PIR: Protein Information Resource

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PIR Protein Information Resource

• Tao Ma
• Georgia Institute of Technology
• 29 June, 2006

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Content

• Overview
• Major Modules
• Search and Analysis Tools
• Demo
• Pros and Cons

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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

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Major Modules

• UniProt?Universal Protein Resource
• iProClass ? Integrated Protein Classification
• iProLink ? Integrated Protein Literature,
  Information and Knowledge
• PIRSF ? PIR Super Family

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UniProt Overview

• The worlds 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

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UniProt Structure
http//pir.georgetown.edu/pirwww/about/brochure.pd
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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

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iProClass Structure
http//pir.georgetown.edu/pirwww/about/brochure.pd
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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

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iProLINK Structure
http//pir.georgetown.edu/pirwww/about/brochure.pd
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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

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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

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• Demo Demo
  Demo
  Demo
  Demo

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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

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Reference

• http//pir.georgetown.edu/pirwww/about/brochure.pd
  f
• 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.