Interoperability With BioMoby 1.0

It’s Better Than Sharing Your Toothbrush!

Photo taken by http://flickr.com/people/mfsarwar/

A brief history of BioMoby

• Model Organism Bring Your own Database Interface Conference, Sept, 2001 (MOBY-DIC) • May 21, 2002 – Genome Canada Platform Award • May 25, 2002 – API Version 0.1 deployed, including object ontology serialization into XML • July 18, 2002 – First Moby Client (Gbrowse Moby) • June 9, 2003 – API Version 0.5 deployed • 2006 – Genome Canada Platform Award • 2007 - Version 1.0 API submitted for publication

MOBY-DIC Chapter VII

7 th Model Organism Bring Your-own Database Interface Conference Vancouver, BC, June 2007.

The Core Ahab’s

Wendy Richard Mylah Martin Eddie

Mark’s Screen… Ivan Paul Andreas

The BioMoby Plan

• Create an

ontology

of bioinformatics data-types • Define a

serialization

of this ontology (data

syntax

) • Create an

open API

over this ontology • Define Web Service inputs and outputs v.v. Ontology • Register Services in an

ontology-aware Registry

• • •

Machines can find an appropriate service Machines can execute that service unattended Ontology is community-extensible

Overview of BioMoby Transactions

MOBY hosts & services Gene names

Sequence Express. Protein Alleles …

MOBY Central

Overview of BioMoby Transactions

Discovery of services That consume things LIKE sequences!

Sequence

Align Phylogeny Primers

MOBY Central

That has these features __ Object ontology

This is SCUFL – Simple Conceptual Unified Flow Language It is a complete record of everything you just did, and it can be saved for use in the Taverna workflow application that we will look at later…

Pipeline discovery “on the fly”

• No explicit coordination between

providers

• Dynamic discovery of ~appropriate

Services

• Automated execution of services

Some BioMoby statistics

Moby: Breadth

• Namespaces (data types): 418 • Objects (data syntaxes): >561 • Service Types (analytical categories): 112 • Providers: ~50 active • Service Instances: ~1200 currently “alive” – In main Moby Central server in Canada – Others in “boutique” Moby registries serving specialized communities worldwide

Moby: Clients

• Gbrowse_moby

(M Wilkinson)

• PlaNet Locus_View

(H Schoof, R Ernst)

• Blue-Jay

(P Gordon)

• Taverna

(T Oinn, M Senger, E Kawas)

• MOWserv

(INB, Spain)

• Remora

(S Carrere, J Gouzy, INRA)

• MOBYLE

(B Néron, P Tufféry, C Letondal, Pasteur Inst.)

• SeaHawk

(P Gordon)

BioMoby in detail

• MOBY Data typing system: Semantic Type • MOBY Data typing system: Syntactic Type • Moby Registry Queries

BioMoby in detail

• MOBY Data typing system: Semantic Type • MOBY Data typing system: Syntactic Type • Moby Registry Queries

Moby Namespaces

• A “Namespace” is a category of identifiers – NCBI has gi numbers (gi Namespace) – GO Terms have accession numbers (GO Namespace) • Namespaces indicate data’s semantic type. – GO:0003476  a Gene Ontology Term – gi|163483  a GenBank record • Though we are using the word “Namespace”

correctly, it causes confusion!

– “Namespace” in XML is tightly associated with an XML document and/or its syntax – In Moby, we are ONLY talking about data entities NOT THEIR SYNTAX

BioMoby in detail

• MOBY Data typing system: Semantic Type • MOBY Data typing system: Syntactic Type • Moby Registry Queries

BioMoby in detail

• MOBY Data typing system: Semantic Type • MOBY Data typing system: Syntactic Type • Moby Registry Queries

The MOBY Object Ontology

• Syntactic types are defined by a GO-like ontology – Class name at each node – Edges define the relationships between Classes – GO used as a model because of its familiarity in the community • Edges define one of three relationships – ISA • Inheritance relationship • All properties of the parent are present in the child – HASA • Container relationship of ‘exactly 1’ – HAS • Container relationship with ‘1 or more’

The Simplest Moby Data Type