際際滷

際際滷Share a Scribd company logo

NCBO DBP

Simon Twigger
Simon Twigger

This document discusses a project to make large biological databases more useful by connecting genes to disease through annotation and integration of data. The project focuses on annotating microarray data in GEO with ontologies, linking these annotations to expression data in GMiner, and developing tools to highlight candidate genes for phenotypes based on integrated data from sources like RGD, OBO and GMiner loaded into a triple store. Next steps include exporting more data to RDF and refining use cases for candidate gene selection and evaluation.

1 of 22
Download to read offline
MCW Driving Biological Project Simon Twigger, PhD 1 Monday, September 27, 2010
Rat Genome Database 2 Monday, September 27, 2010
Whats the problem? large scale repositories with unused or inaccessible information How can these databases be made more useful? How to help researchers 鍖nd and use this information to connect genes to disease? 3 Monday, September 27, 2010
Rat researchers ask... What tissue is this gene expressed in? What expression data is Are any of these genes known for SD (aka SD/NHsd, Harlan Sprague Dawley, associated with my Sprague Dawley) rats? phenotype? Has this gene been seen in the brain? What rat expression studies have been done on Mammary Cancer(aka breast neoplasms/breast cancer/cancer of the breast, breast carcinoma...)? Monday, September 27, 2010
What's the strategy? Focus on GEO GEO Records (microarray) Create Annotation Jobs & Queue Up Q-Out Use NCBO annotator 1..n Annot. Workers to markup text, RabbitMQ Index text review annotations at OBA and then use for tools Q-In Parse Results and visualization Results saved to Put results in to GMiner database queue for save Combine annotations with biological data to derive new insights. 5 Monday, September 27, 2010
Current Ontologies http://bioportal.bioontology.org/ Monday, September 27, 2010
7 Monday, September 27, 2010
8 Monday, September 27, 2010
Progress Monday, September 27, 2010
Linking annotations to data Tm2d1 RGD1306410 Svs4 Hbb Scgb2a1 Alb Monday, September 27, 2010
Linking annotations to data Tm2d1 RGD1306410 Svs4 Hbb Scgb2a1 + Alb Hbb is_expressed_in rat kidney Tm2d1 is_expressed_in rat kidney Human (U133, U133v2.), Mouse (430, U74, U95) and Rat (U34a/b/c, 230, 230v2) 62,000 samples x ca. 25,000 genes/sample = 1.5B data points Monday, September 27, 2010
Probeset results on GMiner Probeset L08490cds_at for Gabra1 - gamma-aminobutyric acid (GABA) A receptor, alpha 1 Hs GABRA1 Monday, September 27, 2010
QTL Hypertensive G G G Phenotype Pathway Strain 1 != Strain 2 G Anatomy G (Kidney) Component Function Process Hypertension Monday, September 27, 2010
QTL Gene Highlighter QTL G G G AllegroGraph Disease/Pheno. GMiner RGD OBO etc Monday, September 27, 2010
RDF/OWL sources Cell Ontology http://www.berkeleybop.org/ontologies/obo-all/cell/cell.owl Mouse Adult Gross Anatomy http://www.berkeleybop.org/ontologies/obo-all/adult_mouse_anatomy/ adult_mouse_anatomy.owl Mammalian Phenotype http://www.berkeleybop.org/ontologies/obo-all/mammalian_phenotype/ mammalian_phenotype.owl GO Function http://www.berkeleybop.org/ontologies/obo-all/molecular_function/molecular_function.owl GO Process http://www.berkeleybop.org/ontologies/obo-all/biological_process/biological_process.owl GO component http://www.berkeleybop.org/ontologies/obo-all/cellular_component/cellular_component.owl Monday, September 27, 2010
Rat Genome Database Wide variety of data types - genomic and physiological many with corresponding ontologies 16 Monday, September 27, 2010
Monday, September 27, 2010
RGD->RDF Existing RGD object types & mappings to SO Monday, September 27, 2010
RGD Gene Monday, September 27, 2010
RGD QTL Monday, September 27, 2010
QTL Highlighter Rails source code will be available on GitHub RDFizer (ruby) http://github.com/simont/MCW-RDF Monday, September 27, 2010
Next Steps Register PURL for RGD Create RGD core object ontology (OWL/RDF) Select appropriate URIs for RGD data Ontology annotations - how best to represent in triple store? Export GMiner data to RDF-> Triple Store Document & re鍖ne biological use cases related to candidate gene selection/evaluation Identify additional data required for candidate gene selection, RDFize as appropriate, load into triple store. Connections to other RDF collections/LOD, etc.? Monday, September 27, 2010

