1. Experiment Data Model for ImmPort Jennifer Cai UT Southwestern Medical Center 9/18/2006

2. Create an integrated database that broadens the usefulness of scientific data and advances hypothesis-driven and hypothesis-generating research. Advance the pace and quality of scientific discovery while extending the value of scientific data in all areas of immunological research. Design, implement and maintain a data warehouse of genomic, proteomic and related data from laboratories. Integrate relevant data sets from public and government databases. Promote rapid availability of important findings, making new discoveries available to the NIAID/DAIT-funded research community for further analysis and interpretation. Provide analysis tools to advance immunological research. Goals for ImmPort

3. ImmPort Experiment Data Model

4. 1.Biological Sample: Definition: Biological material that has undergone isolation, processing and/or treatment prior to use in an experiment. Example: Patient X Blood from patient X Protein lysate from mouse brain RNA isolated from T cells purified from the spleen of patient X with disease phenotype A and placed into cell culture and treated with IL-2 for 2 hrs at 37  C Database entities:

5. Anatomic Part Biological Sample Anatomic Part Biological Sample Accession # Anatomic Part ID Name Description Anatomic Part type Source ID Source Name Source type Purity Weight Value Unit Volume Value Unit Comment Treatment Agent Concentration Value Unit Volume Value Unit Time Value Unit Temperature Value Unit Other Molecular fraction Molecular Fraction Biological Sample Accession # Molecular fraction ID Name Description Molecular fraction type Source ID Source Name Source type Purity Concentration Value Unit Volume Value Unit Treatment Agent Concentration Value Unit Volume Value Unit Time Value Unit Temperature Value Unit Other Comment Cellular Fraction Biological Sample Cellular Fraction Biological Sample Accession # Cellular fraction ID Name Description Description_secondary (e.g. $CELLS: normal human peripheral blood) Cellular fraction type Source ID Source Name Source type Purity Concentration Value Unit Volume Value Unit Treatment Agent Concentration Value Unit Volume Value Unit Time Value Unit Temperature Value Unit Other Comment Subject/Organism Biological Sample Accession # Subject/Organism ID Name Description Description_secondary ($SRC) Taxonomy ID Strain/race Age Value Unit Gender Special genotype Special phenotype (e.g. diabetic) Special phenotype ID (ICD-9 code) Comment Treatment Agent Concentration Value Unit Volume Value Unit Time Value Unit Temperature Value Unit Other One or many One and only one

6. 2.Experiment Sample Reagent Definition: A chemical compound used to measure an Analyte(s). Example: Antibody-conjugated with fluorochrome (flow cytometry) Database entities:

7. Experiment Sample Reagent Experiment Sample Reagent Accession # Experiment Sample Reagent ID Experiment Sample Reagent Name (e.g. FITC-labeled CD45) Experiment Sample Reagent Name_secondary (e.g. $PnS: FITC-labeled CD45) Experiment Sample Reagent Type Experiment Sample Reagent Value Experiment Sample Reagent Description Manufacturer Web link Contact Catalog number Lot Number Reagent Set ID Analyte_n Analyte name_n (e.g. CD19) Analyte description_n Detector name (e.g. anti-CD19) Reporter name (e.g. FITC) Reagent Set SetID Set name Set description Experiment Sample Reagent Acc(s)# Experiment Sample Reagent ID(s)

8. 3. Experiment Sample Definition: The Experiment Sample is a combination of Biological Sample(s), Reagent(s) and Protocol(s) that gives rise to Experiment Sample Results. Example: T cells in one tube stained with CD4-FITC and CD8-PE (flow cytometry) Protein lysate in one anti-CD3-coated well of a 96-well plate (ELISA) RNA hybridized to Affy chip with 40,000 probes (one-color microarray) 1 patient sample hybridized to one well of an Affy SNP chip(genotyping) Database entities:

