germinate_template_4_25_09_04.germinate_template_4_25_09

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.
groups	2	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).
taxonomyproviderslinks	0	2	3	Table
usergroups	2	0	5	Table
projectcollaborators	0	2	5	Table
schema_version	0	0	10	Table
publications	3	0	5	Table
datawarnings	1	0	5	Table
institutions	2	1	11	Table	Defines institutions within Germinate. Accessions may be associated with an institute and this can be defined here.
images	3	1	9	Table
data_import_jobs	0	0	16	Table
locationtypes	1	0	5	Table	Describes a location.
licenses	3	0	5	Table
fileresources	1	2	9	Table
imagetags	1	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.
germplasmdatawarnings	0	2	4	Table
units	2	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
countries	2	0	6	Table	Countries that are used in the locations type tables in Germinate. These are the ISO codes for countries.
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	2	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	12	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.
mcpd	0	4	44	Table
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.
germplasminstitutions	0	2	5	Table
pedigrees	0	4	9	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.
datasetfileresources	0	2	4	Table
entitytypes	1	0	5	Table
maps	1	0	7	Table	Describes genetic maps that have been defined within Germinate.
trialsetup	1	5	15	Table
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 general codes (in boldface) such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. 100) Wild 110) Natural 120) Semi-natural/wild 130) Semi-natural/sown 200) Weedy 300) Traditional cultivar/landrace 400) Breeding/research material 410) Breeder’s line 411) Synthetic population 412) Hybrid 413) Founder stock/base population 414) Inbred line (parent of hybrid cultivar) 415) Segregating population 416) Clonal selection 420) Genetic stock 421) Mutant (e.g. induced/insertion mutants, tilling populations) 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) 423) Other genetic stocks (e.g. mapping populations) 500) Advanced or improved cultivar (conventional breeding methods) 600) GMO (by genetic engineering) 999) Other
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.
userfeedback	0	0	11	Table
phenotypecategories	1	0	5	Table
links	0	1	8	Table	Germinate allows to define external links for different types of data. With this feature you can define links to external resources.
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.
stories	1	2	12	Table
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.
storysteps	0	2	9	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.
data_export_jobs	0	0	12	Table
fileresourcetypes	1	0	5	Table
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.
datasetcollaborators	0	2	6	Table
experiments	1	1	8	Table	Defines ecperiments that are held in Germinate.
datasetmembertypes	1	0	4	Table
mapoverlays	0	1	14	Table
projectpublications	0	2	4	Table
phenotypedata	0	2	7	Table	Contains phenotypic data which has been collected.
climates	1	1	8	Table	Defines climates. Climates are measureable weather type characteristics such as temperature or cloud cover.
grouptypes	1	0	5	Table
germinatebase	8	4	14	Table	Germinatebase is the Germinate base table which contains passport and other germplasm definition data.
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.
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.
projects	6	1	10	Table
phenotypes	1	2	12	Table	Defines phenoytpes which are held in Germinate.
datasettypes	1	0	4	Table
imagetypes	1	0	5	Table
pedigreedefinitions	0	4	8	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 link. The ”placeholder” in the link (from the links table) will be replaced by the value of the ”target column” in the ”target table”
projectgroups	0	2	4	Table
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
datasetlocations	0	2	4	Table
collectingsources	1	0	4	Table	The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. See Multi Crop Passport Descriptors (MCPD V2 2012) for further definitions.
news	0	1	10	Table	Holds news items that are displayed within Germinate.
usergroupmembers	0	1	5	Table
licenselogs	0	1	4	Table
taxonomyproviders	1	0	6	Table
publicationdata	0	1	6	Table
synonyms	0	1	6	Table	Allows the definition of synonyms for entries such as germinatebase entries or marker names.
collaborators	2	1	9	Table
view_stats_biologicalstatus	0	0	3	View
view_table_import_jobs	0	0	7	View
view_table_locations	0	0	14	View
view_table_groups	0	0	12	View
view_table_taxonomies	0	0	7	View
view_table_trait_attributes	0	0	11	View
view_table_institutions	0	0	12	View
view_table_fileresourcetypes	0	0	6	View
view_table_licenses	0	0	6	View
view_table_collaborators	0	0	16	View
view_table_institution_datasets	0	0	16	View
view_table_fileresources	0	0	14	View
view_table_links	0	0	11	View
view_table_mapoverlays	0	0	17	View
view_table_germplasm_deprecated	0	0	31	View
view_table_news	0	0	11	View
view_table_maps	0	0	6	View
view_table_usergroups	0	0	5	View
view_table_datasets	0	0	33	View
view_stats_country	0	0	3	View
view_table_entities	0	0	10	View
view_table_license_definitions	0	0	5	View
view_table_publications	0	0	11	View
view_table_projects	0	0	11	View
view_table_climate_data	0	0	21	View
view_table_traits	0	0	18	View
view_stats_pdci	0	0	2	View
view_stats_taxonomy	0	0	4	View
view_table_stories	0	0	17	View
view_table_pedigrees	0	0	18	View
view_table_images	0	0	11	View
view_table_comments	0	0	8	View
view_table_pedigreedefinitions	0	0	14	View
view_table_climates	0	0	11	View
view_table_germplasm_attributes	0	0	13	View
view_table_dataset_attributes	0	0	10	View

