**caArray** **Use Cases**

Julie Zhu

**Northwestern University**

**Use case 1: Import Microarray dataset as MAGE-ML**

We would like to use caArray to import dataset in MAGE-ML format to an
in-house MAGE-OM compliant Oracle database.

**Use case 2: Export Microarray dataset as MAGE-ML**

We would like to use caArray to export MAGE-ML so that we can export any
data stored in an in-house MAGE-OM compliant Oracle database to any
other MAGE-OM compliant databases.

**Use case 3: Upload Affymetrix Microarray**

We would like to use caArray to upload the MIAME information along with
the following affymetrix microarray files to an in-house MAGE-OM
compliant Oracle database assuming 2 treatments and 4 replicates per
treatment for the experiment to be uploaded. In addition, we would like
to have caArray to store .CEL files in a designated file system
directory for R routines to use.

EXP1_TRT1_REP1.CHP

EXP1_TRT1_REP2.CHP

EXP1_TRT1_REP3.CHP

EXP1_TRT1_REP4.CHP

EXP1_TRT2_REP1.CHP

EXP1_TRT2_REP2.CHP

EXP1_TRT2_REP3.CHP

EXP1_TRT2_REP4.CHP

EXP1_TRT1_REP1.CEL

EXP1_TRT1_REP2.CEL

EXP1_TRT1_REP3.CEL

EXP1_TRT1_REP4.CEL

EXP1_TRT2_REP1.CEL

EXP1_TRT2_REP2.CEL

EXP1_TRT2_REP3.CEL

EXP1_TRT2_REP4.CEL

EXP1_TRT1_REP1.rpt

EXP1_TRT1_REP2.rpt

EXP1_TRT1_REP3.rpt

EXP1_TRT1_REP4.rpt

EXP1_TRT2_REP1.rpt

EXP1_TRT2_REP2.rpt

EXP1_TRT2_REP3.rpt

EXP1_TRT2_REP4.rpt

EXP1_TRT1_REP1.exp

EXP1_TRT1_REP2.exp

EXP1_TRT1_REP3.exp

EXP1_TRT1_REP4.exp

EXP1_TRT2_REP1.exp

EXP1_TRT2_REP2.exp

EXP1_TRT2_REP3.exp

EXP1_TRT2_REP4.exp

In addition, we would like to use caArray to upload the following image
files in a designated file system directory along with the experiment
and store the URL in the Oracle database for future retrieval, viewing
and image reanalyzing when new image analyzing software becomes
available.

EXP1_TRT1_REP1.DAT

EXP1_TRT1_REP2.DAT

EXP1_TRT1_REP3.DAT

EXP1_TRT1_REP4.DAT

EXP1_TRT2_REP1.DAT

EXP1_TRT2_REP2.DAT

EXP1_TRT2_REP3.DAT

EXP1_TRT2_REP4.DAT

**Use case 4: Upload 2-channel Microarray**

We would like to use caArray to upload the MIAME information along with
the following 2-channel microarray files to the backend Oracle database
assuming 2 treatments and 4 replicates per treatment for the experiment
to be uploaded.

EXP1_TRT1_REP1.GPR

EXP1_TRT1_REP2.GPR

EXP1_TRT1_REP3.GPR

EXP1_TRT1_REP4.GPR

EXP1_TRT2_REP1.GPR

EXP1_TRT2_REP2.GPR

EXP1_TRT2_REP3.GPR

EXP1_TRT2_REP4.GPR

EXP1_TRT1_REP1.GAL

EXP1_TRT1_REP2.GAL

EXP1_TRT1_REP3.GAL

EXP1_TRT1_REP4.GAL

EXP1_TRT2_REP1.GAL

EXP1_TRT2_REP2.GAL

EXP1_TRT2_REP3.GAL

EXP1_TRT2_REP4.GAL

With both use cases 3 and 4, we would like to use caArray to assign the
initial ownership of the uploaded experiment so that only the owner can
view the experiment until he/she authorize others to view/analyze the
datasets in a separate module. This owner may or may not be the user
uploading the experiment.

**Relevant issues for Architecture:**

1.  MAGE-OM compliant

2.  Ability to upload large datasets in a reasonable speed

3.  Ability to generate MAGE-ML and import MAGE-ML in a reasonable speed

4.  Ability to track MIAME such as experiment condition, experiment
    design, bio-source, array design, sample extraction condition,
    hybridization condition and scanning parameters et al

5.  Ability to track ownership