Database Properties
Database Type: MySQL - 5.7.22
Tables
Table / View | Children | Parents | Columns | Type | Comments |
---|---|---|---|---|---|
locations | 4 | 2 | 15 | Table | Describes locations. Locations can be collecting sites or the location of any geographical feature such as research institutes or lab locations. |
storagedata | 0 | 2 | 5 | Table | |
dataset_export_jobs | 0 | 1 | 11 | Table | |
groups | 1 | 1 | 8 | Table | Allows the definition of groups within Germinate. Germinate supports a number of different group types such as germinatebase accesion groups and marker groups. |
pedigreenotations | 1 | 0 | 6 | Table | Allows additional supporting data to be associated with a pedigree definition such as the contributing data source. |
markers | 1 | 1 | 5 | Table | Defines genetic markers within the database and assigns a type (markertypes). |
usergroups | 2 | 0 | 5 | Table | |
schema_version | 0 | 0 | 10 | Table | |
institutions | 2 | 1 | 11 | Table | Defines institutions within Germinate. Accessions may be associated with an institute and this can be defined here. |
images | 0 | 1 | 7 | Table | |
data_import_jobs | 0 | 0 | 13 | Table | |
locationtypes | 1 | 0 | 5 | Table | Describes a location. |
licenses | 3 | 0 | 5 | Table | |
imagetags | 0 | 0 | 4 | Table | |
groupmembers | 0 | 1 | 5 | Table | Defines which entities are contained within a group. These can be the primary key from any table. |
units | 3 | 0 | 6 | Table | The ‘units’ table holds descriptions of the various units that are used in the Germinate database. Examples of these would include International System of Units (SI) base units: kilogram, meter, second, ampere, kelvin, candela and mole but can include any units that are required. |
image_to_tags | 0 | 2 | 4 | Table | |
storage | 1 | 0 | 4 | Table | |
compounds | 1 | 1 | 10 | Table | |
countries | 2 | 0 | 6 | Table | Countries that are used in the locations type tables in Germinate. These are the ISO codes for countries. |
compounddata | 0 | 4 | 9 | Table | |
treatments | 1 | 0 | 5 | Table | For trials data the treatment is used to distinguish between factors. Examples would include whether the trial was treated with fungicides or not. |
datasetmembers | 0 | 2 | 6 | Table | |
datasetaccesslogs | 0 | 1 | 9 | Table | If enabled, tracks which user accessed which datasets. |
taxonomies | 1 | 0 | 10 | Table | The species table holds information relating to the species that are deinfed within a particular Germinate instance including common names and ploidy levels. |
datasets | 9 | 4 | 19 | Table | Datasets which are defined within Germinate although there can be external datasets which are links out to external data sources most will be held within Germinate. |
synonymtypes | 1 | 0 | 6 | Table | Synonym type definitions. |
climatedata | 0 | 3 | 9 | Table | Holds montly average climate data such as rainfall, temperature or cloud cover. This is based on locations rather than accessions like most of the other tables in Germinate. |
pedigrees | 0 | 3 | 8 | Table | Holds pedigree definitions. A pedigree is constructed from a series of individial->parent records. This gives a great deal of flexibility in how pedigree networks can be constructed. This table is required for operation with the Helium pedigree viewer. |
entitytypes | 1 | 0 | 5 | Table | |
maps | 1 | 0 | 7 | Table | Describes genetic maps that have been defined within Germinate. |
biologicalstatus | 1 | 0 | 4 | Table | Based on Multi Crop Passport Descriptors (MCPD V2 2012) - The coding scheme proposed can be used at 3 different levels of detail: either by using the |
datasetstates | 1 | 0 | 5 | Table | |
attributedata | 0 | 1 | 6 | Table | Defines attributes data. Attributes which are defined in attributes can have values associated with them. Data which does not warrant new column in the germinatebase table can be added here. Examples include small amounts of data defining germplasm which only exists for a small sub-group of the total database. |
attributes | 1 | 0 | 7 | Table | Describes attributes. Attributes are bits of information that can be joined to, for example, a germinatebase entry. These are bits of data that while important do not warrant adding additional columns in the other tables. Examples would be using this to define ecotypes for germinatebase entries. |
trialseries | 1 | 0 | 4 | Table | Holds the names of trial series. Trial series define the name of the trial to which trials data is associated. Examples would include the overarching project. |
links | 0 | 1 | 8 | Table | Germinate allows to define external links for different types of data. With this feature you can |
