1. Protein Information Resource Protein Information Resource, 3300 Whitehaven St., Georgetown University, Washington, DC 20007 Contact pirmail@georgetown.edu 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. PIR: Integrated Protein Informatics Resource For Genomic & Proteomic Research 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. iProLINK Integrated Protein Literature, Information and Knowledge PIRSF Protein Family Classification System iProClass Integrated Protein Knowledgebase UniProt Universal Protein Resource 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. iProXpress: Platform for analysis of proteomic and genomic data. 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. caBIG™: PIR participates in the voluntary network connecting individuals and institutions, creating a World Wide Web of information on cancer research. NIAID Proteomics Resource: PIR is an administrative resource center providing the scientific community with proteomic information about NIAID's Category A-C biodefense organisms. Additional Projects 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). PIR Team