Medicel Integrator A platform for integrating and analysing biological data

Transcription

1 March 14, 2007 Daniel Nicorici PhD, Application scientist Medicel Integrator A platform for integrating and analysing biological data

2 Outline Medicel's Integrator platform Integration of biological databases Research on Integrator platform

3 What is Medicel Integrator? Medicel Integrator platform is a software environment where biological and medical data can be stored, analyzed, and shared Medicel Integrator offers high functionality and flexibility in biomedical research In practical terms, Medicel Integrator holds all user data, software tools, and documentation. Large databases such as Ensemble, Uniprot, Interpro, Refseq, etc. are included in the Medicel Integrator into a centralized database The centralized database is accessed using User Applications, such as Admin, Query, Report, and Version Graphical User Interfaces are available within Medicel Integrator for biomedical research, such as Experiment, Workflow, Pathway, and Microscopy

4 Challenging issues of integration Heterogenity of available databases: Data stored in different formats Often no schema (i.e. structural definition) available Diversity of data Clashes in concepts & terms, e.g. what is a gene? Lack of metadata External databases No standard accession method Database versions Updated vs. old data No unified model available Amount of data

5 One solution for Integration Oracle 10g External Data Source 1 External Data Source 2 Data Mart Staging Area External Data Source 3... Operational Data Storage Data Warehouse Data Mart Extract, Transform & Load (ETL) Data Evolution Versioning Data Aggregation Data Repository Entity Identity Management Clients

6 Medicel's view

7 own data EBI Spotfire data NCBI Internet own data Laboratory worker... Transition from component-centric to system centric

8 Medicel World data EBI legacy data & annotations data NCBI Internet legacy data & annotations legacy data & annotations data...

9 Integrated databases in Medicel Integrator ENSEMBL NCBI Taxonomy NCBI Refseq Proteins UniProt/Swissprot UniProt/TrEMBL Interpro Mammalian Phenotype Ontology Human Disease Ontology GO (GeneOntology) Cell Ontology Chebi Cytomer Brenda Tissue Ontology PDB

10 Integrated databases in Medicel Integrator cont'd 2,5 million proteins genes, three species transcripts 10 million connections on pathways 1200 different species, having >100 proteins on their pathways

11 Medicel product family Documenting work done with Integrator is stored into the Data Warehouse Repeating already performed work can be easily repeated Reporting Research Reports can be collected automatically based on predefined Report Templates Reports can be composed of formatted text, image captures, configured visualizations, dynamic views of Integrator applications, file contents, database object properties, and Query results

12 Research cycle 12

13 Search background information What do we already know (1)? 13

14 Search background information Use the Data Warehouse to search for proteins related to cancer and display their features 14

15 Search background information What do we already know (2)? 15

16 Search background information Use any text (e.g. PubMed abstracts) to search for sentences on proteins related to cancer 16

17 Search background information Help to formalise the textual information. Visualise objects from the database in the text. 17

18 Laboratory experiment planning Plan a wet-lab project for microarray measurement and data production 18

19 Laboratory experiment planning Planning can be done on several levels of detail. This is a general view of the project 19

20 In silico experiment planning Plan the analysis of the data obtained from the microarray measurement 20

21 In silico experiment planning Planning can be done on several levels of detail. This is a general view of the workflow 21

22 Laboratory experiment refining and updating Laboratory experiment and in silico experiment are part of a whole 22

23 Laboratory experiment planning and execution The progression of the experiment is documented The workflows relating to the experiment are included in the overall plan The same data entity can be shared by the experiment planning application and the workflow application 23

24 In silico experiment planning Analysis of the data obtained from the microarray measurement 24

25 In silico experiment execution The progression is documented All steps and parameters of the analysis are fully documented and saved The process can be instantly repeated with new data when required 25

26 In silico experiment execution Visualisation is accessible among other from the workflow application 26

27 Visualise a set of proteins on a category tree Calculate GO-enrichment for proteins that differed most (workflow, 'particular set') against all human proteins (uniprot, 'background set') 27

28 Visualise a set of proteins on a category tree The relative enrichment of proteins from a particular set can be calculated against a reference background set This enables to unveil e.g. overrepresented categories 28

29 Visualise a set of proteins on a network Display the set of differing proteins on the mother pathway 29

30 Visualise a set of proteins on a network Proteins are connected to each other through different kind of interactions: regulation, assembly, disassembly, etc. 30

31 Visualise a set of proteins on a network Proteins are connected to each other through different kind of interactions: regulation, assembly, disassembly, etc. 31

32 Visualise a set of proteins on a network Find the effect of given SNP haplotypes on... codon transcription... triplet translation... protein domain protein modification (PTM) 3D fold capacity to interact 32

33 Search effect of SNP Use the Data Warehouse to search for genome features and map them to protein features 33

34 Search effect of SNP Use the Data Warehouse to search for the corresponding protein features 34

35 Image interpretation Much research information comes in the form of images. Epithelial tissue images can be annotated as any other data entity in the system 35

36 Handling image data Microscopes are an essential source of biomedical information Image handling and processing is integrated into the rest of the platform Thus images can be subject to analyzes as any quantitative data set 36

37 Getting more information about any database object At any stage and in any application a report of any object can be ordered 37

38 Getting more information about any database object A configurable reporting module can be used to find auxiliary information about any object 38

39 Thank you! 39