diff --git a/_data/sidebars/user_guide.yml b/_data/sidebars/user_guide.yml index 3253fa736..91b974f8c 100644 --- a/_data/sidebars/user_guide.yml +++ b/_data/sidebars/user_guide.yml @@ -85,14 +85,10 @@ subitems: subitems: - title: Creating an ISA-JSON compliant study url: /help/user-guide/studies - - title: Export experiments as ISA-JSON - url: /help/user-guide/exporting-experiments-as-isajson - title: Assays subitems: - title: Creating an ISA-JSON compliant assay url: /help/user-guide/assays - - title: Export experiments as ISA-JSON - url: /help/user-guide/exporting-experiments-as-isajson - title: Experiment Sample Templates subitems: - title: Creating Experiment Sample Templates diff --git a/help/user-guide/adding-assets.md b/help/user-guide/adding-assets.md index a07c5815e..06da155e7 100644 --- a/help/user-guide/adding-assets.md +++ b/help/user-guide/adding-assets.md @@ -31,8 +31,8 @@ Assets in SEEK can be described using a number of fields, for example: * [Tags](general-attributes#tags) * [Attributions](general-attributes#attributions) * [Creators](general-attributes#creators) -* [SOPs](general-attributes#sops) +* [SOPs](sops) * [Data files](general-attributes#data-files) -* [Publications](general-attributes#publications) +* [Publications](publications) * [Experimental assays and Modelling analysis](general-attributes#experimental-assays-and-modelling-analysis) * [Events](general-attributes#events) diff --git a/help/user-guide/assays.md b/help/user-guide/assays.md index fd10b0931..ece05feb2 100644 --- a/help/user-guide/assays.md +++ b/help/user-guide/assays.md @@ -1,5 +1,5 @@ --- -title: Asssays +title: Assays --- The [ISA metadata framework](https://isa-specs.readthedocs.io/en/latest/isamodel.html) requires the description (metadata) of different types of samples, namely Study Sources, Study Samples and Assay Samples. This description is based on customisable Experiment Sample Templates and includes the linking of applied Protocols. Follow the link for an overview about [ISA-JSON compliant experiments](isa-json-compliant-experiment.html). @@ -17,8 +17,8 @@ In the context of an ISA-JSON compliant experiment, we use the terms ISA Investi * Select an Assay Stream, then click on "Design Assay" button at the top right corner of the page. * Fill out the provided form as explained below. -### 2.1 Link the sampling Protocol -Select Protocols already registered in the platform that describe the used method or procedure (SOP) applied to the Assay. See how to [create an SOP](adding-assets) in SEEK. +### 2.1 Link the sampling Protocol +Select Protocols already registered in the platform that describe the used method or procedure (SOP) applied to the Assay. See how to [create an SOP](sops) in SEEK. ### 2.2 Design a Samples table for Assay @@ -39,7 +39,7 @@ The Assay Samples table is a Sample Type associated with the Assay and can only * assay - data file: if the output of the assays are digital data files * organism -![create isaassay 2](/images/user-guide/isajson-compliance/create_isaassay_2.png){:.screenshot} +![create isaassay 2]({{ "/images/user-guide/isajson-compliance/create_isaassay_2.png" | relative_url }}){:.screenshot} * Choose a template from the resulting dropdown menu. * Select "Apply". @@ -51,17 +51,17 @@ The Attributes table can be used to customise the Assay Samples table. However, * If you want to add new attributes of your choice to your Samples table, select “Add new attribute” button. * Fill out the mandatory and optional fields. Note that for ISA-JSON compliant Experiments, the ISA Tag is a mandatory field. -* For ISA tag, select +* For ISA tag, select * in case of ISA Level "assay - material": "other_material_characteristic" or "parameter_value"; * in case of ISA Level "assay - data file": "data_file_comment" or "parameter_value"; - + Note that selecting any other options would generate an error since other options are already selected in the starting template. -![create isaassay 3](/images/user-guide/isajson-compliance/create_isaassay_3.png){:.screenshot} +![create isaassay 3]({{ "/images/user-guide/isajson-compliance/create_isaassay_3.png" | relative_url }}){:.screenshot} ### 2.3 Visualise ISA Assay Upon creation, the newly designed ISA Assay will appear in the tree view on the left sidebar, in Experiment View. Follow the link to know more about [Experiment View](viewing-project-in-single-page). - + ## 3. Adding samples to ISA Assay Follow the link to know how to [create samples in ISA-JSON compliant experiments](create-sample-isajson-compliant), including [Assay Samples](create-sample-isajson-compliant#create-assay-samples). @@ -73,8 +73,8 @@ An assay can only be deleted if it has no samples associated with it. If the ass If the assay is the last one in the assay