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Application 2.2.1 Tool 2.10 - Database 2.10.3 IBDB Genotyping Data Management System (GDMS) Schema v1.0

Structure of the ICIS GDMS database:
Introduction:
GDMS (Genotyping data management system): GDMS aims to provide a comprehensive public repository for marker information, genotype, linkage map and QTL data from crop species.
The underlying database is MySQL. The datasets available for each crop species are displayed with dimension and type descriptions, can be stored and queried and allele data matrices. Access to datasets requires user login.
Data may be currently exported to the following formats: 2x2 matrix, flapjack format and ISMAB formats. Data submission is through templates; upload templates are available for genotype data (separate templates for diversity and mapping populations, type of markers - SNP and SSR data), and mapping populations and marker data templates. The templates are in the form of excel sheets. The GDMS schema will be integrated into the IBDB v1 schema. This schema links to the GMS and DMS tables for the germplasm information and trait and studies information.

GDMS Relationships

Description of Database Tables:
gdms_dataset: This is the primary table of the GDMS database. It stores all the key information of uploaded files like dataset id, dataset name, dataset description etc.

Field Name Description Data type Size
dataset_id Unique identifier for dataset int 4
dataset_name Name of the dataset char 30
dataset_desc Description of dataset varchar 255
dataset_type Type of the dataset whether it is SSR, SNP, DArT or QTL etc. varchar 10
genus Genus name for taxon. char 25
species Taxonomic or common name of
species analyzed.
char 25
template_upload_date The system generates it when a template is uploaded. date  
datatype Whether uploaded data is int or char or map genotyping data enmu
missing_data This is the symbol or characters used by the scientist to represent missing data. varchar 20
remarks Comments on dataset. varchar 255
method Method/Software used to map QTL/MTA ex: PLABQTL (SIM,CIM)/Tassel (GLM,MLM)/ Breeding View varchar 25
score Score type of the QTL/MTA ex: LOD (or) -log10(p) varchar 12


gdms_dataset_user: This table shows the relation between the user table that exists in the GMS database and dataset table of GDMS database. It stores dataset ids and user ids.

Field Name Description Data type Size
dataset_id Identifier for the dataset. int 4
user_id User identification int 4


gdms_char_values: It stores genotyping values of character type.

Field Name Description Data type Size
ac_id Unique identifier for allelic (nucleotide) data. int 4
char_value The allele value, which is normally the expected nucleotide call for SNP data char 4
dataset_id Identifier for the dataset. int 4
Gid Germplasm identifier. int 4
marker_id Marker identifier. int 4


gdms_allele_values: It stores genotyping values of numeric type.

Field Name Description Data type Size
an_id Unique identifier for allelic (fragment) data. int 4
allele_raw_value The raw allele value, which is normally the expected size of SSR fragment. char 20
allele_bin_value The binned allele value, which is normally the expected size of SSR fragment. (binned values ex: after Allelobin) char 20
dataset_id Identifier for the dataset. int 4
Gid Germplasm identifier. int 4
marker_id Marker identifier. int 4


gdms_mapping_pop: This table stores metadata for mapping population.

Field Name Description Data type Size
dataset_id Identifier for the dataset. int 4
mapping_type Type of mapping population ex: Allelic or ABH. varchar 10
parent_a_gid nid for parent a (usually female) in the population. int 4
parent_b_gid nid for parent b (usually male) in the population. int 4
population_size Number of individuals in the mapping population. int 4
population_type Type of population used for mapping. varchar 50
mapdata_desc Description of map. varchar 150
scoring_scheme The name of the scoring scheme used. varchar 150
map_id Unique identifier for map. int 4


gdms_mapping_pop_values: It stores genotyping data values for a mapping population.

Field Name Description Data type Size
mp_id Unique identifier for genotyping data of a mapping population (nucleotide) data. int 4
map_char_value The called genotype value ex: A , B or H char 4
dataset_id Identifier for the dataset. int 4
Gid Germplasm identifier. int 4
marker_id Marker identifier. int 4


gdms_dart_values: It stores genotyping values of DArT type.

