Protein Information Resource

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Protein Information Resource
Protein Information Resource, 3300 Whitehaven
St., Georgetown University, Washington, DC 20007
PIR Integrated Protein Informatics Resource For
Genomic Proteomic Research
For four decades the Protein Information Resource
(PIR) has provided databases and protein sequence
analysis tools to the scientific community
including the Protein Sequence Database
(PIR-PSD), which grew from the Atlas of Protein
Sequence and Structure, edited by Margaret
Dayhoff 1965-1978. PIRs major activities
include i) UniProt - Universal Protein Resource
development ii) iProClass - protein data
integration, iii) PIRSF - protein family
classification, and iv) iProLINK source for
text mining and ontology development.

• iProLINK
• Integrated Protein Literature, Information and
  Knowledge

PIRSF Protein Family Classification System

• iProClass
• Integrated Protein Knowledgebase

UniProt Universal Protein Resource
iProLINK provides annotated literature, protein
name dictionary and other information to
facilitate Natural Language Processing technology
development and protein name tagging and
ontology. When to use iProLINK Use iProLINK for
bibliography mapping, for literature mining of
protein phosphorylation (RLIMS-P), for mapping
protein/gene names to UniProtKB entries, and for
text mining algorithm development.
The PIRSF (superfamily) protein classification
system reflects the evolutionary relationship of
full-length proteins and domains. The primary
PIRSF classification unit is the homeomorphic
family, whose members are both homologous and
homeomorphic (sharing full-length sequence
similarity). When to use PIRSF Use PIRSF to
retrieve curated information on membership,
domain architecture, and function for protein
families.
iProClass provides summary descriptions of
protein family, function and structure for
UniProt protein sequences, with links to over 80
biological databases. When to use iProClass Use
iProClass to retrieve thorough information about
a protein. By integrating data from multiple
sources iProClass presents comprehensive
up-to-date protein information and data mapping.
UniProt is a comprehensive catalog of information
on proteins. UniProt builds upon the solid
foundations laid by the consortium members,
Protein Information Resource, European
Bioinformatics Institute, and Swiss Institute of
Bioinformatics, over many years. When to use
UniProt Use UniProt to retrieve curated,
reliable, comprehensive information on proteins.
PIR Team
Additional Projects
NIAID Proteomics Resource PIR is an
administrative resource center providing the
scientific community with proteomic information
about NIAID's Category A-C biodefense organisms.
caBIG PIR participates in the voluntary network
connecting individuals and institutions, creating
a World Wide Web of information on cancer
research.
iProXpress Platform for analysis of proteomic
and genomic data.
Protein Ontology (PRO) A project geared towards
formally defining protein classes and their
relations. PRO will be developed within the
framework of the Open Biomedical Ontologies (OBO)
Foundry.
CUPID Provides strain-, species- and
genus-specific proteins. Such proteins can
provide insight into the criteria that define an
organism and can also serve as taxon-specific
diagnostic targets.
Acknowledgements PIR activities are supported by
National Institutes of Health (NIH) grant 2U01
HG02712-04 for UniProt, the NIH grants for NIAID
proteomic resource (HHSN266200400061C) and grid
enablement (NCI-caBIG-ICR), and National Science
Foundation grants for protein ontology
(ITR-0205470) and BioTagger (IIS-0430743).
Contact pirmail_at_georgetown.edu