More Related Content

NCBO DBP

  • 1. MCW Driving Biological Project Simon Twigger, PhD 1 Monday, September 27, 2010
  • 2. Rat Genome Database 2 Monday, September 27, 2010
  • 3. Whats the problem? large scale repositories with unused or inaccessible information How can these databases be made more useful? How to help researchers 鍖nd and use this information to connect genes to disease? 3 Monday, September 27, 2010
  • 4. Rat researchers ask... What tissue is this gene expressed in? What expression data is Are any of these genes known for SD (aka SD/NHsd, Harlan Sprague Dawley, associated with my Sprague Dawley) rats? phenotype? Has this gene been seen in the brain? What rat expression studies have been done on Mammary Cancer(aka breast neoplasms/breast cancer/cancer of the breast, breast carcinoma...)? Monday, September 27, 2010
  • 5. What's the strategy? Focus on GEO GEO Records (microarray) Create Annotation Jobs & Queue Up Q-Out Use NCBO annotator 1..n Annot. Workers to markup text, RabbitMQ Index text review annotations at OBA and then use for tools Q-In Parse Results and visualization Results saved to Put results in to GMiner database queue for save Combine annotations with biological data to derive new insights. 5 Monday, September 27, 2010
  • 6. Current Ontologies http://bioportal.bioontology.org/ Monday, September 27, 2010
  • 10. Linking annotations to data Tm2d1 RGD1306410 Svs4 Hbb Scgb2a1 Alb Monday, September 27, 2010
  • 11. Linking annotations to data Tm2d1 RGD1306410 Svs4 Hbb Scgb2a1 + Alb Hbb is_expressed_in rat kidney Tm2d1 is_expressed_in rat kidney Human (U133, U133v2.), Mouse (430, U74, U95) and Rat (U34a/b/c, 230, 230v2) 62,000 samples x ca. 25,000 genes/sample = 1.5B data points Monday, September 27, 2010
  • 12. Probeset results on GMiner Probeset L08490cds_at for Gabra1 - gamma-aminobutyric acid (GABA) A receptor, alpha 1 Hs GABRA1 Monday, September 27, 2010
  • 13. QTL Hypertensive G G G Phenotype Pathway Strain 1 != Strain 2 G Anatomy G (Kidney) Component Function Process Hypertension Monday, September 27, 2010
  • 14. QTL Gene Highlighter QTL G G G AllegroGraph Disease/Pheno. GMiner RGD OBO etc Monday, September 27, 2010
  • 15. RDF/OWL sources Cell Ontology http://www.berkeleybop.org/ontologies/obo-all/cell/cell.owl Mouse Adult Gross Anatomy http://www.berkeleybop.org/ontologies/obo-all/adult_mouse_anatomy/ adult_mouse_anatomy.owl Mammalian Phenotype http://www.berkeleybop.org/ontologies/obo-all/mammalian_phenotype/ mammalian_phenotype.owl GO Function http://www.berkeleybop.org/ontologies/obo-all/molecular_function/molecular_function.owl GO Process http://www.berkeleybop.org/ontologies/obo-all/biological_process/biological_process.owl GO component http://www.berkeleybop.org/ontologies/obo-all/cellular_component/cellular_component.owl Monday, September 27, 2010
  • 16. Rat Genome Database Wide variety of data types - genomic and physiological many with corresponding ontologies 16 Monday, September 27, 2010
  • 18. RGD->RDF Existing RGD object types & mappings to SO Monday, September 27, 2010
  • 21. QTL Highlighter Rails source code will be available on GitHub RDFizer (ruby) http://github.com/simont/MCW-RDF Monday, September 27, 2010
  • 22. Next Steps Register PURL for RGD Create RGD core object ontology (OWL/RDF) Select appropriate URIs for RGD data Ontology annotations - how best to represent in triple store? Export GMiner data to RDF-> Triple Store Document & re鍖ne biological use cases related to candidate gene selection/evaluation Identify additional data required for candidate gene selection, RDFize as appropriate, load into triple store. Connections to other RDF collections/LOD, etc.? Monday, September 27, 2010