stream, it can be removed without affecting the structure of the stream. If it is a midway assay (i.e., not the last assay in the assay stream), the system will automatically update the sample linkage. The input sample of the following assay will always link to the output sample of the preceding assay without requiring manual intervention. To remove, select the assay and click “Actions -> Delete ISA Assay” in the top right corner. ### 4.2 Adding an Assay -Adding a new assay is straightforward when it follows the last assay in the stream. This is permitted even if samples are associated with the assay. Select the last assay in the assay stream, and click the “Design the next Assay” button at the top right. -For adding a midway assay, the next assay in the stream cannot have samples associated with it. Sample linkage is updated automatically, and no manual re-establishment is needed. To add a midway assay, select the preceding assay where you want to add an additional assay, and select “Insert a new Assay”. The new assay will be added after the selected assay. +Adding a new assay is straightforward when it follows the last assay in the stream. This is permitted even if samples are associated with the assay. Select the last assay in the assay stream, and click the “Design the next Assay” button at the top right. +For adding a midway assay, the next assay in the stream cannot have samples associated with it. Sample linkage is updated automatically, and no manual re-establishment is needed. To add a midway assay, select the preceding assay where you want to add an additional assay, and select “Insert a new Assay”. The new assay will be added after the selected assay. ### 4.3 Editing an Assay -Editing an assay follows similar rules to deletion. If an assay has associated samples, certain modifications to the metadata attributes may be restricted. However, it possible to add metadata attributes, or edit the assay’s title, description, etc. +Editing an assay follows similar rules to deletion. If an assay has associated samples, certain modifications to the metadata attributes may be restricted. However, it possible to add metadata attributes, or edit the assay’s title, description, etc. diff --git a/help/user-guide/create-sample-isajson-compliant.md b/help/user-guide/create-sample-isajson-compliant.md index 5af9bb67a..845a7f54d 100644 --- a/help/user-guide/create-sample-isajson-compliant.md +++ b/help/user-guide/create-sample-isajson-compliant.md @@ -102,5 +102,4 @@ Experiment overview table shows an overview of all Sources and Samples in a sear * In ISA Assay, Experiment overview shows Study Samples and Assay samples, up until that experimental step. ## Browsing samples by Experiment Sample templates -[Browsing samples by experiment sample templates](browsing#browsing-samples-by-experiment-sample-templates) - +[Browsing samples by experiment sample templates](browsing#browse-samples-by-experiment-sample-template) diff --git a/help/user-guide/investigations.md b/help/user-guide/investigations.md index e2c283f8f..2d4387629 100644 --- a/help/user-guide/investigations.md +++ b/help/user-guide/investigations.md @@ -7,11 +7,11 @@ The [ISA metadata framework](https://isa-specs.readthedocs.io/en/latest/isamodel In the context of an ISA-JSON compliant experiment, we use the terms ISA Investigation, ISA Study, and ISA Assay when referring to Investigation, Study, and Assay, respectively. ## 1. Creating an ISA Investigation -Select +Select * Create Investigation from header menu bar. -* Alternatively, in Experiment View, select the Design Investigation button at the top right corner +* Alternatively, in Experiment View, select the Design Investigation button at the top right corner Fill out the provided form, check the option for "Make Investigation compliant to ISA-JSON schemas?" and then click the 'Create' button. -![select isajson compliance](/images/user-guide/isajson-compliance/select_isajson_compliance.png){:.screenshot} +![select isajson compliance]({{ "/images/user-guide/isajson-compliance/select_isajson_compliance.png" | relative_url }}){:.screenshot} diff --git a/help/user-guide/isa-json-compliant-experiment.md b/help/user-guide/isa-json-compliant-experiment.md index cc0a310f7..6c545ff8d 100644 --- a/help/user-guide/isa-json-compliant-experiment.md +++ b/help/user-guide/isa-json-compliant-experiment.md @@ -14,6 +14,8 @@ In SEEK, an Investigation becomes an ISA-JSON compliant Investigation (or ISA In ![select isajson compliance]({{ "/images/user-guide/isajson-compliance/select_isajson_compliance.png" | relative_url }}){:.screenshot} +For a step-by-step description on how to set up ISA-JSON compliant Investigation, see [Creating an ISA-JSON compliant Investigation](investigations). + ## ISA