1. PIR: Protein Information Resource
Tao Ma
Georgia Institute of Technology
29 June, 2006

2. Content Overview Major Modules Search and Analysis Tools Demo
Pros and Cons

3. 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

4. Major Modules UniProtUniversal Protein Resource
iProClass  Integrated Protein Classification
iProLink  Integrated Protein Literature, Information and Knowledge
PIRSF  PIR Super Family

5. 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

6. UniProt Structure

7. 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

8. iProClass Structure

9. 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

10. iProLINK Structure

11. 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

12. Search and Analysis Tools
Peptide Match
Pattern Match
Multiple Alignment
Pairwise Alignment
Text Search
Batch Retrieval
BLAST Search
FASTA Search
Related Sequence
ID Mapping
Composition/Molecular Weight Calculation

13. Demo… Demo… Demo… Demo… Demo…

14. 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

15. 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: , 2004.