FAIRDOM-SEEK Docs - Define your own Extended Metadata Type with SEEDs File

Define your own Extended Metadata Type with SEEDs File

If you are managing your own SEEK instance, you have the flexibility to define your project-specific Extended Metadata Types by populating the database with a seed file.

The following are the supported Extended Metadata Attribute Types, each accompanied by a corresponding code snippet for implementation and screenshot in SEEK.

1.String type: the attribute refers to a fixed-length character field. (e.g. “blue”)

 ExtendedMetadataAttribute.new(

    # The attribute's identifier or name (mandatory) .
    title: 'title', 
    
    # Indicates whether this attribute is mandatory for the associated metadata. By default, it is set to false. 
    required: true, 
    
    # Specifies the attribute type, here set to 'String' (mandatory).
    sample_attribute_type: SampleAttributeType.where(title: 'String').first,
    
    # A brief description providing additional details about the attribute. By default, it is set to the empty string. 
    description: 'the title of your study', 
    
    # The label to be displayed in the user interface, conveying the purpose of the attribute. By default, it is set to the value of the 'title' attribute."
    label: 'study title' 
    
)

Text type: the attribute is used for longer, variable-length character fields. (e.g. “The 4th experiment in the batch, it was sampled late, so may not be as accurate” ).

 ExtendedMetadataAttribute.new(title: 'description', required:true, sample_attribute_type: SampleAttributeType.where(title:'Text').first)

Date type: the attribute is used to represent dates. (e.g. January 1, 2015)

 ExtendedMetadataAttribute.new(title: 'study_start_date', required:true, sample_attribute_type: SampleAttributeType.where(title:'Date').first)

Date-Time type: the attribute is used to represent dates and times. (e.g. January 1, 2015 at 14:00 GMT)

 ExtendedMetadataAttribute.new(title: 'study_start_time', required:true, sample_attribute_type: SampleAttributeType.where(title:'Date time').first)

Integer type: the attribute is positive, negative, or zero numbers that do not have a fractional part. (e.g. 1, 2, 3, 4)

 ExtendedMetadataAttribute.new(title: 'study_age', required:true, sample_attribute_type: SampleAttributeType.where(title:'Integer').first)

Real Number: the attribute is used to represent numbers that may have a fractional component or decimal point. (e.g. 180.5)

 ExtendedMetadataAttribute.new(title: 'cholesterol_level', required:true, sample_attribute_type: SampleAttributeType.where(title:'Real number').first)

Boolean: the attribute uses true and false to represent truth values. (e.g. true, false)

 ExtendedMetadataAttribute.new(title: 'resource_use_rights_authors_confirmation', required:true, sample_attribute_type: SampleAttributeType.where(title:'Boolean').first)

Controlled Vocabulary: The attribute is limited to a predefined set of terms, and users must choose from this set. This selection is presented as a single-select dropdown list in the user interface.

def create_sample_controlled_vocab_terms_attributes(array)
  attributes = []
  array.each do |type|
    attributes << { label: type }
  end
  attributes
end


# Create a list of controlled vocablary for the personal title of role name

 role_name_personal_title_cv = SampleControlledVocab.where(title: 'Personal Title').first_or_create!(sample_controlled_vocab_terms_attributes: create_sample_controlled_vocab_terms_attributes(['Mr.', 'Ms.', 'Dr.', 'Prof. Dr.', 'Other']))
 
 ExtendedMetadataAttribute.new(title: 'role_name_personal_title', required:true,
                                                                  sample_attribute_type: SampleAttributeType.where(title:'Controlled Vocabulary').first, sample_controlled_vocab: role_name_personal_title_cv)
    

Controlled Vocabulary List: Unlike a single-select option in Controlled Vocabulary, Controlled Vocabulary List allows users to make multiple selections from a predefined set of terms for a given attribute.

# Create a controlled vocabulary for European study countries.

    study_country_cv = SampleControlledVocab.where(title: 'study_country').first_or_create!(
    sample_controlled_vocab_terms_attributes: create_sample_controlled_vocab_terms_attributes([
      'Albania',
      'Austria',
      'Belgium',
      'Bosnia and Herzegovina',
      'Bulgaria',
      'Croatia',
      'Cyprus',
      'Czech Republic','Denmark',
      'Estonia',
      ....
    ]))

 ExtendedMetadataAttribute.new(title: 'study_country', required:true, sample_attribute_type: SampleAttributeType.where(title:'Controlled Vocabulary List').first, sample_controlled_vocab: study_country_cv)

Nested Extended Metadata: the attribute allows for a hierarchical structure where one Extended Metadata type definition can reference another, resulting in the nesting of these types within a single form. Furthermore, The inner Extended Metadata type can also now be defined as a list, with the form allowing new items to be added or removed.

# Define the inner extended metadata type 'person' with attributes 'first_name' and 'last_name'.
# The 'supported_type' is set to 'ExtendedMetadata' to denote it as the inner extended metadata type.

unless ExtendedMetadataType.where(title: 'person', supported_type: 'ExtendedMetadata').any?

  emt = ExtendedMetadataType.new(title: 'person', supported_type: 'ExtendedMetadata')
  
  # Define 'first_name' attribute as a 'String' type 
  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(
    title: 'first_name',
    sample_attribute_type: SampleAttributeType.where(title: 'String').first
  )
  
  # Define 'last_name' attribute as a 'String' type
  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(
    title: 'last_name',
    sample_attribute_type: SampleAttributeType.where(title: 'String').first
  )
  emt.save!
end

# Define the extended metadata type 'family', which contains the nested extended metadata attributes 
person_emt = ExtendedMetadataType.where(title: 'person', supported_type: 'ExtendedMetadata').first

unless ExtendedMetadataType.where(title: 'family', supported_type: 'Investigation').any?
  emt = ExtendedMetadataType.new(title: 'family', supported_type: 'Investigation')
  
  # Define 'dad' attribute for 'family' linked to the 'person' type
  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(
    title: 'dad',
    sample_attribute_type: SampleAttributeType.where(title: 'Linked Extended Metadata').first,
    linked_extended_metadata_type: person_emt
  )
  
  # Define 'mom' attribute for 'family' linked to the 'person' type
  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(
    title: 'mom',
    sample_attribute_type: SampleAttributeType.where(title: 'Linked Extended Metadata').first,
    linked_extended_metadata_type: person_emt
  )

  # Define 'child' attribute for 'family' linked to the 'person' type (multiple children allowed)
  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(
    title: 'child',
    sample_attribute_type: SampleAttributeType.where(title: 'Linked Extended Metadata (multiple)').first,
    linked_extended_metadata_type: person_emt
  )
end

You can find the complete example here, you need to move the file under the db/seeds folder, then run the seed file using the command bundle exec rake db:seed:family_example from the SEEK instance root path.

How to run the seed file?

Here is a seed file named extended_study_metadata_example.seeds.rb, which creates an Extended Metadata type named “My study metadata” for study.

You can place it under the db/seeds folder, then run the seed file using the command bundle exec rake db:seed:extended_study_metadata_example from the SEEK instance root path.