FACS Data Management Workshop The Immunology Database and Analysis Portal ( ImmPort ) Perspective

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FACS Data Management Workshop The Immunology Database and Analysis Portal ( ImmPort ) Perspective. Bioinformatics Integration Support Contract (BISC) N01AI40076 Richard H. Scheuermann, P.I. 20 September 2006. Bioinformatics Support for Immunology Community. - PowerPoint PPT Presentation


  • FACS Data Management Workshop

    The Immunology Database and Analysis Portal (ImmPort) PerspectiveBioinformatics Integration Support Contract (BISC)N01AI40076

    Richard H. Scheuermann, P.I.

    20 September 2006

  • Bioinformatics Support for Immunology CommunityInvestigators must be able to extract meaningful information from the vast amounts of data generated from advanced research technologiesThis requires the collection, integration and analysis of research data from numerous, diverse sources, and their long-term storage in sustainable databasesTo facilitate these processes, the scientific community must work to jointly develop essential minimum information sets and shared vocabularies for experiment records and knowledge descriptionIn response to these needs, the NIAID/NIH funded the Bioinformatics Integration Support Contract (BISC) in fall of 2004 to provide advanced IT support in the production, analysis, archiving, exchange and integration of genomic, proteomic and related dataThe users of BISC include NIAID/DAIT programs that conduct:basic scientific research of immune system development and functiongenetic determinants of immune diseaseclinical trials to evaluate the safety, toxicity, and efficacy of immune disease therapiesstudies of the underlying mechanisms of therapeutic agentsImmunology Database and Analysis Portal (ImmPort) is being developed to meet these needsImmPort v1.0 deployed on 07NOV2005; currently v1.3www.immport.org

  • The problem(s)The ultimate goal is to provide an infrastructure to support FACS data re-use.The challenges that have been identified by our ImmPort project include:Develop a complete description of the FACS experiment that fits within a generic investigation data model (e.g. FUGE)Develop an approach for the description of gating regionsDevelop an objective way of delineating protein expression classes that is based on the fluorescence intensity distributional characteristicsIntegrate population descriptions based on fluorescence intensity with the OBO Foundry Cell OntologyBroad adoption and compliance with any standards developed

  • Current approaches to addressing these challengesMapping of .fcs standards to the ImmPort System Experiment Data Model, which will align with a FUGE-like standard in the futureCapture gate image and link to results data (unclear whether the GateML standard will be used due to its complexity)Developing new clustering algorithm to rapidly identify cell populations in n-dimensional spaceCollaborated in the development of the immunology content of Cell Ontology as a starting pointWork with user community at an early stage to get their buy-in regarding the importance and use of any standards developed

  • Areas of anticipated frustrationStandards adoption and use, including societal barriersTraining and education in their proper useConfusion between standards designed for experiment replication (e.g. MIAME) and standards designed for data re-use (more focused on capturing key experiment variables)Migration of legacy systems


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