Grid-Enablement of Protein Information Resource (PIR) caBIG ICR Face-to-Face Workspace Columbia University, Irving Cancer Research Center January 26-27, 2006

1
Grid-Enablement of Protein Information Resource
(PIR) caBIG ICR Face-to-Face Workspace
Columbia University, Irving Cancer Research
Center January 26-27, 2006

• Baris Ethem Suzek
• Georgetown University
• Lombardi Cancer Center PIR
• bes23_at_georgetown.edu

Craig Street University of Pennsylvania
Biomedical Informatics Facility street_at_mail.med.up
enn.edu
2
Outline

• Introduction PIR/BMIF
• Data Model
• Overview of the Grid-Enablement of Protein
  Information Resource
• Demo/Screenshots API/caGRID Browser
• Acknowledgements

3
Introduction - PIR

• Protein Information Resource (PIR) Integrated
  Protein Informatics Resource for
  Genomic/Proteomic Research

• UniProt Universal Protein Resource Central
  Resource of Protein Sequence and Function
• PIRSF Family Classification System Protein
  Classification and Functional Annotation
• iProClass Integrated Protein Knowledgebase Data
  Integration and Functional Analysis

http//pir.georgetown.edu
4
Introduction - PIR

• UniProt Universal Protein Resource - Central
  Resource of Protein Sequence and Function

• International Consortium
• PIR at GUMC
• European Bioinformatics Institute (EBI)
• Swiss Institute of Bioinformatics (SIB)
• Unifies PIR-PSD, Swiss-Prot, TrEMBL Protein
  Sequence Databases

http//www.uniprot.org
5
Introduction - PIR

• UniProt Databases

Primary data source for Grid-Enablement of PIR
6
Project Overview

• Grid-Enablement of PIR project is a data service
• Developer PIR _at_ Georgetown University
• Adopter BMIF _at_ University of Pennsylvania
• All the objects in our model exposed to the grid
• API is developed using caCORE SDK 1.0.3.1
• All the PIR and UniProt databases are public gt
  no security layers implemented

7
Data Model

• Protein/Gene related objects

8
Data Model

• Annotation related objects Protein Features

9
Data Model

• Taxonomy related objects (Proposed as Taxonomy
  CDE)

10
Demo and/or Screenshots - API (Example 1)

• Purpose of the script Rudimentary ID Mapper
• Find Corresponding PIR Database Cross Reference
  ID(s) that match EMBL M15034
• Test Script
• public void Demo1_DBXR2DBXR_Reports()
• try
• DatabaseCrossReference source new
  DatabaseCrossReferenceImpl()
• final String id "M15034"
• source.setCrossReferenceId(id)
• source.setDataSourceName("EMBL")
• final String answer "PIR"
• log.info("Find all PIR Database Cross Reference
  ids that match EMBL id " id ")
• try
• String path "edu.georgetown.pir.domain.Databas
  eCrossReference,"
• "edu.georgetown.pir.domain.Protein"
• List resultList appService.search(path,
  source)
• log.info("Size " resultList.size())

11
Demo and/or Screenshots API (Example 1)

• Expected Response

12
Demo and/or Screenshots - API (Example 2)

• Purpose of the script Return all Organisms
  Containing your Favorite Protein of Interest
• Find all Organisms having a Protein Named
  Transferrin receptor protein 1
• Test Script
• public void Demo2_TestProtein2Organism()
• ProteinName source new ProteinNameImpl()
• final String id Transferrin receptor protein
  1"
• source.setValue(id)
• log.info(" Find all Organisms which
  have Protein Name " id " ")
• log.info("COMMON NAME" "\t\t" "SCIENTIFIC
  NAME")
• try
• String path "edu.georgetown.pir.domain.Organi
  sm,"
• "edu.georgetown.pir.domain.Protein,"
• List resultList appService.search(path,
  source)
• for( Iterator it resultList.iterator()
  it.hasNext())
• Organism organism (OrganismImpl)it.next()
• log.info(organism.getCommonName()
• "\t\t"organism.getScientificName())
  

