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Vocabulary and Vocabulary Term
Vocabulary
| Headers | Mandatory |
|---|---|
| Version | Yes |
| Code | Yes |
| Description | Yes |
Vocabulary Term
| Headers | Mandatory |
|---|---|
| Version | Yes |
| Code | Yes |
| Label | Yes |
| Description | Yes |
Example
| VOCABULARY_TYPE | |||
| Version | Code | Description | |
| 1 | $STORAGE.STORAGE_VALIDATION_LEVEL | Validation Level | |
| Version | Code | Label | Description |
| 1 | RACK | Rack Validation | |
| 1 | BOX | Box Validation | |
| 1 | BOX_POSITION | Box Position Validation |
Experiment Type
| Headers | Mandatory |
|---|---|
| Version | Yes |
| Code | Yes |
| Description | Yes |
| Validation script | Yes |
| Ontology Id | No |
| Ontology Version | No |
| Ontology Annotation Id | No |
Example
| EXPERIMENT_TYPE | ||||||||||
| Version | Code | Description | Validation script | |||||||
| 2 | DEFAULT_EXPERIMENT | date_range_validation.py |
Sample Type
| Headers | Mandatory |
|---|---|
| Version | Yes |
| Code | Yes |
| Description | Yes |
| Auto generate codes | Yes |
| Validation script | Yes |
| Generate code prefix | Yes |
| Ontology Id | No |
| Ontology Version | No |
| Ontology Annotation Id | No |
Example
| SAMPLE_TYPE | |||||
| Version | Code | Description | Auto generate codes | Validation script | Generated code prefix |
| 2 | STORAGE_POSITION | TRUE | storage_position_validation.py | STO |
Dataset Type
| Headers | Mandatory |
|---|---|
| Version | Yes |
| Code | Yes |
| Description | Yes |
| Validation script | Yes |
| Ontology Id | No |
| Ontology Version | No |
| Ontology Annotation Id | No |
Example
| DATASET_TYPE | |||
| Version | Code | Description | Validation script |
| 1 | RAW_DATA |
Property Type
A property type can exist unassigned to an entity type or assigned to an entity type.
| Headers | Mandatory Assigned | Mandatory Unassigned |
|---|---|---|
| Version | Yes | Yes |
| Code | Yes | Yes |
| Mandatory | No | Yes |
| Show in edit views | No | Yes |
| Section | No | Yes |
| Property label | Yes | Yes |
| Data type | Yes | Yes |
| Vocabulary code | Yes | Yes |
| Description | Yes | Yes |
| Metadata | No | No |
| Dynamic script | No | No |
| Ontology Id | No | No |
| Ontology Version | No | No |
| Ontology Annotation Id | No | No |
A property type requires a data type to be defined, valid data types are.
| Data type | Description |
|---|---|
| INTEGER | |
| REAL | |
| VARCHAR | Text of any length but displayed as a single line field. |
| MULTILINE_VARCHAR | Text of any length but displayed as a multi line field. |
| HYPERLINK | |
| BOOLEAN | |
| CONTROLLEDVOCABULARY | |
| XML | |
| TIMESTAMP | |
| DATE | |
| SAMPLE | Sample of any type. |
| SAMPLE:<SAMPLE_TYPE> | Sample of the indicated type. |
Example Unassigned Property
In this case, the property is registered without being assigned to a type, and the block of property types uses the PROPERTY_TYPE block.
| PROPERTY_TYPE | ||||||||
| Version | Code | Mandatory | Show in edit views | Section | Property label | Data type | Vocabulary code | Description |
| 1 | $WELL.COLOR_ENCODED_ANNOTATION | FALSE | TRUE | Color Annotation | CONTROLLEDVOCABULARY | $WELL.COLOR_ENCODED_ANNOTATIONS | Color Annotation for plate wells | |
| 1 | ANNOTATION.SYSTEM.COMMENTS | FALSE | TRUE | Comments | VARCHAR | Comments | ||
| 1 | ANNOTATION.REQUEST.QUANTITY_OF_ITEMS | FALSE | TRUE | Quantity of Items | INTEGER | Quantity of Items | ||
| 2 | $BARCODE | FALSE | FALSE | Custom Barcode | VARCHAR | Custom Barcode |
Example Assigned
In this case the property types are assigned to a sample type and the block of property types belong to the entity type block (SAMPLE_TYPE in this case).
