The myGrid project: towards a semantic grid for bioinformatics

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The myGrid project towards a semantic grid
for bioinformatics

• Professor Carole Goble
• http//www.mygrid.org.uk
• Contact mygrid_at_cs.man.ac.uk
• Genes, Proteins and Computing VII
• 12th September 2002
• University of Southampton, UK

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Roadmap

• The information integration bottleneck
• The myGrid project
• Semantics-driven middleware
• A taste of myGrid 0.0 0.1
• Remarks

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Obstacles Everywhere to Information Weaving

• Large amounts of different kinds of data many
  applications.
• Highly heterogeneous.
• Different types, algorithms, forms,
  implementations, communities, service providers
• High autonomy.
• Highly complex and inter-related, volatile.

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Circadian Rhythms

• Has anyone else studied the effect of
  neurotransmitters on the circadian rhythms in
  Drosophila?
• Ive got a cluster of proteins from my
  experiment. How do their functions interrelate?
  And what are the proteins with a particular
  function?
• Is a structure known for my protein? What other
  proteins have a similar structure?
• Can I build a homology 3D model?
• What is known about a homologous protein?

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E-Science Q A

• Who else has asked this question can I
  use/adapt their approach?
• Workflow.
• What were the results at each stage?
• Dynamic Data Repositories.
• When was P12345 last updated?
• Which BLAST did I use?
• Provenance.
• Has PDB changed since I last ran this?
• Notification.

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Personalisation.
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• myGridpersonalised extensible environments
  fordata-intensive in silico experiments in
  biology
• EPSRC eScience pilot project
• official start 01/10/01
• actual 01/01/02
• end 30/03/05
• 16 RAs, 9 studentships (start 09/03)

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myGrid partners
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myGrid upper middleware

• An extensible open platform for data tools
  interoperability
• Service based
• Web services Grid Open Grid Services
  Architecture (OGSA)
• XML, SOAP, WSDL,
• WSIL, UDDI
• WebSphere

Grid
Web Services
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Web Services

• Loosely coupled, stateless, message based
  distributed computing over the internet
• Description separate from implementation

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myGrid integration coordination services

• Databases
• Access.
• Semantic database integration.
• Distributed query processing.
• Workflow
• Dynamic workflow enactment.
• A resource in their own right.
• Workflow replay / repeat / reuse.
• User interactive.
• Linking
• Workflows and derived data

DB2, mySQL XML
WSFL
XML, RDF
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myGrid specialist services

• Information extraction from abstracts
• PASTA from Sheffield
• Grid-enabled BioServices by the EBI
• myGrid 0.1
• EMBOSS
• SRS
• Open BQS
• BLAST
• XEmbl and EmblFetch
• Flybase, Gadfly

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myGrid science services

• Data provenance and resource change management
• Workflow logs.
• Event notification service.
• Incremental view management.
• Personalisation
• Management of views over repositories.
• Personalisation of process flows,.
• Annotation of existing data sets.
• Dynamic creation of personal data sets.

XML, RDF, DBMS
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myGrid metadata services

• Metadata
• Service discovery, publication, composition,
  management.
• Database and data integration.
• Workflow control.
• Portal driving.
• Etc
• The Semantics
• Information models, data types ontologies.
• Object identity.

Web Services
Semantic Web
Grid
XML, XSD,RDF(S), DAMLOIL, OWL
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Metadata

• Metadata computationally accessible data about
  the services
• Ontologies the shared and common understanding
  of a domain
• A vocabulary of terms
• Definition of what those terms mean.
• A shared understanding for people and machines
• Usually organised into a taxonomy.

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myGrid Clients of Services

• e-Scientists
• Configurable portal for service access,
  personalisation community management.
• Wizards for workflow.
• Reference implementation services applications.
• Gene function expression analysis -fly yeast.
• Annotation workbench for the PRINTS pattern
  database.
• Developers
• Protocols and service descriptions.
• myGrid-in-a-Box developers kit of core services.
• Grid-enabled Bio services.

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User Agent
Custom Application
Presentation Services
Collaboration Support
Management Tools
Portal
Client Framework
Semantic Data Integration
Semantic Aspect
Information Extraction
Semantic Workflow Design
Provenance Validation Assessment
Semantic Discovery
Ontology Service
Preferences
Metadata Aspect
Availability
Preferences
Versioning
Third-party Metadata
QoS
QoS
Provenance
QoS
Coordination Services
Distributed Query
Workflow Enactment
Syntactic Discovery
Event Notification
Networked Services
White Pages Yellow Pages Discovery
Personal Repository
Database Access
JobExecution
Device Access
Device Access
Security Authentication Authorization
Distributed Resources
Database
resources data and tools
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myGrid Challenge

• Identifying the most important services.
• Agreeing consistent interfaces.
• Integrating with other Grid services.
• Implementing core services
• Describing services
• Use case scenarios (see Peter Lis poster)
• Rolling programme of prototyping
• April myGrid 0.0, October myGrid 0.1
• Not reinventing the wheel.

