Grid-Enablement of Protein Information Resource (gridPIR)

1
Grid-Enablement of Protein Information Resource
(gridPIR) Georgetown University Medical Center
(Developer) 1 University of Pennsylvania
(Adopter) 2 1 Baris E. Suzek, Hongzhan Huang,
Scott Chung, Hsing-Kuo Hua, Peter McGarvey, Cathy
H. Wu Lombardi Comprehensive Cancer Center,
Georgetown University Medical Center, Washington,
DC, 20057 2 Craig Street, Casey Overby, David
Fenstermacher Abramson Cancer Center, University
of Pennsylvania, Philadelphia, PA 19104
Abstract The Protein Information Resource (PIR)
is an integrated bioinformatics resource that
provides protein databases and analysis tools to
support genomic and proteomic research. A
participant in the Integrative Cancer Research
(ICR) workspace of caBIG, PIR developed gridPIR
in collaboration with the adopter from the
Biomedical Informatics Facility (BMIF) for the
Abramson Cancer Center at the University of
Pennsylvania. gridPIR is one of four reference
projects for demonstrating how a caBIG Silver
compliant data source can be discovered and
consumed on caGrid. gridPIR was developed using a
Model Driven Architecture (MDA) approach and
employs an n-tier architecture. A data layer,
supported by Oracle 9i, stores the UniProt
Knowledgebase (UniProtKB). The object layer
contains 48 domain objects with 51 attributes
registered to caDSR, as required to support
semantic interoperability. A data access layer
utilizing Hibernate provides the mapping between
objects and the relational database. The gridPIR
API exposed to caGrid was generated using caCORE
SDK 1.0.3.1. Upon successful completion on August
1st, 2005, gridPIR became one of the first caBIG
Silver compliant data services on caGrid 0.5. In
compliance with caBIG compatibility guidelines,
gridPIR will continue to improve its services to
better serve as the central proteomic information
resource for cancer research within caBIG.
Protein Science Team (13) Executive Team
Members Dr. Winona Barker, Director Emeritus,
Adjunct Professor Dr. Darren Natale, Protein
Science Team Lead, Research Assistant
Professor Dr. Zhangzhi. Hu, Associate Protein
Science Team Lead, Research Associate
Professor Dr. Lai-Su L. Yeh, Senior Protein
Scientist, Research Assistant Professor Staff
Members Dr. Anastasia Nikolskaya, Senior Protein
Scientist, Research Assistant Professor Dr. Raja
Mazumder, Scientific Coordinator, Research
Assistant Professor Dr. C.R. Vinayaka, Senior
Protein Scientist, Research Assistant
Professor Dr. Sona Vasudevan, Senior Protein
Scientist, Research Assistant Professor Dr.
Cecilia Arighi, Senior Protein Scientist,
Research Assistant Professor Christina Fang,
Research Assistant Natalia Petrova, PhD
Student Paul Ramos, MS Student Ti-Cheng Chang, MS
Student
Developer PIR _at_ GUMC
PIR Director Dr. Cathy Wu Professor
Bioinformatics Team (11) Executive Team
Members Dr. Peter McGarvey, Project Manager,
Research Associate Professor Dr. Hongzhan Huang,
Bioinformatics Team Lead, Research Assistant
Professor Baris Suzek, Associate Bioinformatics
Team Lead, Senior Research Associate Staff
Members Dr. Leslie Arminski, Systems Manager,
Research Assistant Professor Dr. Hsing-Kuo Hua,
Bioinformatics Software Engineer, Research
Assistant Professor Dr. Robel Kashay,
Bioinformatics Scientist, Research Instructor Dr.
Xin Yuan, Bioinformatics Scientist, Research
Instructor Yongxing Chen, Bioinformatics Research
Associate Jing Zhang, Bioinformatics
Programmer Jess Catana, System Administrator
Alireza Amoozmand, MS Student

UniProt Team
Adopter BMIF _at_ UPenn
UML Model
EVS Annotations

• Current model contains 48 objects , 51 attributes
  including Protein/Gene, Taxonomy and Protein
  Feature related objects
• In second year, the model will be extended with
  Protein Annotation and Family-related objects
  from PIRSF

UniProt
Querying using caGrid Browser
http//cagrid-browser.nci.nih.gov/
Search proteins for a gene
caCORE SDK Process Flow
Querying using Java API public void
Demo2_TestProtein2Organism() ProteinName
source new ProteinNameImpl() final String id
Transferrin receptor protein 1"
source.setValue(id) try String path
"edu.georgetown.pir.domain.Organism,"
"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.getC
ommonName() "\t\t"organism.getScientificName
())
Project Page
http//gforge.nci.nih.gov/projects/gridpir
Search organisms containing a protein