| SAMPLE_TYPE | ||||||||||
| Version | Code | Description | Auto generate codes | Validation script | Generated code prefix | |||||
| 1 | ENTRY | TRUE | ENTRY | |||||||
| Version | Code | Mandatory | Show in edit views | Section | Property label | Data type | Vocabulary code | Description | Metadata | Dynamic script |
| 1 | $NAME | FALSE | TRUE | General info | Name | VARCHAR | Name | |||
| 1 | $SHOW_IN_PROJECT_OVERVIEW | FALSE | TRUE | General info | Show in project overview | BOOLEAN | Show in project overview page | |||
| 1 | $DOCUMENT | FALSE | TRUE | General info | Document | MULTILINE_VARCHAR | Document | { "custom_widget" : "Word Processor" } | ||
| 1 | $ANNOTATIONS_STATE | FALSE | FALSE | Annotations State | XML | Annotations State |
Entity Type Validation Script and Property Type Dynamic Script
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In order to refer to a validation or dynamic script (e.g. storage_position_validation.py below), the relative path (from the scripts directory) to the file has to be provided in the relevant column. See the example columns below.
Example
| SAMPLE_TYPE | ||||||||||
| Version | Code | Description | Auto generate codes | Validation scriptƒgre | Generated code prefix | |||||
| 2 | STORAGE_POSITION | TRUE | storage_position_validation.py | STO | ||||||
| Version | Code | Mandatory | Show in edit views | Section | Property label | Data type | Vocabulary code | Description | Metadata | Dynamic script |
| 1 | $STORAGE_POSITION.STORAGE_CODE | FALSE | TRUE | Physical Storage | Storage Code | VARCHAR | Storage Code | |||
| 1 | $STORAGE_POSITION.STORAGE_RACK_ROW | FALSE | TRUE | Physical Storage | Storage Rack Row | INTEGER | Number of Rows | |||
| 1 | $STORAGE_POSITION.STORAGE_RACK_COLUMN | FALSE | TRUE | Physical Storage | Storage Rack Column | INTEGER | Number of Columns | |||
| 1 | $STORAGE_POSITION.STORAGE_BOX_NAME | FALSE | TRUE | Physical Storage | Storage Box Name | VARCHAR | Box Name | |||
| 1 | $STORAGE_POSITION.STORAGE_BOX_SIZE | FALSE | TRUE | Physical Storage | Storage Box Size | CONTROLLEDVOCABULARY | $STORAGE_POSITION.STORAGE_BOX_SIZE | Box Size | ||
| 1 | $STORAGE_POSITION.STORAGE_BOX_POSITION | FALSE | TRUE | Physical Storage | Storage Box Position | VARCHAR | Box Position | |||
| 1 | $STORAGE_POSITION.STORAGE_USER | FALSE | TRUE | Physical Storage | Storage User Id | VARCHAR | Storage User Id | |||
| 1 | $XMLCOMMENTS | FALSE | FALSE | Comments | XML | Comments log | ||||
| 1 | $ANNOTATIONS_STATE | FALSE | FALSE | Annotations State | XML | Annotations State |
Entity Types Versioning
General Usage
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| Warning |
|---|
Repeated headers will result in an error, in case a Property shares Label with an Attribute is encouraged to use the property code instead. |
Space
| Headers | Mandatory |
|---|---|
| Code | Yes |
| Description | Yes |
Example
| SPACE | |
| Code | Description |
| ELN_SETTINGS | ELN Settings |
| DEFAULT_LAB_NOTEBOOK | Default Lab Notebook |
| METHODS | Folder for methods |
| MATERIALS | Folder for th materials |
| STOCK_CATALOG | Folder for the catalog |
| STOCK_ORDERS | Folder for orders |
| PUBLICATIONS | Folder for publications |
Project
| Headers | Mandatory |
|---|---|
| Identifier | Yes on UPDATES, ignored on INSERT |
| Code | Yes |
| Space | Yes |
| Description | Yes |
Example
| PROJECT | |||
| Identifier | Code | Description | Space |
| /DEFAULT_LAB_NOTEBOOK/DEFAULT_PROJECT | DEFAULT_PROJECT | Default Project | DEFAULT_LAB_NOTEBOOK |
