Loading Dominant and Co-dominant Marker Data into ICIS
From ICISWiki
'''THIS PAGE IS STILL UNDER CONSTRUCTION. '''
Contents |
Introduction
Definitions
Sample data
Dataset Description
Row Headings
- Rows 1-3
- Row 1
- Rows 2 and 3
- Row 4
Column Headings
- samples
Results
- 0 marker not present in sample
- 1 marker is present in sample
- x missing data
Storing Data in DMS and GEMS
Data stored in DMS
STUDY, FACTOR and TRAIT tables
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VARIATE, DATA and OINDEX TABLES
Data stored in GEMS
The MarkerNames from DArT data are stored in the gnval field of the gems_names table. A unique ID (gnid) in the gems_names table is assigned to the MarkerName. It is connected to the gems_marker_detector table thru gobjid if the gobjtype field has the value "MARKER_DETECTOR". The gems_marker_detector is connected to gems_pd table thru the mdid field. The pdid field defines the combination of marker_detector and condition/protocol used for the marker_detector. For markers with more than one protocol, multiple pdids are generated.
Unique IDs are assigned to Allele/Molecular Variant of each Marker and is stored in the gems_names table as gobjid with gobjtype equal to "MV" and is also stored in the gems_mv table as mvid. The gems_mv table contains the information on the Molecular Variant and is connected to the gems_marker_detector table
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Loading of Data using ICIS Workbook
Workbook Template for Dominant and Co-dominant Marker Data
[[Media: |Workbook Template for DArT Data]]
Datasheet
The Datasheet below is currently the format that is being delivered to clients. Some DArT formats may include other columns such as discordance and chromosome. This Datasheet is transformed in the Observation format.
Description Sheet
In the Description Sheet, dart clone,PD(Polymorphism Detector), MD(Marker Detector),entry and GID(or samples) are treated as factors. While cloneid, clonename and marker are treated as Labels of the factor markerid. MV, MVNAME and MV STATE are treated as variates. Information about the Study/experiment is also stored in the Description Sheet.
Observation Sheet
The Observation Sheet is created from the Datasheet using a new tool in Workbook for importing Genotype Data. The Observation Sheet is a serialized format of the Datasheet.
The MD(Marker) and MV(Allele) IDs are retrieved from the GEMS database using the Get Marker ID and Get Allele ID tool of the ICIS Workbook. If the Marker or Allele is not yet in the Database, it will be added to the database and a new markerid/alleleid will be assigned to that marker/allele.
Loading Summary/Derived Data
Derived or Summary data such as PIC, Call Rate and P values are stored as a separate workbook with the same study name. A separate description sheet and Observation sheet will be used to load this data into ICIS.
