Provenance in Taverna

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Provenance in Taverna

• Daniele Turi
• University of Manchester
• Chimatica Meeting, Manchester, 24/3/06

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Components

• Identifiers
• LSIDs
• Data
• JDBC data store
• Metadata
• RDF Provenance Plugin
• Browsing
• Provenance Browser Plugin
• Security
• Under development

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LSID
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LSID Life Science Identifier

• URN specification in progress
• 5 part identifier (with optional version id)
• urnlsidwww.mygrid.org.uklsdocumentX1234
• urnlsidncbi.nlm.nlh.gov.lsid.biopathways.orggen
  bank_gi7717376
• protocol for retrieving data and metadata about
  an object
• commitment by the provider to always return the
  same data for an ID

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LSID (ctd)

• Issue
• LSID Authorities
• Resolution
• LSID Resolvers
• abstract, lightweight
• independent from actual storage implementation
• database, file system, application
• both for private and public data sources

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Data
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Data Storage

• Taverna can persist inputs, outputs and
  intermediate results in an SQL database via JDBC
• Optional and can be done by configuring a Baclava
  Data Store
• Allows the LSIDs of data items to be resolved
  against the actual data

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Metadata
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Metadata Generation

• Taverna Provenance Plugin
• Listen to Taverna Events
• WorkflowEventListener
• Faithfully record them as ontological instance
  data
• RDF graphs (one for each Taverna run)

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Metadata

• Representation
• Schema (Ontology)
• Storage
• Query

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Representation

• RDF
• triples
• subject predicate? object
• semantic web language
• XML serialization
• flexible, powerful
• sets of triples gives rise to graphs

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Workflow Run
urnlsidworkflow6
urnlsidorgHY7
runs
belongsTo
urnlsid..wfInstance8
launchedBy
urnlsidperson4
executed
executed
urnlsidprocessRun84
urnlsidprocessRun51
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Schema

• Ontology
• Classes and Properties
• RDF schema
• Taxonomic inferences
• also available as OWL
• opens it up to complex reasoning

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Workflow Run
urnlsidworkflow6
urnlsidorgHY7
runs
belongsTo
urnlsid..wfInstance8
launchedBy
urnlsidperson4
executed
executed
urnlsidprocessRun84
urnlsidprocessRun51
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Typed Workflow Run
launchedBy
Provenance Ontology
executed
Experimenter
Organization
ProcessRun
WorkflowRun
Workflow
belongsTo
runs
urnlsidworkflow6
urnlsidorgHY7
runs
belongsTo
urnlsid..wfInstance8
launchedBy
urnlsidperson4
executed
executed
urnlsidprocessRun84
urnlsidprocessRun51
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Storage

• Named RDF graphs
• retrieve whole graphs (eg workflows)
• implementation in NG4J (Jena MySQL)
• scalability issues
• new implementation almost ready using Sesame2
  native store
• scalable

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Query

• RDF query languages
• TriQL, SeRQL, SPARQL
• Ontology inspection/reasoning
• Canned Queries
• workflows with failed processes
• input/output of past process runs
• workflows with data changed by user

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Browsing
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Provenance Browsing

• Provenance Browser Plugin
• reusing Taverna GUI components
• Matthew Gamble

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Analysis
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Provenance Analysis

• Comparison
• Aggregation
• etc
• see work by Jun Zhao

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Security
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