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.

groups

2

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

5

Table

Defines genetic markers within the database and assigns a type (markertypes).

taxonomyproviderslinks

0

2

3

Table

usergroups

2

0

5

Table

projectcollaborators

0

2

5

Table

schema_version

0

10

Table

publications

3

0

5

Table

datawarnings

1

0

5

Table

institutions

2

1

11

Table

Defines institutions within Germinate. Accessions may be associated with an institute and this can be defined here.

images

3

1

9

Table

data_import_jobs

0

16

Table

locationtypes

1

0

5

Table

Describes a location.

licenses

3

0

5

Table

fileresources

1

2

9

Table

imagetags

1

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.

germplasmdatawarnings

0

2

4

Table

units

2

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

countries

2

0

6

Table

Countries that are used in the locations type tables in Germinate. These are the ISO codes for countries.

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

2

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

12

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.

mcpd

0

4

44

Table

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.

germplasminstitutions

0

2

5

Table

pedigrees

0

4

9

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.

datasetfileresources

0

2

4

Table

entitytypes

1

0

5

Table

maps

1

0

7

Table

Describes genetic maps that have been defined within Germinate.

trialsetup

1

5

15

Table

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 general codes (in boldface) such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. 100) Wild 110) Natural 120) Semi-natural/wild 130) Semi-natural/sown 200) Weedy 300) Traditional cultivar/landrace 400) Breeding/research material 410) Breeder’s line 411) Synthetic population 412) Hybrid 413) Founder stock/base population 414) Inbred line (parent of hybrid cultivar) 415) Segregating population 416) Clonal selection 420) Genetic stock 421) Mutant (e.g. induced/insertion mutants, tilling populations) 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) 423) Other genetic stocks (e.g. mapping populations) 500) Advanced or improved cultivar (conventional breeding methods) 600) GMO (by genetic engineering) 999) Other

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.

userfeedback

0

11

Table

phenotypecategories

1

0

5

Table

links

0

1

8

Table

Germinate allows to define external links for different types of data. With this feature you can define links to external resources.

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.

stories

1

2

12

Table

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.

storysteps

0

2

9

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.

data_export_jobs

0

12

Table

fileresourcetypes

1

0

5

Table

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.

datasetcollaborators

0

2

6

Table

experiments

1

8

Table

Defines ecperiments that are held in Germinate.

datasetmembertypes

1

0

4

Table

mapoverlays

0

1

14

Table

projectpublications

0

2

4

Table

phenotypedata

0

2

7

Table

Contains phenotypic data which has been collected.

climates

1

8

Table

Defines climates. Climates are measureable weather type characteristics such as temperature or cloud cover.

grouptypes

1

0

5

Table

germinatebase

8

4

14

Table

Germinatebase is the Germinate base table which contains passport and other germplasm definition data.

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.

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.

projects

6

1

10

Table

phenotypes

1

2

12

Table

Defines phenoytpes which are held in Germinate.

datasettypes

1

0

4

Table

imagetypes

1

0

5

Table

pedigreedefinitions

0

4

8

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 link. The ”placeholder” in the link (from the links table) will be replaced by the value of the ”target column” in the ”target table”

projectgroups

0

2

4

Table

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

datasetlocations

0

2

4

Table

collectingsources

1

0

4

Table

The coding scheme proposed can be used at 2 different levels of detail: either by using the general codes such as 10, 20, 30, 40, etc., or by using the more specific codes, such as 11, 12, etc. See Multi Crop Passport Descriptors (MCPD V2 2012) for further definitions.

news

0

1

10

Table

Holds news items that are displayed within Germinate.

usergroupmembers

0

1

5

Table

licenselogs