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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

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• Investigators must be able to extract meaningful information from the vast amounts of data generated from advanced research technologies

• This requires the collection, integration and analysis of research data from numerous, diverse sources, and their long-term storage in sustainable databases

• To facilitate these processes, the scientific community must work to jointly develop essential minimum information sets and shared vocabularies for experiment records and knowledge description

• In 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 data

• The users of BISC include NIAID/DAIT programs that conduct:– basic scientific research of immune system development and function– genetic determinants of immune disease– clinical trials to evaluate the safety, toxicity, and efficacy of immune disease therapies– studies of the underlying mechanisms of therapeutic agents

• Immunology Database and Analysis Portal (ImmPort) is being developed to meet these needs

• ImmPort v1.0 deployed on 07NOV2005; currently v1.3

• www.immport.org

Bioinformatics Support for Immunology Community

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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:

1. Develop a complete description of the FACS experiment that fits within a generic “investigation” data model (e.g. FUGE)

2. Develop an approach for the description of gating regions3. Develop an objective way of delineating protein expression classes that

is based on the fluorescence intensity distributional characteristics4. Integrate population descriptions based on fluorescence intensity with

the OBO Foundry Cell Ontology5. Broad adoption and compliance with any standards developed

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Current approaches to addressing these challenges

• Mapping of .fcs standards to the ImmPort System Experiment Data Model, which will align with a FUGE-like standard in the future

• Capture 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 space

• Collaborated in the development of the immunology content of Cell Ontology as a starting point

• Work with user community at an early stage to get their buy-in regarding the importance and use of any standards developed

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Areas of anticipated frustration

• Standards adoption and use, including societal barriers

• Training and education in their proper use

• Confusion 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