Bioinformatics presentation to students University of Minho
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Bioinformatics presentation to students University of Minho

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Bioinformatics presentation to students University of Minho Bioinformatics presentation to students University of Minho Presentation Transcript

  • PROTOFILWW A computational platform for the analysis of the relationships between microorganisms and environmental parameters in activated sludge plants José Fernandes Bioinformatics Master Thesis Prof. Anália Lourenço Prof. Ana Nicolau
  • System requirements • Insertion and retrieval of data has to be done quickly and easily • Should be possible to export the data so it can be analyzed with other informatics systems • Should support statistical assessments • Have user-friendly visualization capabilities • Controlled access to data, based on user roles, accounting for data privacy issues • Easy dissemination of related studies and results • Always online (web-based) • Help finding additional information about the microorganisms present in the biological samples
  • Overview of the workflow of field and lab work PROTOFILWWPROTOFILWW
  • 1.635 lines x 137 columns
  • ProtoFilWW system major components 1. Content Management component: supports the researchers managing and analyzing the data obtained from the WWTP’s samples 2. Text Mining component: finding additional information about the microorganisms present in the biological samples
  • High-level integration perspective of ProtoFilWW Drupal core PLUGINS Import data Reports Access control Other services... PROTOFILWW SQL XLS, TXT, CSV Export dataXLS, TXT, CSV Solr/LuceneViews Solr Backend Views XML Relational Database UIMA
  • Contend Management component • Open source Content Management System (CMS) and Framework (CMF) • Highly modular and with high extensibility • Built in the PHP scripting language
  • WWTP Sample 1. Filamentous bacteria 2. Protozoa 3. Metazoa 4. Physical-chemical 5. Sample characterization
  • User roles use case visitors collaborators WWTP researchers administrators Find studies and results x x x x Contact researchers x x x Analysis of available data x Data insertion x x Creation of reports x Export data x Managing users x Backup data x Text Mining x x x x
  • Dynamic reporting and charting Reports creation Reports display
  • Geolocation of the WWTPs Address geocoding Map display
  • Text Mining component Listing the species mentioned in a document
  • Major Text Mining technologies used • Lucene is a high-performance text search engine library. • Solr is a standalone enterprise search server with a REST-like API • UIMA is a powerful infrastructure for the storage, transport, and retrieval of document and annotation knowledge accumulated in NLP pipeline systems • LINNAEUS is a popular organism name identification system for biomedical literature that is capable of normalizing to unambiguous NCBI taxonomy identifiers
  • Text Mining process in ProtoFilWW Solr/Lucene LINNAEUS Solr UIMA PMC Open Access SubsetPMC Open Access Subset Solr XML documentsSolr XML documents XPath convertion
  • Solr LINNAEUS Annotator UIMA Component Descriptor Editor plugin UIMA type system for LINNAEUS
  • LINNAEUS UIMA wrapper running on CVD
  • Drupal Views Solr Backend
  • Major contributions 1. The Web-based computational system www.protofilww.org 2. The Drupal module Views Solr Backend 3. The Solr UIMA plug-in for LINNAEUS Annotator
  • Em que trabalho após o mestrado…
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