Field Name Description Data type Size
ad_id Unique identifier. int 4
dataset_id Identifier for the dataset. int 4
marker_id Marker identifier. int 4
clone_id Clone identification number int 4
Qvalue It is an estimate of marker quality, which reflects how well the two phases (Present = 1 vs Absent = 0) of the marker are separated in this sample set. It measures the fraction of the total variation across all individuals due to bimodality. Q is based on ANOVA.
float 4
reproducibility Measure in % how reproducible the scoring for replicated samples is. (100 means 100% reproducible). A small number of markers were also analysed in duplicate. A score of X means a scoring discordance between 2 copies of an extract or between 2 copies of a marker. float 4
call_rate Percentage of valid scores in all possible scores for a marker. float 4
pic_value Polymorphism information content (PIC): a maximum of 0.5 when a marker scores 50% 0 and 50% 1. float 4
discordance Measure of reproducibility expressing overall variation of scores within replicated samples. float 4


gdms_marker: It stores primary information of marker.

Field Name Description Data type Size
marker_id Unique identifier for marker. int 4
marker_type Type of marker for ex: SSR, SNP, DArT. char 10
marker_name Name of the marker. char 40
genotype Name of the genotype/accession/germplasm on which the marker was originally discovered. char 40
Ploidy Ploidy of the species ex: haploid, diploid etc. varchar 25
Species Name of species char 25
db_accession_id Gen Bank ID or any other public database ID varchar 50
reference Publication / citation details varchar 255
primer_id Name of the primer varchar 70
remarks Comments on marker varchar 255
assay_type Type of assay ex: golden gate, kaspar etc. varchar 50
Motif Motif values ex: Actual SNP [G/T] or SSR (AT)2 varchar 250
forward_primer Forward Primer/Left flanking sequence for KASPar or Golden Gate assay. varchar 100
reverse_primer Reverse primer/Right flanking sequence for KASPar or Golden Gate assay. varchar 100
product_size Size of the Product. varchar 20
annealing_temp Annealing Temperature. float 4
amplification Amplification status. varchar 12



gdms_marker_details: It stores additional information of marker.

Field Name Description Data type Size
marker_id Unique identifier for marker. int 4
no_of_repeats Number of repeats. int 4
motif_type Type of motif ex: di, tri, tetra, etc... varchar 20
sequence Sequence in which motif is identified Marker. varchar 2500
sequence_length Number of base pairs. int 4
min_allele Minimum allele value. int 4
max_allele Maximum allele value. int 4
ssr_nr Number of identified SSR out of the total number of identified SSRs. int 4
forward_primer_temp Melting Temp of forward primer. float 4
reverse_primer_temp Melting Temp of reverse primer. float 4
elongation_temp Elongation Temperature. float 4
fragment_size_expected Expected size of fragment in bp. int 4
fragment_size_observed Observed size of fragment bp. int 4
expected_product_size Expected product size. int 4
position_on_reference_sequence Position number of SNP on reference sequence. int 4
restriction_enzyme_for_assay Restriction enzyme. varchar 25



gdms_map: This stores metadata about the maps (genetic / sequence / physical)

Field Name Description Data type Size
map_id Unique identifier for map. int 4
map_name Name of the Map. varchar 30
map_type Type of map ex: genetic, sequence, physical. varchar 20
mp_id Unique identifier for genotyping data of a mapping population (nucleotide) data. int 4


gdms_qtl: This stores metadata about the QTL.

Field Name Description Data type Size
qtl_id Unique identifier for QTL int 4
qtl_name Name of the QTL char 30
dataset_id Identifier for the dataset. int 4


gdms_qtl_details: It stores information about QTL.

