PIR: Protein Information Resource

Tao Ma

Georgia Institute of Technology

29 June, 2006

Content• Overview

• Major Modules

• Search and Analysis Tools

• Demo

• Pros and Cons

Overview

• An integrated public resource of functional annotation of protein data

• Support genomic/proteomic research and scientific discovery

• Provide PIRSF family classification system

• Provide iProClass integrated database of protein family, function, and structure

Major Modules

• UniProtUniversal Protein Resource

• iProClass Integrated Protein Classification

• iProLink Integrated Protein Literature, Information and Knowledge

• PIRSF PIR Super Family

UniProt Overview• The world’s most comprehensive catalog of information

on proteins

• Created by joining the information contained in Swiss-Prot, TrEMBL, and PIR

• Retrieve curated, reliable, comprehensive information on proteins

UniProt Structure

http://pir.georgetown.edu/pirwww/about/brochure.pdf

iProClass Overview

• Provide summary descriptions of protein family, function and structure for UniProt sequences

• Link to over 90 biological databases

• Comprise reports for all UniProtKB proteins

• Present comprehensive up-to-date information on proteins and protein data mapping

• Retrieve thorough information about a protein

iProClass Structure

http://pir.georgetown.edu/pirwww/about/brochure.pdf

iProLINK Overview

• Provide annotated literature, protein name dictionary and other information

• facilitate Natural Language Processing technology development

• Obtain literature source that describes protein entries

• Literature mining of protein phosphorylation

• Mapping protein/gene names to UniProtKB entries

• Text mining algorithm development using an annotated data set

iProLINK Structure

http://pir.georgetown.edu/pirwww/about/brochure.pdf

PIRSF Overview• A network with multiple levels of sequence diversity

• From superfamilies to subfamilies

• The primary PIRSF classification unit is the homeomorphic family

Homologous

Homeomorphic

• Manual curation for membership, etc.

• Retrieve reliable curated information for your protein sequence

Search and Analysis Tools• Text Search

• Batch Retrieval

• BLAST Search

• FASTA Search

• Related Sequence

• Peptide Match

• Pattern Match

• Multiple Alignment

• Pairwise Alignment

• ID Mapping

• Composition/Molecular Weight Calculation

•Demo… Demo… Demo… Demo… Demo…

Pros & Cons• Powerful

Provide many DBs and Tools

• Convenient

A Web Based Retrieval System

• PIRSF family classification system

Based on Evolutionary Relationships of Full-length Proteins

• Weak in Supporting Visualization of Data

Reference• http://pir.georgetown.edu/pirwww/about/brochure.pdf

• Wu CH, et al. The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Research, 30: 35-37, 2002.

• Huang H, et al.The PIR integrated protein databases and data retrieval system. Data Science 3: 163-174, 2004.