markertypes | 1 | 0 | 4 | Table | Describes the marker type. Markers (markers) have a defined type. This could be AFLP, MicroSat, SNP and so on. Used to differentiate markers within the markers table and alllows for mixing of marker types on genetic and physical maps. |
comments | 0 | 1 | 8 | Table | Comments can be added to different entries in Germinate such as entries from germinatebase or markers from the markers table. |
mapdefinitions | 0 | 3 | 10 | Table | Relates genetic markers to a map and assigns a position (if known). Maps are made up of lists of markers and positions (genetic or physiscal and chromosome/linkage group assignation). In the case of QTL the definition_start and definition_end columns can be used to specify a range across a linkage group. |
climateoverlays | 0 | 1 | 11 | Table | Climate overlays can be used in conjunction with OpenStreetMap in order to visualize climate data in a geographic context. |
locales | 1 | 0 | 5 | Table | |
commenttypes | 1 | 0 | 5 | Table | Defines the comment type. |
datasetpermissions | 0 | 2 | 6 | Table | This defines which users can view which datasets. Requires Germinate Gatekeeper. This overrides the datasets state. |
newstypes | 1 | 0 | 5 | Table | Defines the news types which are contained the database. The news types are displayed on the Germinate user interface and are not required if the user interface is not used. |
experiments | 1 | 0 | 7 | Table | Defines ecperiments that are held in Germinate. |
datasetmembertypes | 1 | 0 | 4 | Table | |
datasetcollaborators | 0 | 2 | 5 | Table | |
analysismethods | 1 | 0 | 5 | Table | |
phenotypedata | 0 | 6 | 11 | Table | Contains phenotypic data which has been collected. |
climates | 2 | 1 | 8 | Table | Defines climates. Climates are measureable weather type characteristics such as temperature or cloud cover. |
grouptypes | 1 | 0 | 5 | Table | |
germinatebase | 7 | 8 | 32 | Table | Germinatebase is the Germinate base table which contains passport and other germplasm definition data. |
pedigreedescriptions | 2 | 0 | 6 | Table | Description of pedigrees. Pedigrees can have a description which details additional information about the pedigree, how it was constructed and who the contact is for the pedigree. |
mapfeaturetypes | 1 | 0 | 4 | Table | Defines features which can exist on maps. In general this will be the marker type but it can also be used to identify QTL regions. |
phenotypes | 1 | 1 | 8 | Table | Defines phenoytpes which are held in Germinate. |
datasettypes | 2 | 0 | 4 | Table | |
imagetypes | 1 | 0 | 5 | Table | |
pedigreedefinitions | 0 | 3 | 7 | Table | This table holds the actual pedigree definition data. |
linktypes | 1 | 0 | 7 | Table | The link type determines which database table and column are used to construct the final |
licensedata | 0 | 2 | 6 | Table | |
datasetmeta | 0 | 1 | 6 | Table | Defines dataset sizes for the items in the datasets table. This table is automatically updated every hour. |
mlsstatus | 1 | 0 | 4 | Table | |
collectingsources | 1 | 0 | 4 | Table | The coding scheme proposed can be used at 2 different levels of detail: either by using the |
datasetlocations | 0 | 2 | 4 | Table | |
news | 0 | 1 | 9 | Table | Holds news items that are displayed within Germinate. |
usergroupmembers | 0 | 1 | 5 | Table | |
licenselogs | 0 | 1 | 4 | Table | |
synonyms | 0 | 1 | 6 | Table | Allows the definition of synonyms for entries such as germinatebase entries or marker names. |
collaborators | 1 | 1 | 8 | Table | |
view_stats_biologicalstatus | 0 | 0 | 2 | View | |
view_table_locations | 0 | 0 | 13 | View | |
view_table_groups | 0 | 0 | 11 | View | |
view_table_institutions | 0 | 0 | 10 | View | |
view_table_licenses | 0 | 0 | 8 | View | |
view_table_collaborators | 0 | 0 | 13 | View | |
view_stats_overview | 0 | 0 | 8 | View | |
view_table_experiments | 0 | 0 | 10 | View | |
view_table_compound_data | 0 | 0 | 14 | View | |
view_table_trials_data | 0 | 0 | 19 | View | |
view_table_compounds | 0 | 0 | 9 | View | |
view_table_links | 0 | 0 | 11 | View | |
view_table_news | 0 | 0 | 10 | View | |
view_table_maps | 0 | 0 | 6 | View | |
view_table_usergroups | 0 | 0 | 5 | View | |
view_table_datasets | 0 | 0 | 26 | View | |
view_stats_country | 0 | 0 | 3 | View | |
view_table_entities | 0 | 0 | 8 | View | |
view_table_climate_data | 0 | 0 | 20 | View | |
view_table_traits | 0 | 0 | 11 | View | |
view_stats_pdci | 0 | 0 | 2 | View | |
view_stats_taxonomy | 0 | 0 | 4 | View | |
view_table_pedigrees | 0 | 0 | 10 | View | |
view_table_images | 0 | 0 | 9 | View | |
view_table_comments | 0 | 0 | 8 | View | |
view_table_climates | 0 | 0 | 11 | View | |
view_table_climateoverlays | 0 | 0 | 9 | View | |
view_table_germplasm_attributes | 0 | 0 | 12 | View | |
view_table_mapdefinitions | 0 | 0 | 10 | View | |
view_table_dataset_attributes | 0 | 0 | 10 | View | |
view_table_markers | 0 | 0 | 6 | View |