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Demo and/or Screenshots API (Example 2)

• Expected Response

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Demo and/or Screenshots - API (Example 3)

• Purpose of the script Need to Identify Protein
  with Known Molecular Weight from Proteomics
  Experiment
• Find all Proteins with a Molecular Weight of
  26266 Daltons
• Test Script
• public void Demo3_ProteinMeolcularWeight()
• try
• ProteinSequence object new
  ProteinSequenceImpl()
• final Integer id new Integer(26266)
• object.setMolecularWeightInDaltons(id)
• log.info(" Find all Proteins which
  have a Molecular Weight in Daltons of " id ".
  ")
• try
• List resultList appService.search(Protein.cl
  ass, object)
• for( Iterator it resultList.iterator()
  it.hasNext())
• Protein protein (ProteinImpl)it.next()
• List seqs appService.search(ProteinSequence
  .class, protein)
• for(Iterator iseqs.iterator()
  i.hasNext())
• ProteinSequence seq (ProteinSequence)i.nex
  t()
• log.info(protein.getUniprotkbEntryName()"\
  t\t" seq.getMolecularWeightInDaltons())

15
Demo and/or Screenshots API (Example 3)

• Expected Response

16
Demo and/or Screenshots caGRID Browser

• Retrieve the proteins for gene BRCA2 (Breast
  Cancer Gene 2)
• ltcaBIGXMLQuery name"testGene2Protein"gt
• ltTarget name"edu.georgetown.pir.domain.Protein
  gt
• ltObjects name"edu.georgetown.pir.domain.Gene"
  gt
• ltProperty namename predicate"equal
  valueBRCA2"/gt
• lt/Objectsgt
• lt/Targetgt
• lt/caBIGXMLQuerygt

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Demo and/or Screenshots caGRID Browser

• Retrieve the proteins for gene BRCA2 (Breast
  Cancer Gene 2) RESPONSE
• ltgridDataServiceResponse xmlns"http//ogsadai.org
  .uk/namespaces/2003/07/gds/types"gt
• .
• ltuniprotkbPrimaryAccessiongtO35923lt/uniprotkbPrim
  aryAccessiongt
• ltuniprotkbEntryNamegtBRCA2_RATlt/uniprotkbEntryNam
  egt
• ltuniprotkbPrimaryAccessiongtP51587lt/uniprotkbPrima
  ryAccessiongt
• ltuniprotkbEntryNamegtBRCA2_HUMANlt/uniprotkbEntryN
  amegt
• .....
• ltvaluegtMPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPY
  NSEPAEES
• EHKNNNYEPNLFKTPQRKPSYNQLASTPIIFKEQGLTLPLYQSPVKELDK
  
• ..
• ltuniprotkbPrimaryAccessiongtP97929lt/uniprotkbPrima
  ryAccessiongt
• ltuniprotkbEntryNamegtBRCA2_MOUSElt/uniprotkbEntryN
  amegt
• ..
• lt/edu.georgetown.pir.domain.impl.ProteinImplgtgtlt
  /resultgt
• lt/gridDataServiceResponsegt

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Demo and/or Screenshots caGRID Browser

• Find all the proteins that contain the domain
  BRCA2 repeat (PFAMPF00634, a domain in Breast
  cancer type 2 susceptibility protein)
• ltcaBIGXMLQuery name"testPfam2Protein"gt
• ltTarget nameedu.georgetown.pir.domain.Protein
  gt
• ltObjects name"edu.georgetown.pir.domain
  .DatabaseCrossReference"gt
• ltProperty name"crossReferenceId"
  predicate"equal" value"PF00634"/gt
• lt/Objectsgt
• lt/Targetgt
• lt/caBIGXMLQuerygt

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Demo and/or Screenshots caGRID Browser

