Mouse BIRN Data Integration. Maryann Martone Mouse All Hands Meeting

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1 Mouse BIRN Data Integration Maryann Martone 2005 Mouse All Hands Meeting

2 Specific Aims Specific Aim 1: Data Access and Management Continue development of multi-scale databases along existing lines extending database schemas to support expanded data models, collections and domains, and; continue development of data integration approaches that address the requirements presented by these multi-scale databases. Specific Aim 2: Expansion Expand the MBIRN federation by integrating additional data sources and incorporating additional ontologies, with a concentration on sources of gene expression information. These additions will help provide valuable insights into the molecular biology underlying degenerative brain disease. Specific Aim 3: Software Integration Continue to develop tools integrating data management, presentation, visualization and processing such that the investigator can query, process, analyze and visualize data across all data sources.

3 Data Resources: Current Status

4 Collaborative environment for pooling expertise BIRN Virtual Data Grid Group and individual permissions

5 Authentication and Auditing Ability to set permissions through portal has been greatly improved Audit trails easily recovered

6 Shared Tools Duke MRM volume Segmentation using NCMIR s Xvoxtrace

7 Multiscale Data Mediation 1. Create databases at each site 2. Create conceptual links to a shared ontology 4. Use mediator to navigate and query across data sources 3. Situate the data in a common spatial framework

8 Site Databases

9 Database Mediation for BIRN Find animal models of movement disorders where the volume of basal ganglia structures are decreased and where loss of spines from medium spiny neurons is observed. Integrated View Definition Integrated View Mediator Database Team: Sally Gewalt, Duke Jeff Brandenburg, Duke Mike Fehnel, Duke Edriss Merchant, Cal Tech Yujun Wang, UCSD Julia Sun, UCSD Karen Crawford, UCLA Wrapper Wrapper Wrapper Wrapper UCSD Cal Tech Duke UCLA

10 Calsequestrin in Cerebellum

11 Mouse BIRN Data Federation Yujun Wang Willy Wong Josh Tran Vadim Astakhov Amarnath Gupta Accessible from the portal: integrated view

12 Steps Required Data sources (Duke, Cal Tech, CCDB) registered to mediator Exported certain tables Conceptual global schema defined for Mouse BIRN data sources Emphasized general imaging workflow Integrated view created across CCDB and Duke Required understanding relationships between tables, fields and values and the conceptual global schema Required additional knowledge sources to make connections among sources UMLS Bonfire: disease mapping Mouse BIRN shared project database

13 Mouse BIRN Project Database Maps individual institutions project ID s to common BIRN ID

14 Mouse BIRN Ontologies Navigating through Multi-resolution information Linking animal and human imaging data brain cerebellum Entopeduncular nucleus Globus pallidus, internal segment cerebellar cortex Animal Model Disease Process Purkinje cell dendritic spine

15 Knowledge Maps Parkinson s Disease C Pathological feature symptom neuronal degeneration C akinesia C tremor rigidity Lewy Body C Dopamine neuron C Cell inclusion C Motor deficit C Filamentous inclusion C Substantia nigra C neurons Abnormal filaments glia ubiquitin C Alpha synuclein C C C cortex C Basal forebrain

16 Knowledge Map: Animal Model transgenic animal C a-synuclein mouse Alpha synuclein C Cellular phenotype Behavioral phenotype Cellular inclusion Motor deficit C nuclear inclusion C Cytoplasmic inclusion C ubiquitin C Alpha synuclein C neurons C glia C

17 Knowledge Maps Parkinson s Disease a-synuclein mouse Pathological feature nuclear inclusion Cellular phenotype Lewy Body Cytoplasmic inclusion Cellular inclusion Alpha synuclein Filamentous inclusion neurons ubiquitin glia

18 Spatial referencing of brain data Mediator wrapper wrapper wrapper wrapper SRB UCSD Cal Tech Duke UCLA

19 Specific Aim 1: Data Access and Management Adapt database schemas for additional data domains and data types Transgenic tables Behavioral tables, clinical assessment tables Novel data types for query-by-content type queries Continue improvement of mouse BIRN virtual data grid Adapt tools to work with BVDG Further development of data mediation tools and interfaces XML standards for data exchange (look at human work) API s Semantic mark-up of schema and data

