Phase II Additions to LSG

1
Phase II Additions to LSG

• Search capability to Gene Browser
• Though GUI in Gene Browser
• BLAST plugin that invokes remote EBI BLAST
  service
• Working set manager
• State retention between sessions
• Provenance viewer
• Displays annotated provenance
• Accepts RDF representations

2
Knowledge Discovery through Provenance
Collection, Representation, and Use in the Life
Science Grid (LSG) Phase II Final Report
Architectural and Technical Details

• Beth Plale
• Director, Center for Data and Search Informatics
• Indiana University

3
Key contribution to LSG proper (provenance aside)

• Introduction of state

4
LSG Space
user
Annotated Provenance Graph
Working Set Manager
RDF Viewer
Lilly CAB Bus
S-OGSA Service
Entrez
Karma Framework
Provenance Graphs
OPM RDF Interface
Gene Ontology
Karma Services
Lilly to Karma Events Reflector
Provenance DB
Semantic Binding
Gene Browser
BLAST
Events Capture
Karma structure ontology
Proxy
Karma Events Bus (WSLSG)
Services and data ontology (myGrid)
SAWSDL Registry
Service Annotations
Resources (public private)
Open Provenance Model v1.01
5
BLAST support
6
Working Set support for user state
7
Demo 1 Phase II Use Case

• Select gene from database list, list will show
  in Gene Browser
• Submit gene to NCBI
• Open tab of BLAST plugin, download FASTA sequence
• Run BLAST
• Add results to Working Set
• Annotate Working set

8
Working Set Manager listens to CAB bus. It uses
Entrez ID and/or all or partial of BLAST result
as input to working set, or imports csv file into
working set. Working set WS2 was generated from
working set WS1 by Delete Rows. WS2 can be
exported as csv file.
9
Demo II Query provenance database

• Query BLAST related data.
• Query 1 get the latest Blast_Plugin.
• create or replace view v1 as
• select process_id, service_id, process_initializat
  ion_time
• from process
• where service_id like 'Blast_Plugin' and
• process_initialization_time (select
  max(process_initialization_time)
• from process
• where service_id like
  'Blast_Plugin)
• select from v1
•  
• Query 2 get the service (Blast_Ebi_Web_Service)
  invoked by Blast_Plugin.
• select invoker_id, invokee_id, p.service_id
• from invocation, process p, v1
• where invoker_id v1.process_id and invokee_id
  p.process_id

10
Demo II Query provenance database

• Query 3 get input to Blast Ebi Web Service
• select p.service_id, artifact_id,artifact_value
• from artifact_used au,artifact a, process p, v1
• where au.artifact_no a.artifact_no and
• au.process_id p.process_id and
• p.process_id v1.process_id 1 and
  p.service_id like 'Blast_Ebi_Web_Service
• Query 4 get output from Blast Ebi Web Service
• select p.service_id, artifact_id,artifact_value
• from artifact_generated ag,artifact a, process
  p,v1
• where ag.artifact_no a.artifact_no and
• ag.process_id p.process_id and
• p.process_id v1.process_id 2 and
  p.service_id like 'Blast_Ebi_Web_Service

11
Suggested Future Work

• Next steps
• Engagement of users or,
• Expanded functionality set
• Build in development time if we must do this
  ourselves
• Represent to user combined visualization and
  process provenance
• Write research quality paper
• Requires user study, or comparison, or
• Formally integrate provenance collection tools
  into non-public LSG

12
Suggested Future Work Technical

• Support BLAST in asynchronous mode,
• extend NCBI Entrez to work on other NCBI
  databases, and
• design rich provenance queries.