Here comes the semantics!!
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Wheres the Grid?

• Resource sharing coordinated problem solving in
  dynamic, multi-institutional virtual
  organizations
• On-demand, ubiquitous access to computing, data,
  and services
• New capabilities constructed dynamically and
  transparently from distributed services
• Ian Foster

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Courtesy of Mark Wilkinson (BioMOBY)
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Courtesy of Mark Wilkinson (BioMOBY)
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Service Discovery

• Find appropriate type of services
• sequence alignment
• Find appropriate instances of that service
• BLAST (an algorithm for sequence alignment), as
  delivered by NCBI
• Assist in forming an appropriate assembly of
  discovered services.
• Find, select and execute instances of services
  while the workflow is being enacted.
• Knowledge in the head of expert bioinformatian

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Finding a Service

• Words
• Syntactic signature type of inputs, outputs
  number
• Semantics What it does, whats it for, who wrote
  it -gt ontologies
• All of the above

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Why have ontologies for services?

• A shared vocabulary for describing a service
• that can evolve and say as little or as much as
  necessary.
• Service classifications
• Service discovery, organisation indexing
• Service matching and substitution
• BLAST Finds tblastx, tblastn, psi-blast, and
  marks_super_blast.
• Alignment Finds ClustalW, Blast,
  Smith-Waterman, Needleman-Wunsch
• Expanded selection of services presented based on
  expansion of in-hand object

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Why have ontologies for services?

• Controlling service composition
• Outputs of service A semantically compatible with
  inputs of service B.
• A service description is plausible.
• Blastn compares a nucleotide query sequence
  against a nucleotide sequence database

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Metadata Classification

• Domain metadata
• the domain coverage of the service, or its
  function.
• BLASTn is a tool for computing sequence homology
  that uses the BLAST algorithm over nucleotides
• Business metadata
• data quality, quality of service, cost,
  geographical location, authorisation, provenance
  of data and so on.
• BLASTn service offered by the NCBI is 80
  reliable.

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Four tiered service descriptions
Domain semantic

• Class of service
• a protein sequence alignment, a protein sequence
  database.
• Specific example of an abstract service
• BLAST, SWISS-PROT.
• Instance service description of a specific
  service
• BLAST, SWISS-PROT as offered by the EBI.
• Invoked instance service description
• BLAST as offered by the EBI on a particular date,
  with particular parameters when a service was
  actually enacted.

Business operational
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DAMLOIL/OWL

• DAML OIL designed to describe ontologies
• Ontologies incorporate information about classes,
  properties, and individuals, each of which can
  have an ID which is URI reference.
• Ontologies can reference XML Schema datatypes by
  a name for the datatype.
• Automated reasoning for inferring classification
  lattice and checking concepts are consistent
• OWL Web Ontology Language 1.0 Reference
• W3C Working Draft 29 July 2002
• http//www.w3.org/TR/owl-ref/

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Ontology editing OilEd
http//oiled.man.ac.uk/
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Reasoning in DAMLOIL

• Consistency check if knowledge is meaningful
• Subsumption structure knowledge, compute
  classification
• Equivalence check if two classes denote same
  set of instances
• Instantiation check if individual i instance of
  class C
• Retrieval retrieve set of individuals that
  instantiate C

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Why isnt a tree enough?

• BLASTn description implicitly describes a service
  that operates over nucleotides (and not
  proteins). protein pairwise alignment doesnt
  exist despite the fact that this is a likely
  service description.

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Why isnt a tree enough?

• Classify descriptions by operation (alignment,
  pairwise, multiple), by data source (protein,
  nucleotide, sequence), or by algorithm
  (SmithWaterman, BLAST).

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Why isnt a tree enough?

• Constraints are missing for the descriptions.
  BLASTp only operates over proteins.
• tBLASTn compares a protein sequence query against
  a nucleotide sequence database dynamically
  translated in 6 reading frames.
• Alignment is an operation that only applies to
  sequences and not pathways, and at least two
  inputs are required.

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• class-def defined BLAST-n_service_operation
• subclass-of atomic_service_operation
• has_Class performs_task
• (aligning has_Class has_feature local
• has_Class has_feature pairwise)
• has_Class produces_result
• (report has_Class is_report_of
  sequence_alignment)
• has_Class uses_resource
• (database has_Class contains
• (data has_Class encodes
• (sequence has_Class is_sequence_of
• 
  nucleic_acid_molecule)))
• has_Class requires_input
• (data has_Class encodes
• (sequence has_Class is_sequence_of
• 
  nucleic_acid_molecule))
• has_Class is_function_of (BLAST_application)