9. Experiment Sample Experiment Sample Accession # Experiment Sample ID Name Name_secondary (e.g. $SMNO: A7) Description Description_secondary ($COM: Incubation time 47 mins) Biological Sample Accession #(s) Biological Sample ID(s) Results File Set Accession # Replicate Group ID Reagent Accession #(s) Protocol Accession #(s) Protocol ID(s) Protocol Name(s) Experiment sample parameter_n Name_n (e.g. $TOT, the tag in the.fcs file become the value in this field, the value will be translated from “$TOT” to “Total number of events in the data set”) Value_n (e.g. 2000000) Reagent Set ID

10. 4.Experiment Definition: One or more Experimental Sample(s) containing at least one biological sample from which responding variable(s) are measured, evaluated, or collected for the purposes of testing hypotheses or theories, demonstrating known facts or theories or measuring/collecting data. Example: A series of Affy gene expression chips A series of cDNA chips 4 tubes of T cells stained with CD4-FITC, CD8-PE, none, or both T cells+CD4-FITC T cells+CD8-PE T cells+CD4-FITC+CD8-PE T cells Database entities:

11. Experiment Experiment Accession Number Experiment Type Experiment Measurement Technique Title Description Hypothesis Keywords Rationale Quality Control Measures Submitter Experiment Group ID(s) Experiment Protocol ID(s) Experiment Sample ID(s) and short description Experiment Sample Replicate Group ID(s) Links to publications, supplemental websites or database accession numbers Experiment Conditional/Manipulated Variable Type Descriptor/value Experiment Constant Type Descriptor/value

12. 5.Protocol Experiment related protocols: Biological Sample Preparation protocol Definition: A protocol file submitted by the user that describes how a Biological Sample was isolated, enriched, processed, treated, or otherwise prepared for experimental use. Example Sample Protocol Definition: A protocol file which the user may submit that describes how an Experimental Sample was processed for an experiment. Example: Staining using CD4-FITC antibody (flow cytometry) Experiment Protocol Definition: A protocol file which the user may submit that describes how an Experiment was performed. It is applied to all Experimental Samples associated with an experiment.

13. Protocol Protocol Accession # Protocol Name File Name Description File Name Protocol type Keywords Summary Biological Sample Set Accession #(s), etc. Biological Sample Set Name(s), etc. Instrument Experiment Sample ID Instrument type (e.g. flow cytometer) Instrument name Instrument name_secondary (e.g. $CYT: FACSCalibur) Instrument settings Instrument setting type (e.g. parameter // gating // compensation matrix) Instrument setting name Instrument setting description Instrument setting value

14. 6.Data Analysis: Data Transformation Application Protocol Data in Data out Example: Data Input Data Transformation Data Out Application Protocol Database entities: Cell Population Proportion Fluorescence Intensity Gate Strategy Calculation Equation

15. Data Transformation Protocol Application Protocol Application ID Filter ID(s) Protocol Application type (e.g. population proportion) Protocol Application/Calculation Equation Protocol Application/Calculation Description (e.g. No. of events in with characteristic R6/Total number of event) Filter Filter ID Filter components ID(s) Filter name Filter description Filter image file ID Parameter Profile ID(s) Parameter Profile Parameter Profile ID name (e.g. FITC, FSC, Cell Count, ) value type value (e.g. +/-, dim/high, 100-200)

16. 7.Experiment Sample Result Set Definition: The file or set of files generated from an Experimental Sample. Examples: Primary FCM data file:.fcs file Analyzed FCM data: %population of cells, #Cell Count, etc Database entities Experiment Sample Results File Set Experiment Sample Results File Set Accession # Experiment Sample Results File Name(s) Experiment sample result file name_secondary (e.g. $FIL: 071494.001) Acquisition date (e.g. $DATE: 01-OCT-1994) Experiment Sample Accession #(s) FACS Analyzed Result Experiment Sample ID Calculation information n Data Transformation Protocol Application ID n Calculated Value and Unit n

17. + Exp Sample Reagent + Protocol Subject Biological Sample Experiment Sample + Exp Sample Reagent + Protocol

18. BISC Team –Dr. Scheuermann –UT BISC team Jamie lee Megan Kong Max Qian Jyoti Shah Nishan Marthandan –NG BISC team