| /METHODS/PROTOCOLS | PROTOCOLS | Protocols | METHODS |
| /STOCK_CATALOG/PRODUCTS | PRODUCTS | Products | STOCK_CATALOG |
| /STOCK_CATALOG/SUPPLIERS | SUPPLIERS | Suppliers | STOCK_CATALOG |
| /STOCK_CATALOG/REQUESTS | REQUESTS | Requests | STOCK_CATALOG |
| /STOCK_ORDERS/ORDERS | ORDERS | Orders | STOCK_ORDERS |
| /ELN_SETTINGS/TEMPLATES | TEMPLATES | Templates | ELN_SETTINGS |
| /PUBLICATIONS/PUBLIC_REPOSITORIES | PUBLIC_REPOSITORIES | Public Repositories | PUBLICATIONS |
Experiment
| Headers | Mandatory |
|---|---|
| Identifier | Yes on UPDATES, ignored on INSERT |
| Code | Yes |
| Project | Yes |
| Property Code | No |
| Property Label | No |
Example
| EXPERIMENT | ||||
| Experiment type | ||||
| COLLECTION | ||||
| Identifier | Code | Project | Name | Default object type |
| /METHODS/PROTOCOLS/GENERAL_PROTOCOLS | GENERAL_PROTOCOLS | /METHODS/PROTOCOLS | General Protocols | GENERAL_PROTOCOL |
| /STOCK_CATALOG/PRODUCTS/PRODUCT_COLLECTION | PRODUCT_COLLECTION | /STOCK_CATALOG/PRODUCTS | Product Collection | PRODUCT |
| /STOCK_CATALOG/SUPPLIERS/SUPPLIER_COLLECTION | SUPPLIER_COLLECTION | /STOCK_CATALOG/SUPPLIERS | Supplier Collection | SUPPLIER |
| /STOCK_CATALOG/REQUESTS/REQUEST_COLLECTION | REQUEST_COLLECTION | /STOCK_CATALOG/REQUESTS | Request Collection | REQUEST |
| /STOCK_ORDERS/ORDERS/ORDER_COLLECTION | ORDER_COLLECTION | /STOCK_ORDERS/ORDERS | Order Collection | ORDER |
| /ELN_SETTINGS/TEMPLATES/TEMPLATES_COLLECTION | TEMPLATES_COLLECTION | /ELN_SETTINGS/TEMPLATES | Template Collection | |
| /PUBLICATIONS/PUBLIC_REPOSITORIES/PUBLICATIONS_COLLECTION | PUBLICATIONS_COLLECTION | /PUBLICATIONS/PUBLIC_REPOSITORIES | Publications Collection | PUBLICATION |
Sample
| Headers | Mandatory |
|---|---|
| $ | No |
| Identifier | Yes on UPDATES, ignored on INSERT |
| Code | No |
| Project | No |
| Experiment | No |
| Auto generate code | No |
| Parents | No |
| Children | No |
| Property Code | No |
| Property Label | No |
Example
| SAMPLE | ||||||
| Sample type | ||||||
| ORDER | ||||||
| $ | Identifier | Code | Space | Project | Experiment | Order Status |
| /ELN_SETTINGS/TEMPLATES/ORDER_TEMPLATE | ORDER_TEMPLATE | ELN_SETTINGS | /ELN_SETTINGS/TEMPLATES | /ELN_SETTINGS/TEMPLATES/TEMPLATES_COLLECTION | Not yet ordered |
Defining Parent and Children in Samples
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| Warning |
|---|
| Parents and children SHOULD be separated by an end of line, each sample should be in its own line. |
| SAMPLE | ||||||||
| Sample type | ||||||||
| ORDER | ||||||||
| $ | Parents | Children | Identifier | Code | Space | Project | Experiment | Order Status |
| /ELN_SETTINGS/TEMPLATES/ORDER_TEMPLATE_A | ORDER_TEMPLATE | ELN_SETTINGS | /ELN_SETTINGS/TEMPLATES | /ELN_SETTINGS/TEMPLATES/TEMPLATES_COLLECTION | Not yet ordered | |||
| $B | /ELN_SETTINGS/TEMPLATES/ORDER_TEMPLATE_B | ORDER_TEMPLATE | ELN_SETTINGS | /ELN_SETTINGS/TEMPLATES | /ELN_SETTINGS/TEMPLATES/TEMPLATES_COLLECTION | Not yet ordered | ||
/ELN_SETTINGS/TEMPLATES/ORDER_TEMPLATE_A $B | /ELN_SETTINGS/TEMPLATES/ORDER_TEMPLATE_D | /ELN_SETTINGS/TEMPLATES/ORDER_TEMPLATE_C | ORDER_TEMPLATE | ELN_SETTINGS | /ELN_SETTINGS/TEMPLATES | /ELN_SETTINGS/TEMPLATES/TEMPLATES_COLLECTION | Not yet ordered | |
| /ELN_SETTINGS/TEMPLATES/ORDER_TEMPLATE_D | ORDER_TEMPLATE | ELN_SETTINGS | /ELN_SETTINGS/TEMPLATES | /ELN_SETTINGS/TEMPLATES/TEMPLATES_COLLECTION | Not yet ordered |
Properties and Sample Variables
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