Transcript Slide 1

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]. PIR’s 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.
UniProt
iProClass
PIRSF
iProLINK
Universal Protein Resource
Integrated Protein
Knowledgebase
Protein Family Classification
System
Integrated Protein
Literature, Information and
Knowledge
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.
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-todate protein information and
data mapping.
The PIRSF (superfamily) protein
classification system reflects the
evolutionary relationship of fulllength 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.
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 (RLIMSP), for mapping protein/gene
names to UniProtKB entries, and
for text mining algorithm
development.
Additional Projects
PIR Team
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
[email protected]