Study ISA Study can only be associated to an ISA Investigation. It is not possible to associate an ISA Study to an Investigation which is not ISA-JSON compliant. @@ -26,6 +28,8 @@ An ISA Study is a central unit that must contain the description (metadata) of: 3. *Sample(s)* - the physical material which results from the sampling protocol (e.g. leaves, biopsies, aliquotes). +For a step-by-step description on how to set up ISA-JSON compliant Study, see [Creating an ISA-JSON compliant Study](studies). + ## Assay Stream An Assay Stream constitutes a structured sequence of sequential assays, interconnected through the flow of samples. Within an Assay Stream, the sample output of one assay serves as the input for the subsequent one. Each Assay Stream aligns with a single Assay in the ISA metadata framework. It is typically associated with one specific technology or technique, such as Metabolomics or Sequencing. @@ -49,6 +53,7 @@ The outputs of an Assay can only be used as inputs by the next Assay in the same * physical materials (e.g. nucleic acids extracts, RNA libraries) generated from an experimental step; * data files (e.g. files containing measurements, rawdata.fastq, processed data, reads.counts.txt). +For a step-by-step description on how to set up ISA-JSON compliant Assay, see [Creating an ISA-JSON compliant Assay](assays). ## Experiment Sample Templates @@ -72,11 +77,6 @@ The "level" of the Experiment Sample Template applied to generate a Sample Type See [Working with Samples in ISA-JSON compliant Experiments](create-sample-isajson-compliant) for more information. -## Designing ISA-JSON compliant Experiments - -See [Designing ISA-JSON compliant Experiments](designing-experiments-isajson-compliant) for a step-by-step description -of how to set up ISA-JSON compliant Experiments. - ## ISA-JSON export [Export Experiments as ISA-JSON](exporting-experiments-as-isajson) diff --git a/help/user-guide/publications.md b/help/user-guide/publications.md index db08b0873..ae55244bf 100644 --- a/help/user-guide/publications.md +++ b/help/user-guide/publications.md @@ -5,8 +5,8 @@ title: Publications ## Publications If your asset is directly related to a publication you can link the two together in SEEK. You can select publications within your project form the drop-down menu. If the publication is in another project you need to check the box that says associate publications from other projects. -![add publication 1](/images/user-guide/add_publication_1.png){:.screenshot} +![add publication 1]({{ "/images/user-guide/add_publication_1.png" | relative_url }}){:.screenshot} When a publication is added a preview will be shown in the bottom right hand corner of SEEK. It can be removed easily if needed. -![add publication 2](/images/user-guide/add_publication_2.png){:.screenshot} \ No newline at end of file +![add publication 2]({{ "/images/user-guide/add_publication_2.png" | relative_url }}){:.screenshot} diff --git a/help/user-guide/studies.md b/help/user-guide/studies.md index 64e8e23f2..3f3d57be3 100644 --- a/help/user-guide/studies.md +++ b/help/user-guide/studies.md @@ -6,14 +6,14 @@ The [ISA metadata framework](https://isa-specs.readthedocs.io/en/latest/isamodel In the context of an ISA-JSON compliant experiment, we use the terms ISA Investigation, ISA Study, and ISA Assay when referring to Investigation, Study, and Assay, respectively. -## 21. Creating an ISA Study +## 1. Creating an ISA Study ISA Study can only be associated to an ISA Investigation. It is not possible to associate an ISA Study to an Investigation which is not ISA-JSON compliant. To start designing an ISA Study within the Investigation in Experiment View, select the Investigation and then select the "Design Study" button at the top right corner. Fill out the provided form as explained below. -## 1.1 Design a Sources table for Study Sources +### 1.1 Design a Sources table for Study Sources The Sources table can be used to register metadata about Study Sources material. * Biological material and its origin or provenance * Environmental and/or experimental conditions of the Sources in the Study @@ -24,23 +24,23 @@ The Sources table can be used to register metadata about Study Sources material. The Study Sources table is a Sample Type associated with the Study and can only be accessed through the Study interface. The Study Sources table can only be created starting from an existing Experiment Sample Templates. -### 1.1.1 Choose one Experiment Sample Template +#### 1.1.1 Choose one Experiment Sample Template * Choose one Experiment Sample Templates by clicking on "Existing Experiment Sample Templates" button. -![create isastudy source 1](/images/user-guide/isajson-compliance/create_isastudy_source_1.png){:.screenshot} +![create isastudy