• Find all the proteins that contain the domain
  BRCA2 repeat (PFAMPF00634, a domain in Breast
  cancer type 2 susceptibility protein) RESPONSE
• ltgridDataServiceResponse xmlns"http//ogsadai.org
  .uk/namespaces/2003/07/gds/types"gt
• ..
• ltuniprotkbPrimaryAccessiongtO35923lt/uniprotkbPrim
  aryAccessiongt
• ltuniprotkbEntryNamegtBRCA2_RATlt/uniprotkbEntryNam
  egt
• ..
• ltuniprotkbPrimaryAccessiongtP51587lt/uniprotkbPrim
  aryAccessiongt
• ltuniprotkbEntryNamegtBRCA2_HUMANlt/uniprotkbEntryN
  amegt
• .
• ltuniprotkbPrimaryAccessiongtP70098lt/uniprotkbPrim
  aryAccessiongt
• ltuniprotkbEntryNamegtQ5TBJ7_HUMANlt/uniprotkbEntry
  Namegt
• .
• ltuniprotkbPrimaryAccessiongtQ7RG20lt/uniprotkbPrim
  aryAccessiongt
• ltuniprotkbEntryNamegtQ7RG20_PLAYOlt/uniprotkbEntry
  Namegt
• .
• lt/gridDataServiceResponsegt

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Demo and/or Screenshots caGRID Browser

• ID mapping Find all the database
  cross-references from various databases
  corresponding to RefSeq Accession NP_061820
• ltcaBIGXMLQuery name"testIDMapping"gt
• ltTarget name"edu.georgetown.pir.domain.DatabaseC
  rossReference pathedu.georgetown.pir.domain.Pro
  teingt
• ltObjects name"edu.georgetown.pir.domain.Databa
  seCrossReference"gt
• ltProperty name"dataSourceName"
  predicate"equal" value"RefSeq"/gt
• ltProperty name"crossReferenceId"
  predicate"equal" value"NP_061820"/gt
• lt/Objectsgt
• lt/Targetgt
• lt/caBIGXMLQuerygt

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Demo and/or Screenshots caGRID Browser

• ID mapping Find all the database
  cross-references from various databases
  corresponding to RefSeq Accession NP_061820
• ltgridDataServiceResponse xmlns"http//ogsadai.org
  .uk/namespaces/2003/07/gds/types"gt
• .
• ltdataSourceNamegtEMBLlt/dataSourceNamegt
• ltcrossReferenceIdgtM22877lt/crossReferenceIdgt
• .
• ltdataSourceNamegtPIRlt/dataSourceNamegt
• ltcrossReferenceIdgtCCHUlt/crossReferenceIdgt
• .
• ltdataSourceNamegtGenPeptlt/dataSourceNamegt
• ltcrossReferenceIdgtAAH09579lt/crossReferenceIdgt
• .
• ltdataSourceNamegtNCBI GIlt/dataSourceNamegt
• ltcrossReferenceIdgt14250124lt/crossReferenceIdgt
• .
• ltgridDataServiceResponsegt

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Acknowledgements

• 3rd Millenium
• Juli Klemm
• Brian Davis
• BAH
• Mark Adams
• Arumani Manisundaram

NCI Center for Bioinformatics Peter
Covitz George Komatsoulis Avinash Shanbhag Tara
Akhavan William Sanchez Manav Kher Jijin
Yan Clarie Wolfe Nicole Thomas Himanso
Sahni Jennifer Zeng Nafis Zebarjani
Georgetown University Cathy Wu (Faculty
Lead) Hongzhan Huang (Chief Architect) Peter
McGarvey (Domain Expert) Baris Suzek (Project
Manager) Sehee Chung (SW Developer) Hsing-Kuo Hua
(DB Developer) Jess Cannata (System Admin) Robert
Clarke Steve Moore Arnie Miles Panther
Informatics Brian Gilman (Consultant)
University of Pennsylvania - BMIF David
Fenstermacher Craig Street Vishal Nayak Casey
Overby