MBAT Programmers Meeting From MBAT to WOMBAT Web-based Ontology-based

Architecture Basic data type abstraction (or physical databases) Sources Gene expression 2D images 2D vector segmentations 3D volumes 4+D volumes (FMRI) Time series Phenotype/behavioral surfaces Methods over the abstract representation – Shall have common signatures getExpressed(gene, feature) translate (coords) convet (formats) registries Clients: MBAT etc. Data integration tools

HIS example Time series data model Time series objects Time series catalogs Methods over time series databases Multiple clients

Brainstorming: gene expression subjects features genes probes getSubjects (GeneExpression, source, filter) getFeatures (GeneExpression, source, subject, filter) getGenes (GeneExpression, source, subject, feature, filter) getAvgGeneExpression (GeneExpression, source, subject, feature, gene) createImage? getAvgGeneExpression (…user-defined shape, gene) Array Express +MaxdSQL (European Bioinfo inst) GenX (open source, NCGR) Gene Expression Omnibus (NLM) Stanford Microarray DB EMAP!! Bill asks Rob about typical scenarios – formalize them as method signatures, Looking at BIOMOBY, FuGO. Make sure Steve’s general signatures can be run Against multiple sources – then write wrappers, and document them. Another step is: catalog of gene expression sources, and search API over it Steve + Bill

Also: ochemweb.or g/databases. shtml ochemweb.or g/databases. shtml

Need to outline Data types: –upload on wiki examples of each data type? - everybody –Sample APIs over each type of data - for discussion (lead: Steve?) –Data cutter API? Sources –Sources of gene expression: GEO + David +GN + Desmond +Daniel (need to wrap and –Sources of 2D images: images in CCDB; images in SRB (as exposed through ArcIMS or similar) – Gensat (downloadable, but working on services), MBL (in SRB) : UCSD (Asif + Willy) Controlled vocabularies Spatial reference systems –Stereotaxic Paxinos style –image based on corner points as referenced to Stereotaxic –Alternate stereotaxic –conversion routines across all. Conversions won’t be perfect at the beginning. Establish the conversions as web services and as Java library Tools for generating and registering resources –Image registration workflow (UCSD + Bill) – make forks for different registration base and warping methods Web services for: data access; catalog searching; data format conversion, coordinate conversion, ontological operations

Front-end A survey to find common clients? Portal-based client Workspaces = portlets? –Portalizing MBAT

1. API for data retrieval and transformation Settle on common BIRN-supported data formats: –2D raster formats, 2D vector formats (e.g. ArcIMS services) –3D formats –XML exchange standards Settle on a common spatial and ontological references –Stereotaxic, plus conversion routines –Ontologies is an ongoing effort Common web services API for data access (CCDB web services!)

2. API for atlas catalogs Spatial registry: –Image registration pipeline –Services over the registry Other registries: –Web services –Data sources of each type

3. API for state exchange First version available, and supported by three atlases (Shiva, SA, NT) –Agreed-upon protocol and ROI description, plus Java API; –Agreed-upon coordinate framework; –Synchronizing mouse positions Need to implement, test, publish…

Universal description of location and spatial relationships?? Across scales and coordinate systems Location description: –By geometries (in common coordinates: there are three of them at least) –By feature names (in shared ontology) – Neuronames most likely –By relationships (in common mereotopology terms): need engines for description “packing” and “unpacking” –NEED TRANSLATIONS BETWEEN THE THREE

Outline Morning: general architecture Afternoon: Immediate steps Possible focus: –gene expression, 2D images –For them: canonical representation, conversion to canonical representation or wrapping, registration workflows, web service API over data sources; web service API over registries

Reviewing minutes Need to add some high level technical specs – but not excruciatingly detailed –Because time consuming, and in flux –Based on use cases and requirements –Define a process for using/updating/validating the high-level specs Deconstructing MBAT… and re-building Need to separate pieces that need to communicate tightly, versus those that communicate via server

MBAT deconstruction Components that require tight Integration (client-client) Components that can communicate Via server, and where web service Interfaces are appropriate N coordinated vis panes (currently required by Shiva to communicate efficiently); however NT SDK implements the same via client-server connection Querying UMLS Querying gene expression, etc. Searching catalogs… MBAT will connect to the following servers: - ArcIMS services wrapped in SOAP, with functions like getImage(), - GEO gene expression data wrapped In SOAP and responding to getGenes(), Etc. - Bill sends a document outlining breakdown of components

Standard operations over Gene Expression Data Will come later

Steps Bill’s architectural description –Specifying approx effort Documenting existing web services: NT, CCDB Possibly services available from others – need a catalog Guidelines for use of services by web clients – put on the web Services against a few common data types –Gene expression services (web service API, web wrappers over common sources and/or canonical representation + loader) –2D image services (web service API over ArcIMS and images in SRB, image registration workflow)