20 Information models are available and well described Interoperable Data Resources cabig guidelines for compatibility ( documentation) Programmatic interfaces that are well described, containing service oriented components (grid-services) Use of publicly accessible controlled vocabularies which include unambiguous definitions of terms Common data elements

21 Example: Integration of 2 Cell-level databases, each containing complementary information Interopeability between UCSD and Yale Programmatic interface Query of Senselab returns results both from Senselab (Yale) and CCDB (UCSD) Points to the need for semantic mark up of resources From CCDB (UCSD)

22 Expansion of Mouse BIRN Data Resources Additional knowledge sources Continue to build the BIRN ontologies Extensions via Bonfire Disease maps: mapping of animal models of neurological disease onto the human condition Incorporate additional data and knowledge sources Register the MBL and WebQTL databases and libraries with the BIRN mediator BAMS, Mouse Phenomics Database, genetic resources Develop integrated views for Mouse BIRN defining a global schema across the various MBIRN resources, incorporating additional knowledge sources where necessary to create the bridges between related but not directly joinable data elements Develop a set of interoperable query interfaces for MBIRN data federation

23 Current BIRN Knowledge Sources UMLS Neuronames Bonfire Disease Maps Rodent brain nomenclature Knowledge map Extension tools BAMS (proposed)

24 Software Integration Create tools to enhance interoperability and integration with databases Utilize BIRN authentication and authorization utilities Can read and write to BIRN data grid Available through the BIRN portal Create tools to enhance interoperability and integration with databases Debabeler: file format conversion Metadata moderator: automatic population of database tables Workflow management tools LONI pipeline, portlets Data tracking tools Cal Tech electronic laboratory notebook

25 Discussion Topics Who: working groups data federation working group Programmers and scientists Description of resources (programmatically and semantically) Interfaces and integrated views Terminology group? Portal group? What: deliverables Mouse BIRN data federation Data and data standards Ontologies/terminology Interoperable data resources Integrated views Interfaces Documentation CVS Advertisements Where: BIRN portal, Wiki, individual sites? Need to enhance/redesign Mouse BIRN portal resources When: timeline 3 month, 6 month, 12 month goals for data integration How: training and tutorials Gridsphere? Data integration tools? What else?

26 BIRN Wide Committees Data sharing task force Rob Williams and Mark Ellisman and Art Toga Ontology Task Force Maryann Martone, Bill Bug, Allan MacKenzie Graham Cross Over Team Al Johnson, Jyl Boline, Yoni Nissanov Intellectual Property?

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28 My impressions Terminology for imaging in existing knowledge sources is very poor Semantic network in UMLS is very sparse Build semantic networks in addition to terminology base Semantic type is very important How close do you have to be? Proper description of resources both from the human and machine view is critical for current mediation Current tools for building knowledge bases, e.g., Protégé, are non-intuitive for the domain scientist

29 Atlas interfaces Interoperable Atlases Ontology Browsers Metadata Images and Volumes Genomic Data

30 Terminologies Experiences with existing knowledge sources UMLS Gene Ontology Neuronames Bonfire Controlled Vocabulary: terms and definitions Metathesaurus: synonyms Taxonomy: Concepts linked by is a relationship Ontology: is a and has a relationship

31 CCDB Dictionary Term Ontology ConceptID Semantic Type Definition Cerebellum UMLS C Body Part, Organ, or Organ Component Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement. (MSH) Glial Fibrillary Acidic Protein UMLS C Amino Acid, Peptide, or Protein, Biologically Active Substance An intermediate filament protein found only in glial cells or cells of glial origin. MW 51,000. (MSH) Medium Spiny Neuron Bonfire BF_C Cell Small (10-15 µm in diameter) projection neurons found in neostriatum, possessing a rougly spherical dendritic tree composed of 3-5 primary dendrites. Dendrites are covered with dendritic spines. Purkinje cell UMLS C Cell large branching neurons of the middle layer of cerebellar cortex, characterized by vast arrays of dendrites; the output neurons of the cerebellar cortex.

32 Documentation and Tutorials

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