source 1]({{ "/images/user-guide/isajson-compliance/create_isastudy_source_1.png" | relative_url }}){:.screenshot} * Filter existing Experiment Sample Templates based on: * the repository that will store metadata about your Study Sources (e.g. ENA, ArrayExpress or your institutional repository). Select "Project specific templates" if you want to use a template made for or by a specific Project * organism -![create isastudy source 2](/images/user-guide/isajson-compliance/create_isastudy_source_2.png){:.screenshot} +![create isastudy source 2]({{ "/images/user-guide/isajson-compliance/create_isastudy_source_2.png" | relative_url }}){:.screenshot} * Choose a template from the resulting dropdown menu. * Select "Apply". * Give a Title to the Study Sources table. -### 1.1.2 Customise the Study Sources table +#### 1.1.2 Customise the Study Sources table The Attributes table can be used to customise the Study Sources table. However, be aware that applying changes may compromise the compliance to the original template. @@ -48,23 +48,23 @@ The Attributes table can be used to customise the Study Sources table. However, * Fill out the mandatory and optional fields. Note that for ISA-JSON compliant Experiments, the ISA Tag is a mandatory field. * For ISA tag, select "source_characteristic". Note that selecting "source" would generate an error since a "source" is already selected in the starting template. -![create isastudy source 3](/images/user-guide/isajson-compliance/create_isastudy_source_3.png){:.screenshot} +![create isastudy source 3]({{ "/images/user-guide/isajson-compliance/create_isastudy_source_3.png" | relative_url }}){:.screenshot} -## 1.2 Link the sampling Protocol -Select Protocols already registered in the platform that describe the used method or procedure (SOP) used to collect Samples from Sources in your Study (Samples collection protocol). See how to [create an SOP](adding-assets) in SEEK. +### 1.2 Link the sampling Protocol +Select Protocols already registered in the platform that describe the used method or procedure (SOP) used to collect Samples from Sources in your Study (Samples collection protocol). See how to [create an SOP](sops) in SEEK. -## 1.3 Design a Samples table for Study Samples +### 1.3 Design a Samples table for Study Samples Follow the same steps described for designing the Study Sources table to create and customise the Study Samples table. -## 1.4 Visualise ISA Study +### 1.4 Visualise ISA Study Upon creation, the newly designed ISA Study will appear in the tree view on the left sidebar, in Experiment View. Follow the link to know more about [Experiment View](viewing-project-in-single-page). ## 2. Adding Sources to ISA Study After you have designed the Sources table, you can then start by creating and describing your Study Sources according to the designed table. -Follow the link to know how to [create samples in ISA-JSON compliant experiments](create-sample-isajson-compliant), including [Study Sources](create-sample-isa-json-compliant#create-study-sources). +Follow the link to know how to [create samples in ISA-JSON compliant experiments](create-sample-isajson-compliant), including Study Sources. ## 3. Adding Samples to ISA Study -Follow the link to know how to [create samples in ISA-JSON compliant experiments](create-sample-isajson-compliant), including [Study Samples](create-sample-isajson-compliant#create-study-samples). \ No newline at end of file +Follow the link to know how to [create samples in ISA-JSON compliant experiments](create-sample-isajson-compliant), including [Study Samples](create-sample-isajson-compliant#create-study-samples). diff --git a/tech/extended-metadata/create-extended-metadata-type-with-seeds-file.md b/tech/extended-metadata/create-extended-metadata-type-with-seeds-file.md index 87ec8b470..9601d4a74 100644 --- a/tech/extended-metadata/create-extended-metadata-type-with-seeds-file.md +++ b/tech/extended-metadata/create-extended-metadata-type-with-seeds-file.md @@ -2,7 +2,7 @@ title: 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. +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. ## Supported types and vocabularies @@ -15,23 +15,23 @@ 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, - + 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', - + + # 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' - + label: 'study title' + ) ``` -![](/images/user-guide/extended-metadata/atrribute_string_type.png) +![]({{ "/images/user-guide/extended-metadata/atrribute_string_type.png" | relative_url }}) {:.screenshot} ### 2. Text type @@ -40,7 +40,7 @@ The attribute is used for longer, variable-length character fields. (e.g. "The 4 ``` ExtendedMetadataAttribute.new(title: 'description', required:true, sample_attribute_type: