Division of Allergy, Immunology, and Transplantation (DAIT)

NIAID Bioinformatics Integration Support Contract (BISC)

Immunology and Data Analysis Portal (ImmPort) Website

Description of Project

The goal of the NIAID BISC is to advance the discovery and generation of new hypotheses for immune-mediated diseases and to further our understanding of innate and adaptive immunity by

• Providing an integrated data repository
• Providing advanced computer support for handling scientific data
• Disseminating best practices in scientific data analysis including research data standards for data sharing and ontologies of immunology, disease phenotype and clinical research
• Building a platform for integrated research and data sharing

The BISC will provide the means for scientists to easily access, store, analyze, and exchange complex high-quality data sets.

Specifically, BISC will provide the following resources to scientific researchers:

• A data repository
• A suite of bioinformatics analysis tools
• A suite of data integration tools
• Consulting advice on technical and data management issues
• Technical support data submission
• An archive facility

The data repository houses a variety of data types in the areas of both clinical and basic research. This unique integrated resource facilitates the translation of mechanistic data generated from the bench to improve public health and treatment of immune-mediated diseases. Access to these data and analysis tools are facilitated by user-friendly web interfaces for data query, import, export and analysis.

The BISC was awarded to a multidisciplinary team of bioinformaticians, computer scientists and scientific domain experts. The team consists of:

• Northrop Grumman Information Technology - Prime Contractor
• University of Texas Southwestern Medical Center

For more information please refer to the NIAID BISC Project Officer.

Resources Generated from the BISC Project

• Immunology and Data Analysis Portal (ImmPort) Web site
• ImmPort gene lists
• DAIT minimum information guidelines for experimental data
• Data templates for experiment data submission
• ImmPort system documentation
• ImmPort user’s guide
• Immunology ontology

Publications Related to the BISC Activities

• Diehl et al. Ontology development for biological systems: immunology. Bioinformatics. 2007 Apr 1; 23(7):913-5.
• Lee et al. MIFlowCyt: the minimum information about a flow cytometry experiment. Cytometry A.2008 Oct; 73(10):926-30.
• Smith et al. The OBO Foundry: coordinate devolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007 Nov; 25(11):1251-5.
• Taylor et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol. 2008 Aug; 26(8):889-96.
• Karp et al Ethical and practical issues associated with aggregating databases. PLoS Med. 2008 Sep 23;5(9):e190.
• Scheuermann et al Ontology-based Knowledge Representation of Experiment Metadata in Biological Data Mining. Biological Data Mining, edited by Jake Chen and Stefano Lonardi, pp. 529-560. Boca Raton: Taylor and Francis.
• Karp et al. Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis. Hum Mol Genet.2010 Feb 15;19(4):707-19. Epub 2009 Nov 18.
• Thomson et al, Sequence feature variant type (SFVT) analysis of the HLA genetic association in juvenile idiopathic arthritis. Pac Symp Biocomput. 2010:359-70.
• Malin et al. Technical and policy approaches to balancing patient privacy and data sharing in clinical and translational research. J Investig Med. 2010 Jan; 58(1):11-8.
• Qian et al. Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data. Cytometry B Clin Cytom. 2010;78 Suppl 1:S69-82.
• Diehl et al. Hematopoietic cell types: Prototype for a revised cell ontology. J Biomed Inform. 2010 Feb 1. [Epub ahead of print]
• Kong et al. Toward an ontology-based framework for clinical research databases. J Biomed Inform. 2010 May 10. [Epubahead of print]

DAIT-Funded Projects Depositing Data into ImmPort

• Immune Tolerance Network (ITN)
• Atopic Dermatitis and Vaccinia Network (ADVN)
• Population Genetics Analysis Program
• Immune Function and Biodefense in Children, Elderly, and Immunocompromised Populations
• HLA Region Genetics in Immune-Mediated Diseases
• Modeling Immunity for Biodefense

Non-federal Related Web Sites

• Northrop Grumman Information Technology
• University of Texas Southwestern Medical Center