1 / 26

Ma DAS

Ma DAS. a collaborative tool for sequence annotation. Current annotation model. Limitations of current model. Prediction methods are unable to generate high quality data in many of the cases.

apu
Download Presentation

Ma DAS

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. MaDAS a collaborative tool for sequence annotation. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  2. Currentannotation model http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  3. Limitations of current model • Prediction methods are unable to generate high quality data in many of the cases. • Biologists, with high confidence data, are unable to contribute in a effective way to the process of sequence annotation. • Information is provided by only a few groups, compared with the number of people that use this information. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  4. Collaborative model for sequence annotation http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  5. What could a collaborative application look like? http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  6. Provide a user comunity Users have a profile information that can be used to exchange knowledge http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  7. Project workspace Researchers can build their own projects. A project is the fundamental unit in the research field. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  8. Plug-in system Integration with external bioinformatic resources is possible through several plug-ins. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  9. Data source plug-ins. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  10. Data source plug-ins Researchers can upload their data or get it from different repositories. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  11. General data source plug-ins Users can set their sequence reference from Ensembl, Uniprot or provide a new one. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  12. General data source plug-ins Researchers have full control over their annotations http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  13. General data source plug-ins Load GFF files http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  14. Specific data source plug-ins Load information from a gene expression experiment. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  15. Specific data source plug-ins Load information from specific databases like Treefam http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  16. Specific data source plug-ins Connect to a Postgres SQL server and import the annotations. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  17. Visualizationplug-ins. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  18. Visualization plug-ins. Madasmap Google maps like representation of genome or protein annotations http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  19. Visualization plug-ins Users can filter their annotations http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  20. Visualization plug-ins Internal and Pubmed searches. In Pubmed search, a text mining tool (BiocreativeMetaserver) is used to automatically extract genes from the articles. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  21. Search results The query results are mapped to the sequence and displayed in the map. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  22. Manual annotations Users can manually add or edit their annotations http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  23. Other plug-in for geneexpression Visualization of a Up/down regulated genes for a given q-value. The search and edit capability also work with this plug-in. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  24. The central plug-in. DAS server All the information stored in MaDAS is available trough DAS. http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  25. Other applications used by MaDAS Metaserver: Leitner F et al. Introducing meta-services for biomedical information extraction. Genome Biology 2008, 9(Suppl 2):S6 Bionemo: Carbajosa, G. et al. Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Res 37, D598-602(2009). http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

  26. Thanks! URL: http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es http://madas2.bioinfo.cnio.es Contact: vdelatorre@cnio.es

More Related