SampleAttributeType.where(title:'Text').first) ``` -![](/images/user-guide/extended-metadata/attribute_text_type.png) +![]({{ "/images/user-guide/extended-metadata/attribute_text_type.png" | relative_url }}) {:.screenshot} ### 3. Date type @@ -48,7 +48,7 @@ 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) ``` -![](/images/user-guide/extended-metadata/attribute_date_type.png) +![]({{ "/images/user-guide/extended-metadata/attribute_date_type.png" | relative_url }}) {:.screenshot} ### 4. Date-Time type @@ -57,7 +57,7 @@ The attribute is used to represent dates and times. (e.g. January 1, 2015 at 14: ``` ExtendedMetadataAttribute.new(title: 'study_start_time', required:true, sample_attribute_type: SampleAttributeType.where(title:'Date time').first) ``` -![](/images/user-guide/extended-metadata/attribute_time_type.png) +![]({{ "/images/user-guide/extended-metadata/attribute_time_type.png" | relative_url }}) {:.screenshot} ### 5. Integer type @@ -66,7 +66,7 @@ The attribute is positive, negative, or zero numbers that do not have a fraction ``` ExtendedMetadataAttribute.new(title: 'study_age', required:true, sample_attribute_type: SampleAttributeType.where(title:'Integer').first) ``` -![](/images/user-guide/extended-metadata/attribute_integer_type.png) +![]({{ "/images/user-guide/extended-metadata/attribute_integer_type.png" | relative_url }}) {:.screenshot} ### 6. Real Number @@ -75,7 +75,7 @@ The attribute is used to represent numbers that may have a fractional component ``` ExtendedMetadataAttribute.new(title: 'cholesterol_level', required:true, sample_attribute_type: SampleAttributeType.where(title:'Real number').first) ``` -![](/images/user-guide/extended-metadata/attribute_real_number_type.png) +![]({{ "/images/user-guide/extended-metadata/attribute_real_number_type.png" | relative_url }}) {:.screenshot} ### 7. Boolean @@ -84,7 +84,7 @@ 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) ``` -![](/images/user-guide/extended-metadata/attribute_boolean_type.png) +![]({{ "/images/user-guide/extended-metadata/attribute_boolean_type.png" | relative_url }}) {:.screenshot} ### 8. Controlled Vocabulary @@ -103,17 +103,17 @@ 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) - + ``` -![](/images/user-guide/extended-metadata/attribute_cv_type.png) +![]({{ "/images/user-guide/extended-metadata/attribute_cv_type.png" | relative_url }}) {:.screenshot} ### 9. 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. +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. @@ -134,11 +134,11 @@ Unlike a single-select option in Controlled Vocabulary, Controlled Vocabulary Li ExtendedMetadataAttribute.new(title: 'study_country', required:true, sample_attribute_type: SampleAttributeType.where(title:'Controlled Vocabulary List').first, sample_controlled_vocab: study_country_cv) ``` -![](/images/user-guide/extended-metadata/attribute_cvlist_type.png) +![]({{ "/images/user-guide/extended-metadata/attribute_cvlist_type.png" | relative_url }}) {:.screenshot} ### 10. 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. +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. ``` @@ -148,13 +148,13 @@ Furthermore, The inner Extended Metadata type can also now be defined as a list, 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 + + # 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', @@ -163,19 +163,19 @@ unless ExtendedMetadataType.where(title: 'person', supported_type: 'ExtendedMeta emt.save! end -# Define the extended metadata type 'family', which contains the nested extended metadata attributes +# 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', @@ -192,7 +192,7 @@ unless ExtendedMetadataType.where(title: 'family', supported_type: 'Investigatio end ``` -![](/images/user-guide/extended-metadata/attribute_nested_type.png) +![]({{ "/images/user-guide/extended-metadata/attribute_nested_type.png" | relative_url }}) {:.screenshot} You can find the [complete example here](https://github.com/seek4science/seek/blob/main/db/seeds/extended_metadata_drafts/family_example.seeds.rb), you need to move the file under the `db/seeds` folder, then run the seed file using the command @@ -200,7 +200,7 @@ You can find the [complete example here](https://github.com/seek4science/seek/bl ## How to run the seed file -Here is a seed file named **[extended_study_metadata_example.seeds.rb](https://github.com/seek4science/seek/blob/main/db/seeds/extended_metadata_drafts/extended_study_metadata_example.seeds.rb)**, which creates an Extended Metadata type named **"My study metadata"** for study. +Here is a seed file named **[extended_study_metadata_example.seeds.rb](https://github.com/seek4science/seek/blob/main/db/seeds/extended_metadata_drafts/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.