Field Name Description Data type Size
qtl_id Unique identifier for qtl int 4
map_id Unique identifier for linkage map int 4
linkage_group Chromosome number/ Linkage group number varchar 20
min_position Minimum position of QTL float 4
max_position Maximum position of QTL float 4
trait Name of the Trait varchar 40
experiment dataset id from DMS or qtl mapping s/w or location or environment; mandatory field char 100
left_flanking_marker Marker which is left of the QTL varchar 50
right_flanking_marker Marker which is right of the QTL varchar 50
effect +ve effect or -ve effect on the trait numeric value. float 4
position Position of QTL float 4
score_value Value of Log 10 base ratio float 4
r_square % of total phenotypic variation float 4
interactions Epistatic or environmental conjunction varchar 255
clen Chromosome length float 4
se_additive Standard error of additive effect varchar 15
hv_parent Parent of High value allele varchar 225
hv_allele High value allele for particular char 20
lv_parent Parent of Low value allele varchar 225
lv_allele Low value allele for particular char 20


gdms_markers_onmap: It stores the map information and the marker loci.

Field Name Description Data type Size
map_id Unique identifier for map int 4
marker_id Unique identifier for marker int 4
linkage_group Chromosome number/ Linkage group number varchar 50
start_position Start position of marker double 8
end_position End position of marker double 8
map_unit Linkage group units ex: cm(Centimorgan), bp(basepair) varchar 15


gdms_marker_user_info: It stores the contact details of principal investigator of the marker.

Field Name Description Data type Size
marker_id Unique identifier for marker int 4
principal_investigator Principal investigator name varchar 50
Contact Address of principal investigator varchar 200
Institute Institute name varchar 100


gdms_marker_alias: Marker alias names are stored in this table.

Field Name Description Data type Size
marker_id Unique identifier for marker int 4
Alias Alias name of marker char 40


gdms_acc_metadataset: It stores accession/germplasm ids of each dataset.

Field Name Description Data type Size
dataset_id Identifier for the dataset. int 4
Gid Germplasm identifier int 4
Nid Unique identifier for the name from GMS database. int 4


gdms_marker_metadataset: It stores marker ids of each dataset.

Field Name Description Data type Size
dataset_id Identifier for the dataset. int 4
marker_id Unique identifier for marker int 4


gdms_track_data: It stores the previously retrieved data upon prompting the user.

Field Name Description Data type Size
track_id Unique identifier for data track int 4
track_name Name for the selected group of markers / accessions int 4
user_id User identification int 4


gdms_track_markers: It stores the marker ids.

Field Name Description Data type Size
track_id Unique identifier for data track int 4
marker_id Marker identifier int 4


gdms_track_acc: It stores the germplasm ids.

Field Name Description Data type Size
track_id Unique identifier for data track int 4
Gid Germplasm identifier int 4


gdms_mat: It stores information about Marker trait association.

Field Name Description Data type Size
mat_id Unique identifier for mta int 4
marker_id Unique identifier for marker int 4
dataset_id Identifier for the dataset. int 4
map_id Unique identifier for linkage map int 4
linkage_group Chromosome number/ Linkage group number varchar 20
position Position of QTL float 4
trait Name of the Trait varchar 40
experiment dataset id from DMS or qtl mapping s/w or location or environment; mandatory field char 100
hv_allele High value allele for particular char 20
effect +ve effect or -ve effect on the trait numeric value. float 4
score_value Value of Log 10 base ratio float 4
r_square % of total phenotypic variation float 4



VIEWS:
gdms_dataset_size: This view shows number of markers and germplasms contained in each dataset.
gdms_genotypes_count: This view contains the number of genotypes screened for a particular marker.
gdms_mapping_data: It contains marker position on map, marker name, and map name.
gdms_marker_retrieval_info: It contains marker information like marker id, name, principle investigator of the marker, and number of genotypes screened for a particular marker.

Downloads:
GDMS Database Script version 1.0
GDMS Database Script version 1.0.1 Minor changes in database schema

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