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• class-def defined pairwise_sequence_alignment_se
  rvice
• subclass-of atomic_service_operation
• has_Class performs_task
• (aligning has_Class has_feature local
• has_Class has_feature pairwise)
• has_Class produces_result
• (report has_Class is_report_of
  sequence_alignment)
• has_Class uses_resource
• (database has_Class contains
• (data has_Class encodes
• (sequence has_Class is_sequence_of
• 
  nucleic_acid_molecule)))
• has_Class requires_input
• (data has_Class encodes
• (sequence has_Class is_sequence_of
• 
  nucleic_acid_molecule))
• has_Class is_function_of (BLAST_application)

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Suite
Specialises. All concepts are subclassed from
those in the more general ontology.
Contributes concepts to form definitions.
Upper level ontology
Publishing ontology
Informatics ontology
Molecularbiology ontology
Organisationontology
Task ontology
Bioinformatics ontology
Web serviceontology
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Suite
Specialises. All concepts are subclassed from
those in the more general ontology.
Contributes concepts to form definitions.
Upper level ontology
Publishing ontology
Informatics ontology
Molecularbiology ontology
Organisationontology
Task ontology
parameters input, output, precondition,
effect performs_task uses-resource is_function_of
Bioinformatics ontology
Web serviceontology
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Suites Coverage
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Client framework
myGrid 0.0
Portal
Repository Client
Ontology Client
Workflow Client
Personal Repository
Workflow Repository
(Metadata) Ontology Server
DAMLOIL Reasoner (FaCT)
(Metadata) Service Type Directory
Workflow enactment
Matcher and Ranker
Service instance directory
Bioinformatics services
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How do the functions of a cluster of proteins
interrelate?

• Some proteins in my personal repository

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Find services that takes a protein and gives
their functions and pick the best match.
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Find another that displays the proteins base on
their function. Ontology restricts inputs
outputs
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Build a workflow of composed services linked
together
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See if a workflow that is appropriate already
exists. It could have been made anyone who will
share with you.
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Pick one and enact it.
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While its running it picks the best service
instance that can run the service at that time.
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While its running it picks the best service
instance that can run the service at that
time. Or you choose.
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The workflow finishes with the final display
service
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Results are put into your personal repository,
with a concept from the ontology to tell you and
myGrid what they mean.
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And full provenance record kept, and linked with
the results. We could redo or reuse the workflow.
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Other uses of the ontology

• Labelling data items in databases
• Semantic typing for controlling inputs and
  outputs
• Use by distributed query processing
• Labelling and hence indexing linking browsing
  any myGrid information component
• Workflow descriptions, people, provenance
• Link with the Life Science Identifier (I3C)
• Generate BioMOBY Central service classification
  link with BioMOBY objects.

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What about other efforts?

• Integration
• DAS "Distributed Annotation System"
• ISYS Integration of Desktop Tool
• DiscoveryLink wrapper and distributed query
  environment
• GO Gene Ontology etc
• Service discovery and common typing
• BioMOBY Integration of online biological
  databases and analysis services
• Tackling parts of the problem.
• myGrid is a framework for a platform.

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Thoughts to hold on to

• Application driven by use cases
• Open Source
• Data object types, APIs, protocols, ontologies
  have longer life span that s/w
• Components are useful dont have to buy into
  the whole shooting match.
• Dont reinvent the wheel
• Get everyone else to build services.
• Keep it simple.
• Its distributed global and a continuum.

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myGrid Summary

• myGrid aims to develop infrastructure middleware
  for an e-Biologists workbench.
• The setting is bioinformatics but the results are
  intended to be generally applicable to e-Science.
• A mix of standard, vanguard and bleeding edge
  technologies, advanced development and (some)
  research.
• Academic commercial partnership.

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The myGrid team

• Carole Goble
• Norman Paton
• Brian Warboys
• Stephen Pettifer
• Alvaro Fernandes
• Luc Moreau
• Dave De Roure
• Chris Greenhalgh
• Tom Rodden
• John Brooke
• Paul Watson
• Alan Robinson
• Rob Gaizauskas
• Robert Stevens
• Ian Horrocks
• Neil Wipat

• Matthew Addis
• Nick Sharman
• Rich Cawley
• Simon Harper
• Karon Mee
• Simon Miles
• Vijay Dailani
• Xiaojian Liu
• Tom Oinn
• Martin Senger
• Milena Radenkovic
• Kevin Glover
• Angus Roberts
• Chris Wroe

• Mark Greenwood
• Phil Lord
• Neil Davis
• Darren Marvin
• Justin Ferris
• Peter Li
• Nedim Alpdemir
• Luca Toldo
• Robin McEntire
• Anne Westcott
• Tony Storey
• Bernard Horan
• Paul Smart
• Robert Haynes

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Downloads

• All tools ontology available from
• http//www.mygrid.org.uk
• Forthcoming publication
• A suite of DAMLOIL Ontologies to Describe
  Bioinformatics Web Services and Data Chris Wroe,
  Robert Stevens, Carole Goble, Angus Roberts, Mark
  Greenwood
• To appear in International Journal of
  Cooperative Information Systems.