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On the Integration of Biomedical Databases: a Naive Approach

On the Integration of Biomedical Databases: a Naive Approach. José Luis Oliveira Univ. Aveiro, IEETA, PT, jlo@ua.pt http://bioinformatics.ua.pt. Objectives. To integrate the most relevant clinical and genetic information available in public databases, for genetic diseases

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On the Integration of Biomedical Databases: a Naive Approach

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  1. On the Integration of Biomedical Databases: a Naive Approach José Luis Oliveira Univ. Aveiro, IEETA, PT, jlo@ua.pt http://bioinformatics.ua.pt

  2. Objectives • To integrate the most relevant clinical and genetic information available in public databases, for genetic diseases  It’s a excellent case study for BMI

  3. Main Questions: what are the … ? • symptoms of the disease? • main publications about this disease? • drugs available for the disease? • gene therapies or clinical trials for the disease? • laboratories that perform genetic tests? • genes that cause the disease? • chromosomes for these genes? • mutations found in these genes? • names used to refer to these genes? • proteins coded by these genes? • the functions of the gene product? • 3D structure for these proteins? • enzymes associated to these proteins?

  4. Public Resources

  5. Navigation Model

  6. Methods • Navigation protocol • Described in a formal language (XML) • Disease cards • Each card contains a set of biomedical concepts • A web crawler for each concept • The crawler specify where to search and what to retrieve • Used just for the construction of the card • Multithreading • No physical integration!

  7. www.diseasecard.org

  8. Diseases List

  9. Navigation Protocol

  10. Card Information

  11. Disease Forum

  12. Concepts – available information

  13. Conclusions • Biomedical portal for rare diseases www.diseasecard.org • Navigation from the symptom to gene • Integrated view • Accurate information • Well known databases, continuously updates • No need to master biological databases • Avoids dealing with search boxes, nomenclatures, etc. • Information retrieval engine based on web wrappers • Easy configuration

  14. Main Credits • InfoBioMed NoE • ISCIII, SP • Fernando Martin-Sanchez, Javier Vicente • UPM, SP • Victor Maojo • Univ. Aveiro, PT • Gaspar Dias, Hugo Pais, José Luis Oliveira www.diseasecard.org

  15. MIND José Luis Oliveira Univ. Aveiro, IEETA, PT, jlo@ua.pt http://bioinformatics.ua.pt

  16. Objectives • Management of microarray experiments workflow • Focus on • Integration (from the lab to the final scientific outcomes) • Usability (less pain to the researcher) • Public access

  17. The Experiment is the central element of the system. It describes the experiment as a hole and aggregates several BioAssays. By selecting this option and choosing an experiment will start a process that converts the data to the MAGE-TAB format. The output files can be submitted into the ArrayExpress database. The Biomaterial describes the steps that a biosample take to be used in an BioAssay The feature extraction files are uploaded and converted to an internal format. Documentation of the set of steps taken in a procedure. Quality control enables the user to detect systematic errors on the production of microarrays. Describes construction of the physical array used in a BioAssay. General Workflow

  18. MAGE package that describes the array layout and design The complete set of bioassays (hybridizations) and their descriptions performed as an experiment for a common purpose. Here we take experiment to mean an observational or perturbing study. An experiment will be often equivalent to a publication. Documentation of the set of steps taken in a procedure. Description of the processing state of the biomaterial for use in the microarray hybridization. Workflow Steps

  19. Main page

  20. General Workflow GUI

  21. Experiment Example

  22. Quality Control • Background subtraction, • Normalization • Data filtering • ...

  23. Results http://bioinformatics.ua.pt/mind • All-in-one system • LIMS, Quality control, Data processing • Public web-based interface • With private and public area • Rich user interface and usability • Standard compliance • MIAME and MAGE (MAGE-ML, MAGE-TAB) Demo: http://bioinformatics.ua.pt/mind2 user: demo@ua.pt pass: demo

  24. Main Credits • InfoBioMed NoE • ISCIII • Univ. Edinburgh • Univ. Aveiro

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