Transcript Slide 1
PIR and caBIG™ Baris E. Suzek, Hongzhan Huang, Hsing-Kuo Hua, Peter McGarvey and Cathy H. Wu Protein Information Resource, Georgetown University, Washington, DC 20007 The cancer Biomedical Informatics Grid, or caBIG™, is a voluntary network or grid connecting individuals and institutions to enable the sharing of data and tools, creating a World Wide Web of cancer research. https://cabig.nci.nih.gov/ The goal is to speed the delivery of innovative approaches for the prevention and treatment of cancer. The infrastructure and tools created by caBIG™ also have broad utility outside the cancer community. caBIG™ is being developed under the leadership of the National Cancer Institute's Center for Bioinformatics. Grid-Enablement of Protein Information Resource (gridPIR) PIR developed one of four reference projects for the first year of caBIG. The initial development phase of gridPIR has been completed and the UniProKB data is currently available and searchable on the first release of the caGrid. Enterprise Vocabulary System Annotations Common Data Elements http://cagrid-browser.nci.nih.gov/ Object Model caBIG Query Language Search proteins for a gene using caBIG Query language Development Process Flow Structure Family Protein Sequence PDB SCOP CATH PDBSum MMDB PIRSF InterPro Pfam Prosite COG UniProt UniRef UniParc RefSeq GenPept … … … Function/Pathway iProClass Integrated Protein Knowledgebase … Protein Expression Interaction Ontology … … Taxonomy GO RESID PhosphoBase … GeneConnect GEO GXD ArrayExpress CleanEx SOURCE OMIM HapMap … SEED … Disease/Variation Swiss-2DPAGE PMG Modification GenBank/EMBL/DDBJ LocusLink UniGene MGI TIGR Gene Expression EC-IUBMB KEGG BioCarta EcoCyc WIT System Overview Gene/Genome DIP BIND … NCBI Taxon NEWT Literature PubMed GeneConnect Database IDs are linked by Direct Annotation,Mappings Inferred Annotation, or Sequence Alignment Proposed Identifier Ensembl Gene Entrez Gene Gene SEED (http://theseed.uchicago.edu/FIG/index.cgi) is a powerful tool for the analysis and annotation of genomes. The University of Chicago and Argonne National Labs have modified SEED for caBIG to better serve the cancer research community. PIR, as caBIG adopter for this project, worked with the developers to help design and test the SEED modifications. Object Model GeneConnect is an identifier mapping service designed to facilitate data integration and semantic interoperability. PIR is caBIG adopter for this project, working with the developers to help design and test the GeneConnect software. UniGene GenBank mRNA (no RefSeq) mRNA Ensembl Transcript RefSeq mRNA Ensembl Protein RefSeq Protein GenBank Protein (no RefSeq) Protein UniProtKB Thick lines indicate links where exact and inexact matches are possible Revised Vocabulary and Common Data Elements (VCDE) Workspace Participation • Mentoring and reviewing caBIG funded software projects to ensure caBIG compatibility guidelines are met SEED Web Interface System Overview http://pir.georgetown.edu/pirwww/cabig.shtml • Development and/or review of data and vocabulary standards to enhance semantic interoperability Contact [email protected]