReBIL: Relating Biological Information through Literature.1st Annual Meeting of Portuguese Proteomic Network - ProCura: Functional Genomics And Proteomics Inst. Nacional de Saúde Dr Ricardo Jorge, Lisboa, November, 2003.

| Document | Presentation | BibTeX source
Francisco Couto, Mário J. Silva 2003: ProFAL: PROtein Functional Annotation through Literature. JISBD 2003 - VIII Jornadas de Ingeniería del Software y Bases de Datos.

| Document | Presentation | BibTeX source
Francisco Couto, Mário J. Silva, Improving Information Extraction through Biological Correlation.Data Mining and Text Mining for Bioinformatics Workshop at the ECML/PKDD2003 Dubrovnik-Cavtat, Croatia, September, 2003.

| Document | BibTeX source
Francisco Couto, Bruno Martins, Mário J. Silva, Classifying Biomedical Articles using Web Resources: application to KDD Cup 02 Technical Report. DI/FCUL TR 3-24. FCUL, July 2003.

| Document | Presentation | BibTeX source
Francisco Couto, Mário J. Silva, Curating Extracted Information through the Correlation between Structure and Function.Third meeting of the special interest group on Text Mining at the Intelligent Systems for Molecular Biology (ISMB) Brisbane, Australia, June, 2003.

| Document | Poster | BibTeX source
Francisco Couto, Mário J. Silva, Pedro M Coutinho, ReBIL: Relating Biological Information through Literature.Poster at Intelligent Systems for Molecular Biology (ISMB) Brisbane, Australia, June, 2003.


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