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MIAMExpress and the development of annotation ontologies for gene expression experiments

MIAMExpress and the development of annotation ontologies for gene expression experiments Ele Holloway Microarray Informatics European Bioinformatics Institute. Microarrays and Data Mining 10 th -11 th December 2002. Outline. Capturing information Ontologies MIAMExpress.

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MIAMExpress and the development of annotation ontologies for gene expression experiments

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  1. MIAMExpress and the development of annotation ontologies for gene expression experiments Ele Holloway Microarray Informatics European Bioinformatics Institute Microarrays and Data Mining 10th-11th December 2002

  2. Outline • Capturing information • Ontologies • MIAMExpress

  3. Capturing information • Lab book – only useful for the individual Need information understandable by all • Annotate in a controlled way Allows easy retrieval • Submit information to a database / LIMS Available to other researchers

  4. What is an ontology? • A kind of controlled vocabulary (CV) expressed in a structured way.

  5. Components of an ontology = container for information. • Class Has a definition and a relationship to other classes (is-a, part-of, kind-of). e.g. An exon is part of a gene • Instance Terms that are contained within a class.

  6. An ontology – what can it do? • Captures knowledge • Shared understanding • Structure enriches CV • Computer ‘readable’

  7. Why do we need an ontology for the database? • To help users annotate their data usefully and easily • To perform structured queries • To accurately compare data • To avoid problems with free text searching • To avoid excessive curation workload in future

  8. Free text Natural language processing Database Annotation Data mining Controlled vocabulary

  9. Standards and Ontologies for Functional Genomics 17 – 20th November 2002 Hinxton Aim: To bring together scientists (biologists and bioinformaticians) developing standards and ontologies http://www.ebi.ac.uk/SOFG

  10. Examples of ontologies and CVs • NCBI Taxonomy - All organisms represented in the genetic databases • GO – Gene Ontology • EMAP – Edinburgh Mouse Atlas Project • FlyBase – Drosophila genome database • MGED Ontology – For describing samples used in microarray experiments

  11. Local MIAMExpress installations MIAMExpress EBI Array manufacturers Submissions www www www MAGE-ML Data pipelines MAGE-ML Queries LIMS Data analysis Expression Profiler Data analysis software MAGE-ML import/export Microarray software External bioinformatics databases Other microarray databases Infrastructure ArrayExpress (Oracle)

  12. MIAME requirements • Experimental design • Array design • Samples • Hybridizations • Measurements • Normalization controls Nature Genetics 29(4): 365-371

  13. MGED MEDLINE Experiment details Publication details EMBL NCBI taxonomy Gene acc. no. Species GO CAS/ Merck Chemical compd. Gene name Mouse stage Genew EMAP External links 6 parts of a microarray experiment Experiment Sample Hybridization Array Normalization Data

  14. MGED Ontology • Community effort - MGED Society • Supports efforts of MAGE • Describes the parts of a microarray experiment • References out to external ontologies

  15. MGED Ontology • Structured in DAML+OIL using OilEd 3.4

  16. MIAMExpress • Submission and annotation tool • Based on MIAME concepts • Array, Experiment and Protocol submissions • Perl-CGI, MySQL database

  17. Login New/Pending Experiment Sample protocol Extraction protocol Sample 1 Sample 2 Sample 3 Sample 4 Labeling protocol Extracts 1….n Extracts 1….n Extracts 1….n Extracts 1….n E1 E2 En E1 E2 En E1 E2 En E1 E2 En Hybridization protocol Lab. Extr. 1….n Lab. Extr. 1….n Lab. Extr. 1….n Lab. Extr. 1….n LE LE LE LE LE LE LE LE LE LE LE LE Scanning protocol Hybridizations Array1 Array2 Array3 Arrayn Image analysis protocol Data1 Data2 Data3 Datan Transformation protocol Combined Experiment Data Submit Submission process

  18. Tour of MIAMExpress • Login +Password • Multi-user environment • Control over data access http://www.ebi.ac.uk/miamexpress

  19. Login New/Pending Experiment Sample 1 Sample 2 Sample 3 Sample 4

  20. Login New/Pending Experiment Sample 1 Sample 2 Sample 3 Sample 4 Extracts 1….n Extracts 1….n Extracts 1….n Extracts 1….n E1 E2 En E1 E2 En E1 E2 En E1 E2 En

  21. Login New/Pending Experiment Lab. Extr. 1….n Lab. Extr. 1….n Lab. Extr. 1….n Lab. Extr. 1….n LE LE LE LE LE LE LE LE LE LE LE LE Sample 1 Sample 2 Sample 3 Sample 4 Extracts 1….n Extracts 1….n Extracts 1….n Extracts 1….n E1 E2 En E1 E2 En E1 E2 En E1 E2 En

  22. Login New/Pending Experiment Sample 1 Sample 2 Sample 3 Sample 4 Extracts 1….n Extracts 1….n Extracts 1….n Extracts 1….n E1 E2 En E1 E2 En E1 E2 En E1 E2 En Lab. Extr. 1….n Lab. Extr. 1….n Lab. Extr. 1….n Lab. Extr. 1….n LE LE LE LE LE LE LE LE LE LE LE LE Array1 Array2 Array3 Arrayn Hybridizations Data1 Data2 Data3 Datan

  23. Submission successful • Curation • Export of MAGE-ML • Loading to ArrayExpress

  24. C MGED Ontology C BiomaterialDescription C Sex C Gender documentation: Subclass of sex applicable to heterogametic species (i.e., those in which the sexes produce gametes of markedly different size). Males produce small numerous gametes. Females produce small numbers of large gametes. Hermaphrodites are individuals with both male and female characteristics. Mixed refers to a population of individuals with more than one type of gender. used in individuals: female,hermaphrodite,male,mixed_sex,unknown_sex Curation of user defined terms, before inclusion in the ontology Ontology instances propagated to submission/annotation web forms User defined terms collected via forms MIAMExpress ArrayExpress RAD MAGE-ML data exchange

  25. Resources • Microarray Informatics Group http://www.ebi.ac.uk/microarray/ • MIAMExpress http://www.ebi.ac.uk/miamexpress/ • MGED Ontology Working Group http://mged.sourceforge.net/ontologies/ • Sourceforge • http://sourceforge.net/

  26. Acknowledgements ArrayExpress Ugis Sarkans Gonzalo Garcia Ahmet Oezcimen Anjan Sharma Alvis Brazma • Curation • Helen Parkinson • Gaurab Mukherjee • Philippe Rocca-Serra • Susanna Sansone • MIAMExpress • Mohammad Shojatalab • Niran Abeygunawardena • Sergio Contrino • MGED Ontology • Chris Stoeckert • (U. Penn)

  27. GO • http://www.geneontology.org • EMAP • http://genex.hgu.mrc.ac.uk/ • FlyBase • http://flybase.bio.indiana.edu/ • NCBI Taxonomy • http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/

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