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myGridTaverna Provenance

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Title: myGridTaverna Provenance

1
myGrid/Taverna Provenance

Daniele Turi
University of Manchester
OMII f2f Meeting, London, 19-20/4/06

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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
Examples
myGrid
Long Term Ecological Research Network
BioPathways Consortium

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LSID (ctd 2)

abstraction
lightweight
independent from actual storage implementation
database
file system
application
both for private and public data sources

8
Data
9
Data Storage (current)

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

10
Data Storage (future)

Domain-specific databases
use outside myGrid
Develop
taverna processor for JDBC/OGSA-DAI
associated interface (cf BioMart)
Users will be able to study the contents of an
existing database and
write queries that extract data from the
database, where the query may be parameterised
with values passed in from the workflow
write requests that insert data from the workflow
into a named table in the database.

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Metadata
12
Metadata Generation

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

13
Metadata

Representation
Ontology (Schema)
Storage
Query
Browsing

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Representation

RDF
triples
subject predicate? object
URIs (hence easy data integration)
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
RDF schema
Taxonomic inferences
also available as OWL
opens it up to complex reasoning

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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
19
Storage

Named RDF graphs
retrieve whole graphs (eg workflows)
implementation in
NG4J (Jena MySQL)
scalability issues
Sesame2 native store
scalable
Java 5

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Query

RDF query languages
TriQL, SeRQL, SPARQL
query languages for named RDF graphs
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
26
Provenance Analysis

Comparison
Aggregation
etc
see work by Jun Zhao

27
Security
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29

User sends LSID ref and credentials to the Access
Point
Access Point returns data and metadata or denies
access as follows
credentials are passed to a User Directory
User Directory passes the corresponding user to
the Authorization Authority
Authorization Authority returns the user
attributes in the form of a (possibly signed)
SAML assertion
this assertion, together with the lsid and its
corresponding metadata, is passed to the Policy
Enforcement Point (PEP)
PEP uses these three inputs to form an XACML
request that is passed to a Policy Decision Point
(PDP) that is preloaded with an XACML Policy Set.
PDP evaluates the request against its policy set
and returns an XACML response to PEP
PEP decodes the response and either allows
data/metadata to be returned to the user or
denies access.